Genotyping of Clostridium difficile isolates

Epidemiologic surveillance of Clostridium difficile diarrhea in a freestanding pediatric hospital and a pediatric hospital at a university medical center

To describe the epidemiology of Clostridium difficile in children, we cultured stool specimens from patients at the Children's Hospital Central California, Madera, CA (CHCC, n = 676) and at the University of California Davis Medical Center Pediatric Hospital, Sacramento, CA (UCDMC-PH, n = 301) for C. difficile, and toxins A and B genes and strain identity of the isolates were determined by polymerase chain reaction assays. A higher percentage of patients from UCDMC-PH were culture positive (148/301, 49%) and colonized with toxigenic strains (45/301, 15%) compared with CHCC (colonized = 178/676, 26%; toxigenic = 96/676, 14%, P < or = .001). Multiple logistic regression analysis showed decreased colonization with inpatient status (odds ratio [OR] = 0.64; 95% confidence interval [CI] = 0.46, 0.89; P = .007) and use of H-2 antagonists (OR = 0.55; 95% CI = 0.36, 0.84; P = .006), whereas underlying conditions (colonization: OR = 1.42; 95% CI = 1.02, 1.96; P = .04; toxin positive: OR = 1.60; 95% CI = 1.04, 2.44; P = .03) and exposure to > or =2 antiinfectives (colonization: OR = 1.56; 95% CI = 1.10, 2.20; P = .01; toxin positive: OR = 1.71; 95% CI = 1.10, 2.66; P = .02) increased colonization. Most isolates appear to be community acquired, although molecular analysis suggests some nosocomial transmission at UCDMC-PH. These data suggest that the epidemiology of colonization with C. difficile in children is different than previously reported.

Molecular characterization ofClostridium difficileisolates from horses in an intensive care unit and association of disease severity with strain type

OBJECTIVE

To determine molecular characteristics, antimicrobial susceptibility, and toxigenicity of Clostridium difficile isolates from horses in an intensive care unit and evaluate associations among severity of clinical disease with specific strains of C difficile.

DESIGN

Prospective study.

ANIMALS

130 horses.

PROCEDURES

Feces were collected from horses admitted for acute gastrointestinal tract disease with loose feces and submitted for microbial culture and immunoassay for toxin production. Polymerase chain reaction assays were performed on isolates for toxins A and B genes and strain identification.

RESULTS

Isolates were grouped into 3 strains (A, B, and C) on the basis of molecular banding patterns. Toxins A and B gene sequences were detected in 93%, 95%, and 73% of isolates of strains A, B, and C, respectively. Results of fecal immunoassays for toxin A were positive in 40%, 63%, and 16% of horses with strains A, B, and C, respectively. Isolates in strain B were resistant to metronidazole. Horses infected with strain B were 10 times as likely to have been treated with metronidazole prior to the onset of diarrhea as horses infected with other strains. Duration from onset of diarrhea to discharge (among survivors) was longer, systemic inflammatory response syndromes were more pronounced, and mortality rate was higher in horses infected with strain B than those infected with strains A and C combined.

CONCLUSIONS AND CLINICAL RELEVANCE

Horses may be infected with a number of heterogeneous isolates of C difficile. Results indicated that toxigenicity and antimicrobial susceptibility of isolates vary and that metronidazole-resistant strains may be associated with severe disease.

Prevalence of the ermB Gene in Clostridium difficile Strains Isolated at a University Teaching Hospital from 1987 through 1998

We analyzed 226 strains of Clostridium difficile for the presence of erythromycin ribosomal methylase B (ermB) genes. Forty-four strains (19.4%) carried ermB genes and were resistant to erythromycin. Toxin A and toxin B gene sequences were identified in 81.9% of these 44 strains. Strains of C. difficile that carry ermB genes are common etiologic agents of C. difficile-associated diarrhea.

Molecular epidemiology of hospital-associated and community-acquired Clostridium difficile infection in a Swedish county

All episodes of Clostridium difficile associated diarrhea (CDAD) diagnosed in a defined population of 274,000 including one tertiary and two primary hospitals and their catchment areas were studied during 12 months. The annual CDAD incidence in the county was 97 primary episodes per 100,000, and 78% of all episodes were classified as hospital associated with a mean incidence of 5.3 (range, 1.4 to 6.5) primary episodes per 1,000 admissions. The incidence among hospitalized individuals was 1,300-fold higher than that in the community (33,700 versus 25 primary episodes per 100,000 persons per year), reflecting a 37-fold difference in antibiotic consumption (477 versus 13 defined daily doses [DDD]/1,000 persons/day) and other risk factors. Three tertiary hospital wards with the highest incidence (13 to 36 per 1,000) had CDAD patients of high age (median age of 80 years versus 70 years for other wards, P < 0.001), long hospital stay (up to 25 days versus 4 days), or a high antibiotic consumption rate (up to 2,427 versus 421 DDD/1,000 bed days). PCR ribotyping of C. difficile isolates available from 330 of 372 CDAD episodes indicated nosocomial acquisition of the strain in 17 to 27% of hospital-associated cases, depending on the time interval between index and secondary cases allowed (2 months or up to 12 months), and only 10% of recurrences were due to a new strain of C. difficile (apparent reinfection). In other words, most primary and recurring episodes were apparently caused by the patient's endogenous strain rather than by one of hospital origin. Typing also indicated that a majority of C. difficile strains belonged to international serotypes, and the distribution of types was similar within and outside hospitals and in primary and relapsing CDAD. However, type SE17 was an exception, comprising 22% of hospital isolates compared to 6% of community isolates (P = 0.008) and causing many minor clusters and a silent nosocomial outbreak including 36 to 44% of the CDAD episodes in the three high-incidence wards.

Clostridium difficile infections in animals with special reference to the horse. A review

In human medicine, Clostridium (C.) difficile is since many years a well-known cause of nosocomial diarrhea induced by antibiotic treatment. In horses, C. difficile was recently suggested as a possible enteric pathogen. The bacterium is associated with acute colitis in mature horses following treatment with antibiotics. C. difficile, and/or its cytotoxin, is also associated with acute colitis in mares when their foals are being treated with erythromycin and rifampicin for Rhodococcus equi pneumonia. The colitis can have resulted from an accidental ingestion of erythromycin by the mares. In an experimental study it was also demonstrated in mature horses that erythromycin can induce severe colitis associated with proliferation of C. difficile. A new interesting finding was that in healthy foals younger than 14 days, C. difficile was isolated from every third foal whereas older foals proved negative. In this paper the current state of knowledge of C. difficile infections in animals, especially in horses, is reviewed. A short description is given of the historical background of Clostridium difficile and the antibiotic-associated colitis and diarrhea caused by infection with this bacterium. The taxonomy of Clostridium difficile is described extensively. A summary is given of the diseases associated with clostridia infections in animals. Special attention is paid to the pathogenesis, epidemiology, clinical symptoms, laboratory diagnosis, and pathology of Clostridium difficile infections in horses. Finally, some other bacterial causes of colitis in horses are discussed shortly.

Characterization of Clostridium difficile isolates from foals with diarrhea: 28 cases (1993-1997)

OBJECTIVE

To determine molecular characteristics of Clostridium difficile isolates from foals with diarrhea and identify clinical abnormalities in affected foals.

DESIGN

Retrospective study.

ANIMALS

28 foals with C difficile-associated diarrhea.

PROCEDURE

Toxigenicity, molecular fingerprinting, and antibiotic susceptibility patterns were determined. Information on signalment, clinical findings, results of clinicopathologic testing, whether antimicrobials had been administered prior to development of diarrhea, and outcome was obtained from the medical records.

RESULTS

Twenty-three (82%) foals survived. Toxin A and B gene sequences were detected in isolates from 24 of 27 foals, whereas the toxin B gene alone was detected in the isolate from 1 foal. Results of an ELISA for toxin A were positive for fecal samples from only 8 of 20 (40%) foals. Ten of 23 (43%) isolates were resistant to metronidazole. Molecular fingerprinting revealed marked heterogeneity among isolates, except for the metronidazole-resistant isolates. Sixteen foals had tachypnea. Hematologic abnormalities were indicative of inflammation. Common serum biochemical abnormalities included metabolic acidosis, hyponatremia, hypocalcemia, azotemia, hypoproteinemia, hyperglycemia, and high enzyme activities. Passive transfer of maternal antibodies was adequate in all 12 foals evaluated.

CONCLUSIONS AND CLINICAL RELEVANCE

Results suggest that a large percentage of C difficile isolates from foals with diarrhea will have the toxin A and B gene sequences. Because of the possibility that isolates will be resistant to metronidazole, susceptibility testing is warranted. Clostridium difficile isolates from foals may have a substantial amount of molecular heterogeneity. Clinical and hematologic findings in affected foals are similar to those for foals with diarrhea caused by other pathogens.

Resistance to moxifloxacin in toxigenic Clostridium difficile isolates is associated with mutations in gyrA

Clostridium difficile is the etiological agent of antibiotic-associated colitis and the most common cause of hospital-acquired infectious diarrhea. Fluoroquinolones such as ciprofloxacin are associated with lower risks of C. difficile-associated diarrhea. In this study, we have analyzed 72 C. difficile isolates obtained from patients with different clinical courses of disease, such as toxic megacolon and relapses; the hospital environment; public places; and horses. They were investigated for their susceptibilities to moxifloxacin (MXF), metronidazole (MEO), and vancomycin (VAN). Mutants highly resistant to fluoroquinolones were selected in vitro by stepwise exposure to increasing concentrations of MXF. The resulting mutants were analyzed for the presence of mutations in the quinolone resistance-determining regions of DNA gyrase (gyrA), the production of toxins A and B, and the epidemiological relationship of these isolates. These factors were also investigated using PCR-based methods. All strains tested were susceptible to MEO and VAN. Twenty-six percent of the clinical isolates (19 of 72) were highly resistant to MXF (MIC > or = 16 microg/ml). Fourteen of these 19 strains contained nucleotide changes resulting in amino acid substitutions at position 83 in the gyrA protein. Resistant strains selected in vitro did not contain mutations at that position. These findings indicate that resistance to MXF in a majority of cases may be due to amino acid substitution in the gyrA gene.

Isolation and molecular characterization of Clostridium difficile strains from patients and the hospital environment in Belarus

Toxigenic Clostridium difficile is the most common etiologic agent of hospital-acquired diarrhea in developed countries. The role of this pathogen in nosocomial diarrhea in Eastern Europe has not been clearly established. The goal of this study was to determine the prevalence of C. difficile in patients and the hospital environment in Belarus and to characterize these isolates as to the presence of toxin genes and their molecular type. C. difficile was isolated from 9 of 509 (1.8%) patients analyzed and recovered from 28 of 1,300 (2. 1%) environmental sites cultured. A multiplex PCR assay was used to analyze the pathogenicity locus (PaLoc) of all isolates, and strain identity was determined by an arbitrarily primed PCR (AP-PCR). The targeted sequences for all the genes in the PaLoc were amplified in all C. difficile strains examined. A predominantly homogeneous group of strains was found among these isolates, with five major AP-PCR groups being identified. Eighty-three percent of environmental isolates were classified into two groups, while patient isolates grouped into three AP-PCR types, two of which were also found in the hospital environment. Although no data on the role of C. difficile infection or epidemiology of C. difficile-associated diarrhea (CDAD) in this country exist, the isolation of toxigenic C. difficile from the hospital environment suggests that this pathogen may be responsible for cases of diarrhea of undiagnosed origin and validates our effort to further investigate the significance of CDAD in Eastern Europe.

Single primer polymerase chain reaction fingerprinting for Pasteurella multocida isolates from laboratory rabbits

OBJECTIVE

To evaluate a rapid polymerase chain reaction (PCR) fingerprinting technique for discriminating among Pasteurella multocida isolates from laboratory rabbits.

SAMPLE POPULATION

33 P multocida isolates from rabbits with clinical pasteurellosis.

PROCEDURE

PCR assays were conducted with 2 minisatellites (core sequence and modified core sequence of phage M13) and 2 microsatellites ([GTG]5 and [GACA]4). Each bacterium was assigned to a PCR type for each of the primers used. Boiled bacterial extracts and purified genomic DNA were compared by use of PCR assays for phage M13 and (GACA)4. Plasmids were isolated from each bacterium, and their influence on PCR fingerprint was determined, using boiled extracts as a DNA source.

RESULTS

M13 core sequence and M13 modified core sequence yielded 5 and 8 PCR types, respectively. The microsatellites (GTG)5 and (GACA)4 yielded 4 and 9 PCR fingerprint types, respectively. Fingerprint patterns obtained by use of isolated DNA differed from those obtained by use of boiled extracts, although discrimination among P multocida isolates was similar. The presence or absence of plasmids did not affect PCR fingerprints.

CONCLUSION

Single primer PCR fingerprinting with minisatellite and microsatellite primers is an efficient and reproducible method for the discrimination of P multocida isolates from rabbits and can be performed directly, using boiled bacterial extracts as a source of template, although more bands were obtained from pure genomic DNA.

Clostridium difficile: a survey of fecal carriage in cats in a veterinary medical teaching hospital

Fecal samples collected from 245 cats over a 6-month period were analyzed for the presence of Clostridium difficile. After culture on selective media, isolates were identified by a latex agglutination test, and the presence of toxin A and toxin B gene sequences was determined by polymerase chain reaction. Clostridium difficile was isolated from 23 (9.4%) of the cats, and 34.8% of that group were colonized with toxigenic strains. All of the cats colonized with toxigenic C. difficile had > or = 1 of the risk factors (antibiotic use, antineoplastic therapy, immunosuppressive virus infection) associated with C. difficile infection in humans. Clostridium difficile was not found in any of the cats from a clinically healthy outpatient group of cats examined from the same hospital nor in cats from a specific-pathogen-free research colony on the same campus tested during the same time period. The data obtained in this study confirm the presence of C. difficile in cats at a veterinary teaching hospital. DNA fingerprinting analysis of these isolates allowed separation of the strains into 5 groups. Type 4 strain found in 7 cats was also recovered from the floor drain in the same hospital, suggesting a possible source of infection. Whether the organism is of clinical significance in diarrheal diseases of cats remains to be determined.

Detection of Bacteroides fragilis enterotoxin gene by PCR

Bacteroides fragilis constitutes about 1% of the bacterial flora in intestines of normal humans. Enterotoxigenic strains of B. fragilis have been associated with diarrheal diseases in humans and animals. The enterotoxin produced by these isolates induces fluid changes in ligated intestinal loops and an in vitro cytotoxic response in HT-29 cells. We developed a nested PCR to detect the enterotoxin gene of B. fragilis in stool specimens. After DNA extraction, a 367-bp fragment was amplified with two outer primers. The amplicon from this reaction was subjected to a second round of amplification with a set of internal primers. With these inner primers, a 290-bp DNA fragment was obtained which was confirmed as part of the B. fragilis enterotoxin gene by Southern blotting with a nonradioactive internal probe and a chemiluminescence system. By this approach, B. fragilis enterotoxin gene sequences were detected in eight known enterotoxigenic human isolates and nine enterotoxigenic horse isolates. No amplification products were obtained from DNA extracted from 28 nonenterotoxigenic B. fragilis isolates or B. distasonis, B. thetaiotaomicron, B. uniformis, B. ovatus, Escherichia coli, or Clostridium difficile. The sensitivity of this assay allowed us to detect as little as 1 pg of enterotoxin DNA sequences or 100 to 1,000 cells of enterotoxigenic B. fragilis/g of stool. Enterotoxin production of all isolates was confirmed in vitro in HT-29 cells. A 100% correlation was obtained between enterotoxin detection by cytotoxin assay and the nested PCR assay. This rapid and sensitive assay can be used to identify enterotoxigenic B. fragilis and may be used clinically to determine the role of B. fragilis in diarrheal diseases.

Comparison of PCR-based approaches to molecular epidemiologic analysis of Clostridium difficile

Representative isolates of the 10 serogroups of Clostridium difficile and 39 clinical isolates (30 toxigenic and 9 nontoxigenic), including 5 isolates from a confirmed nosocomial outbreak, were analyzed by using two previously described arbitrary-primer PCR (AP-PCR) molecular typing methodologies (AP-PG05 and AP-ARB11) and PCR ribotyping. The two AP-PCR methods investigated gave comparable results; AP-PG05 and AP-ARB11 identified 8 and 7 groups among the serogroup isolates and classified the clinical isolates into 21 and 20 distinct groups, respectively. PCR ribotyping also identified 8 unique groups among the serogroup isolates but classified the clinical isolates into 23 groups. In addition, when results obtained by the PCR methods were compared with typing data generated by pulsed-field gel electrophoresis (PFGE), PCR ribotyping and PFGE were found to be in agreement for 83% (29 of 35) of isolates typeable by both techniques while AP-PG05 was in agreement with PFGE for 60% (20 of 33) and AP-ARB11 was in agreement with PFGE for only 44% (17 of 36). These results indicate that PCR ribotyping is a more discriminatory approach than AP-PCR for typing C. difficile and, furthermore, that this technique generates results that are in higher concordance with those obtained by using an established method for differentiating isolates of this organism on a molecular level than are results generated by using AP-PCR.

Clostridium difficile infection

The spore-forming anaerobe Clostridium difficile has become a serious enteropathogen. Changes in the composition of natural intestinal flora, mainly due to antibiotic therapy, permit its colonization of, and multiplication in, the colon. The disease is caused by (entero)toxin A and (cyto)toxin B, and infection ranges from asymptomatic carrier state and mild diarrhea to pseudomembranous colitis. The clinical diagnosis is made by observing inflammatory, sometimes bloody, diarrhea and by the colonoscopic detection of epithelial necrosis, ulceration, and, in the advanced state, pseudomembrane formation. The laboratory supports the diagnosis by detecting toxin A and/or B by an enzyme-linked immunoassay with high specificity, but sometimes less sensitivity than with the cytotoxin assay in tissue culture cells. Fecal leukocytes or fecal lactoferrin may be found. Culture for the isolation and identification of toxigenic C. difficile is time consuming but necessary for epidemiological studies. Polymerase chain reaction (PCR) tests have been tested for detection of the toxin B gene directly in stool. Therapy consists of stopping all systemic antibiotic treatment and the use of oral metronidazole or vancomycin. There may be more relapses after vancomycin therapy, and the increasing vancomycin resistance of Enterococcus is worrisome. Prevention, especially of nosocomial spread, requires isolation and enforced handwashing. For epidemiological studies, the bacteria can be typed by molecular DNA analyses, including PCR, protein electrophoresis, and immunological tests.

Comparison of arbitrarily primed PCR with restriction endonuclease and immunoblot analyses for typing Clostridium difficile isolates

Arbitrarily primed PCR (AP-PCR) was used to genotype 26 clinical isolates of Clostridium difficile previously analyzed by immunoblotting (IB) and 20 isolates typed by restriction endonuclease analysis (REA) with HindIII. Two levels of differentiation were achieved with the AP-PCR approach by use of two different arbitrary primers. With the 19-mer arbitrary primer T-7 (first level of differentiation), a good correlation was found between IB and AP-PCR typing. Twenty isolates grouped into six IB types were separated into seven major AP-PCR types. These seven AP-PCR groups were further discriminated into 12 subtypes after genotyping with the arbitrary primer PG-05 (second level of differentiation). The remaining six isolates, all of different IB types, showed a unique and distinct DNA banding pattern with both of the arbitrary primers, T-7 and PG-05. Twenty isolates representing 20 REA types from 15 REA groups were resolved into 13 AP-PCR DNA profiles with the arbitrary primer T-7. A good correlation was found at this level of differentiation between the major REA groups, Y and M, and AP-PCR typing. While AP-PCR with this primer failed to differentiate isolates in REA groups J, G, R, and B, AP-PCR with PG-05 resolved these four isolates into four distinct AP-PCR types. In addition, one of three M strains and one of four Y strains displayed a slightly different DNA banding pattern by AP-PCR (with PG-05) from that of the other strains in the group. We conclude that AP-PCR is a rapid and sensitive method which not only complements other typing schemes but also may be a substitute and prove to be especially suited for immediate epidemiological tracking of nosocomial infections due to C. difficile.

Use of pulsed-field gel electrophoresis for investigation of an outbreak of Clostridium difficile infection among geriatric patients

A six-month outbreak of Clostridium difficile infection among elderly residents of a middle-term-care facility was investigated. Pulsed-field gel electrophoresis was used to genotype 22 outbreak strains and 30 epidemiologically unrelated strains. A prospective case-control study was conducted to identify risk factors for epidemic Clostridium difficile-associated diarrhea. All epidemiologically unrelated Clostridium difficile strains of the same serogroup could be differentiated by their DNA patterns with two restriction enzymes (SmaI and KspI). Among clustered strains, two epidemic serogroups (C and K) were identified. Two different DNA patterns were identified among serogroup C strains and three among serogroup K strains. Multivariate analysis showed that the risk of Clostridium difficile infection increased with antimicrobial chemotherapy (beta-lactam agents and pristinamycin) and the presence of a feeding tube. This study confirms the high discriminative power of restriction fragment length polymorphism analysis by pulsed-field gel electrophoresis to describe Clostridium difficile epidemiology. The typing results confirm that infection was principally exogenous in this outbreak. Furthermore, they indicate the need to improve all measures limiting transmission of infection.

PCR ribotyping and arbitrarily primed PCR for typing strains of Clostridium difficile from a Polish maternity hospital

Detection of the source of Clostridium difficile strains is of importance for the control of the nosocomial spread of this microorganism. For this purpose, vaginal and rectal swabs from 183 mothers, duplicate fecal samples (taken on days 1 and 4 after birth) from 183 neonates, and 94 environmental samples were cultured for C. difficile. The microorganism was never detected in the meconium obtained on day 1 after birth. On the other hand, an incidence of 17% C. difficile positivity was noted in the fecal samples obtained on day 4 after birth. Forty-two percent of the 31 colonized neonates had been delivered with complications. The bacteria were never encountered in the rectal swabs of the mothers, and C. difficile was identified in only one vaginal swab. In contrast, 13% of the environmental samples were positive for C. difficile. No major difference was encountered between patient and environmental isolates with respect to toxigenicity (58 to 65% toxigenic isolates). All strains were subsequently typed by PCR amplification of the 16S-23S ribosomal intergenic spacer regions and by arbitrarily primed PCR (AP-PCR) with different primers and combinations thereof. All environmental isolates and 11 of 31 neonatal strains were of a single type. The vaginal strain was unique, and among the maternity ward- and neonate-related isolates, only two additional AP-PCR types were identified. When a collection of C. difficile strains from patients hospitalized in other institutions and suffering from antibiotic-associated diarrhea or pseudomembranous colitis was analyzed in a similar manner, it appeared that the strain from the maternity ward was unique. The other strain commonly encountered among the neonates was also identified frequently among the isolates from patients with antibiotic-associated diarrhea or pseudomembranous colitis, indicating its general occurrence. On the basis of both epidemiological studies and PCR-mediated genotyping, it was shown that the environment and not the birth canal is the major source of C. difficile acquisition by neonates in this maternity hospital setting. Furthermore, AP-PCR appears to be a fast and useful method for epidemiologically relevant typing of C. difficile isolates.

Apparent outbreaks of Clostridium difficile-associated diarrhea in horses in a veterinary medical teaching hospital

Intestinal colonization with toxigenic strains of Clostridium difficile was documented in 9 of 10 horses with acute onset diarrhea in a veterinary medical teaching hospital, whereas a similar isolate was detected in only 1 of 23 other horses without diarrhea in the hospital. One horse with diarrhea was infected simultaneously with both C. difficile and Salmonella krefeld. Clostridium difficile was detected by fecal culture on selective medium, confirmed with a latex particle agglutination test, and identified as toxigenic by polymerase chain reaction amplification of toxin A and toxin B gene sequences. Using an arbitrarily-primed polymerase chain reaction, 6 distinct C. difficile isolates were detected in the feces of the 9 affected horses at the time of the outbreak of diarrhea.

Genomic fingerprinting of epidemic and endemic strains of Stenotrophomonas maltophilia (formerly Xanthomonas maltophilia) by arbitrarily primed PCR

Arbitrarily primed PCR (AP-PCR) was used to type 64 clinical isolates of Stenotrophomonas maltophilia from 60 patients and the hands of one nurse. Forty-seven different patterns were observed, most patients having isolates with unique genomic fingerprints. A single pattern, however, was obtained from six of eight patients involved in an intensive care nursery outbreak, confirming the suspected nosocomial transmission of this microorganism. This strain was also found in four other patients hospitalized at the same time but in different units. AP-PCR typing results had a good correlation with the 49 patterns obtained when the isolates were typed by contour-clamped homogeneous electric field gel electrophoresis. Although AP-PCR is slightly less discriminatory than contour-clamped homogeneous electric field gel electrophoresis, it offers several advantages and should be considered as a practical option for molecular typing during investigations of outbreaks.