Detection and Isolation of Clostridium difficile Asymptomatic Carriers During Clostridium difficile Infection Outbreaks: An Exploratory Study.

During 4 Clostridium difficile infection outbreaks, unit-wide screening of 114 patients led to detection and isolation of 15 (13%) C. difficile asymptomatic carriers. Carriage prevalence varied between outbreaks, from 0% to 29% (P = .004). Isolating carriers was not associated with significantly shorter outbreak durations, compared with historical controls.

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications.

Relative microorganism abundance is a parameter describing biodiversity, referring to how common a bacterial species is within the total bacterial flora. Anal, rectal, skin, mucal, and respiratory swabs are typical clinical samples where knowledge of relative bacterial abundance might make distinction between asymptomatic carriers and symptomatic cases. Assays trying to measure total bacterial load are usually based on the amplification of universal segments of 16S rRNA genes. Previous assays were not adoptable to "direct" PCR protocols, and/or they were not compatible with hydrolysis-based detection. Using the latest summary of universal 16S sequence motifs present in literature and testing our design with 500 liquid and 50 formed stool samples, we illustrate the performance characteristics of a new 16S quantitative PCR (qPCR) assay, which addresses well-known technical problems, including a) positive priming reaction in the absence of intended target due to self-priming and/or mispriming of unintended targets; b) amplification bias due to nonoptimal primer/probe coverage; and c) too large amplicons for clinical qPCR. Stool swabs ranked into bins of different bacterial loads show significant correlation with threshold cycle values of our new assay. To the best of our knowledge, this is the first description of qPCR assay measuring individual differences of total bacterial load present in human stool.

Predictors of asymptomatic Clostridium difficile colonization on hospital admission.

BACKGROUND: Clostridium difficile (CD) is the leading cause of health care-associated diarrhea and can result in asymptomatic carriage. Rates of asymptomatic CD colonization on hospital admission range from 1.4%-21%. The objective of this study was to evaluate host and bacterial factors associated with colonization on admission. METHODS: The Consortium de recherche québécois sur le Clostridium difficile study provided data for analysis, including demographic information, known risk factors, and potential confounding factors, prospectively collected for 5,232 patients from 6 hospitals in Quebec and Ontario over 15 months from 2006-2007. Stool or rectal swabs were obtained for culture on admission. Pulsed-field gel electrophoresis was performed on the isolates. The presence of antibody against CD toxins A and B was measured. RESULTS: There were 212 (4.05%) patients colonized with CD on admission, and 5,020 patients were not colonized with CD. Multivariate logistic regression analysis showed that hospitalization within the last 12 months, use of corticosteroids, prior CD infection, and presence of antibody against toxin B were associated with colonization on admission. Of patients colonized on admission, 79.4% had non-NAP1, non-NAP2 strains. CONCLUSION: There are identifiable risk factors among asymptomatic CD carriers that could serve in their detection and provide a basis for targeted screening.

Significantly improved performance of a multitarget assay over a commercial SCCmec-based assay for methicillin-resistant Staphylococcus aureus screening: applicability for clinical laboratories.

Detection of the SCCmec gene is a common strategy for methicillin-resistant Staphylococcus aureus (MRSA) screening assays. However, if SCCmec is used alone, it may not be specific for detecting MRSA. Herein, we describe an in-house MSRA PCR-based screening assay involving detection of three targets (nuc, coa, and mecA). The assay is suitable for a wide range of real-time PCR platforms used in clinical microbiological laboratories. Performance characteristics of the in-house assay were significantly improved compared with the commercial assay, leading to an increase of positive predictive value by 40%. Compared with the bacterial culture, the sensitivity, specificity, and positive and negative predictive values of the in-house PCR assay were 100% (95% CI >83.2%), 99.2% (95% CI = 98.2% to 99.8%), 80% (95% CI = 59.3% to 93.2%), and 100% (95% CI >99.2%), respectively.

Host and pathogen factors for Clostridium difficile infection and colonization.

BACKGROUND: Clostridium difficile infection is the leading cause of health care-associated diarrhea, and the bacterium can also be carried asymptomatically. The objective of this study was to identify host and bacterial factors associated with health care-associated acquisition of C. difficile infection and colonization. METHODS: We conducted a 15-month prospective study in six Canadian hospitals in Quebec and Ontario. Demographic information, known risk factors, potential confounding factors, and weekly stool samples or rectal swabs were collected. Pulsed-field gel electrophoresis (PFGE) was performed on C. difficile isolates to determine the genotype. Levels of serum antibodies against C. difficile toxins A and B were measured. RESULTS: A total of 4143 patients were included in the study; 117 (2.8%) and 123 (3.0%) had health care-associated C. difficile infection and colonization, respectively. Older age and use of antibiotics and proton-pump inhibitors were significantly associated with health care-associated C. difficile infection. Hospitalization in the previous 2 months; use of chemotherapy, proton-pump inhibitors, and H(2) blockers; and antibodies against toxin B were associated with health care-associated C. difficile colonization. Among patients with health care-associated C. difficile infection and those with colonization, 62.7% and 36.1%, respectively, had the North American PFGE type 1 (NAP1) strain. CONCLUSIONS: In this study, health care-associated C. difficile infection and colonization were differentially associated with defined host and pathogen variables. The NAP1 strain was predominant among patients with C. difficile infection, whereas asymptomatic patients were more likely to be colonized with other strains. (Funded by the Consortium de Recherche sur le Clostridium difficile.).

Community-acquired Clostridium difficile-associated diarrhea, Montréal, 2005-2006: frequency estimates and their validity.

A retrospective search for community-acquired Clostridium difficile-associated diarrhea in 15 hospitals revealed important discrepancies with numbers for the same period reported in real time to the surveillance system. Several of the observed problems could be solved by implementing case-by-case notification with subsequent investigation by local public health, as for other reportable diseases.

Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile.

Clostridium difficile is a common cause of infectious diarrhea in hospitalized patients. A severe and increased incidence of C. difficile infection (CDI) is associated predominantly with the NAP1 strain; however, the existence of other severe-disease-associated (SDA) strains and the extensive genetic diversity across C. difficile complicate reliable detection and diagnosis. Comparative genome analysis of 14 sequenced genomes, including those of a subset of NAP1 isolates, allowed the assessment of genetic diversity within and between strain types to identify DNA markers that are associated with severe disease. Comparative genome analysis of 14 isolates, including five publicly available strains, revealed that C. difficile has a core genome of 3.4 Mb, comprising ∼ 3,000 genes. Analysis of the core genome identified candidate DNA markers that were subsequently evaluated using a multistrain panel of 177 isolates, representing more than 50 pulsovars and 8 toxinotypes. A subset of 117 isolates from the panel had associated patient data that allowed assessment of an association between the DNA markers and severe CDI. We identified 20 candidate DNA markers for species-wide detection and 10,683 single nucleotide polymorphisms (SNPs) associated with the predominant SDA strain (NAP1). A species-wide detection candidate marker, the sspA gene, was found to be the same across 177 sequenced isolates and lacked significant similarity to those of other species. Candidate SNPs in genes CD1269 and CD1265 were found to associate more closely with disease severity than currently used diagnostic markers, as they were also present in the toxin A-negative and B-positive (A-B+) strain types. The genetic markers identified illustrate the potential of comparative genomics for the discovery of diagnostic DNA-based targets that are species specific or associated with multiple SDA strains.

Evidence of viremia in 2 cases of severe pandemic influenza A H1N1/09.

The recent pandemic of the 2009 pandemic influenza A (H1N1) infrequently caused severe disease. We describe 2 cases of 2009 H1N1 influenza with rapid progression resulting in respiratory failure and need for prolonged intensive care support. Real-time polymerase chain reaction amplification for influenza A (using a Centers for Disease Control and Prevention protocol) and the 2009 H1N1 influenza (using an in-house protocol) was performed on serial respiratory and serum specimens from both patients collected over 3 weeks. Both patients repeatedly demonstrated 2009 H1N1 influenza in respiratory specimens. Evidence of influenza A viremia was also detected in both cases, although it was confirmed as 2009 H1N1 influenza in only one. The presence of viremia in cases of severe 2009 H1N1 influenza has potential prognostic and therapeutic implications. Detection of viremia may be useful as a predictive marker for severe disease. Antiviral agents with low serum levels may be ineffective if administered to patients with influenza viremia.

Impact of strain type on detection of toxigenic Clostridium difficile: comparison of molecular diagnostic and enzyme immunoassay approaches.

A multicenter clinical trial assessed the performance of the Cepheid Xpert C. difficile assay on stool specimens collected from patients suspected of having Clostridium difficile infection (CDI). A total of 2,296 unformed stool specimens, collected from seven study sites, were tested by Xpert C. difficile enrichment culture followed by cell culture cytotoxicity testing of the isolates (i.e., toxigenic culture with enrichment) and the study sites' standard C. difficile test methods. The methods included enzyme immunoassay (EIA), direct cytotoxin testing, and two- and three-step algorithms using glutamate dehydrogenase (GDH) screening followed by either EIA or EIA and an in-house PCR assay. All C. difficile strains were typed by PCR-ribotyping. Compared to results for toxigenic culture with enrichment, the sensitivity, specificity, and positive and negative predictive values of the Xpert assay were 93.5, 94.0, 73.0, and 98.8%, respectively. The overall sensitivity of the EIAs compared to that of enrichment culture was 60.0%, and the sensitivity of combined GDH algorithms was 72.9%; both were significantly lower than that of Xpert C. difficile (P < 0.001 and P = 0.03, respectively). The sensitivity of the EIA was significantly lower than that of the Xpert C. difficile assay for detection of ribotypes 002, 027, and 106 (P < 0.0001, P < 0.0001, and P = 0.004, respectively, Fisher's exact test), and the sensitivity of GDH algorithms for ribotypes other than 027 was lower than that for Xpert C. difficile (P < 0.001). The Xpert C. difficile assay is a simple, rapid, and accurate method for detection of toxigenic C. difficile in unformed stool specimens and is minimally affected by strain type compared to EIA and GDH-based methods.

Patterns of antibiotic use and risk of hospital admission because of Clostridium difficile infection.

BACKGROUND: Previous observations have indicated that infection with Clostridium difficile occurs almost exclusively after exposure to antibiotics, but more recent observations have suggested that prior antibiotic exposure may be less frequent among cases of community-acquired disease. METHODS: We used 2 linked health databases to perform a matched, nested case-control study of elderly patients admitted to hospital with community-acquired C. difficile infection. For each of 836 cases among people 65 years of age or older, we selected 10 controls. We determined the proportion of cases that occurred without prior antibiotic exposure and estimated the risk related to exposure to different antibiotics and the duration of increased risk. RESULTS: Of the 836 cases, 442 (52.9%) had no exposure to antibiotics in the 45-day period before the index date, and 382 (45.7%) had no exposure in the 90-day period before the index date. Antibiotic exposure was associated with a rate ratio (RR) of 10.6 (95% confidence interval [CI] 8.9-12.8). Clindamycin (RR 31.8, 95% CI 17.6-57.6), cephalosporins (RR 14.9, 95% CI 10.9-20.3) and gatifloxacin (RR 16.7, 95% CI 8.3-33.6) were associated with the highest risk. The RR for C. difficile infection associated with antibiotic exposure declined from 15.4 (95% CI 12.2-19.3) by about 20 days after exposure to 3.2 (95% CI 2.0-5.0) after 45 days. Use of a proton pump inhibitor was associated with increased risk (RR 1.6, 95% CI 1.3-2.0), as were concurrent diagnoses of inflammatory bowel disease (RR 4.1, 95% CI 2.6-6.6), irritable bowel syndrome (RR 3.4, 95% CI 2.3-5.0) and renal failure (RR 1.7, 95% CI 1.2-2.2). INTERPRETATION: Community-acquired C. difficile infection occurred in a substantial proportion of individuals with no recent exposure to antibiotics. Among patients who had been exposed to antibiotics, the risk declined markedly by 45 days after discontinuation of use.

Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

BACKGROUND: Although drug resistance is a major challenge in HIV therapy, the effect of drug resistance mutations on HIV evolution in vivo is not well understood. We have now investigated genetic heterogeneity in HIV-1 by performing drug resistance genotyping of the PR-RT regions of viruses derived from plasma and peripheral blood mononuclear cells (PBMCs) of a single patient who had failed multiple regimens of anti-retroviral therapy. RESULTS: Patterns of drug resistance mutations showed that the viral populations in PBMCs were more heterogeneous than in plasma. Extensive analysis of HIV from infected PBMCs in this patient showed that high-level diversity existed among 109 cloned PR-RT sequences and that the majority of mutations were related to drug resistance. Moreover, the PBMCs included archival species that reflected the treatment history of the patient while those in plasma were mainly related to the most recent treatment. Some of the proviral clones contained single or multiple mutations in various combinations. Approximately eighteen percent of the proviral clones derived from infected PBMCs were defective, i.e. 5.5% contained single nucleotide deletions (frameshift mutations) and 12.8% encoded in-frame stop codons (nonsense mutations). Amino acid substitutions in PR and the polymerase region of RT occurred in 12-15% of cases but were much less frequent in the RNase H region of RT, which might not have been under drug selection pressure. CONCLUSION: Selective drug pressure can yield multiple drug-resistant quasispecies that include archival and replication-incompetent species in PBMC reservoirs.

A protocol for the in vitro selection of specific oligonucleotide probes for high-resolution DNA typing.

The confident discrimination of nucleic acids that share a high degree of sequence identity is the major obstacle for the widespread applicability of multiplex DNA-based techniques. This diagnostic uncertainty originates in the insufficient specificity of hybridization, allowing cross-hybridization between unwanted probe-target combinations. Starting from a random mixture of oligonucleotides, we describe a protocol to selectively amplify the probes that bind to the target but not to the similar, unintended targets. The procedure involves five forward hybridizations to generate pools of probes with significant affinity, but not necessarily specificity, for the target. Specificity is then achieved during subtractive hybridization steps, where only probes having differential diagnostic performance are retained. Iterative hybridizations, cloning, sequencing and testing of the performance of selected probes can all be fully automated. Eight weeks are required for the full completion of a project composed of 40 probe-target pairs, even when targets share as much as 87% of sequence identity. While alternative, computer-assisted, rational oligonucleotide design may produce an uncertain outcome, the present protocol generates robust and specific probes suitable for a variety of multiplex, nucleic acid-based detection/typing platforms.

Antimicrobial drugs and community-acquired methicillin-resistant Staphylococcus aureus, United Kingdom.

We report results of a case-control study of the association between receipt of antimicrobial agents and diagnosis of community-acquired methicillin-resistant Staphylococcus aureus (MRSA) in the United Kingdom. Eligible adults, selected from the General Practice Research Database, had no previous diagnosis of MRSA, no hospitalization in the past 2 years, and > or = 2 years of follow-up recorded in the database. For 2000-2004, we identified 1,981 MRSA case-patients and 19,779 matched control-patients. The odds ratios (ORs) and 95% confidence intervals (CIs) of MRSA diagnosis for patients who were prescribed 1, 2-3, or > or = 4 antimicrobial drugs were 1.57 (CI 1.36-1.80), 2.46 (CI 2.15-2.83), and 6.24 (CI 5.43-7.17), respectively. Risk for community-acquired MRSA increased with number of antimicrobial drug prescriptions, appeared to vary according to antimicrobial drug classes prescribed the previous year, and was highest for quinolones (OR 3.37, CI 2.80-4.09) and macrolides (OR 2.50, CI 2.14-2.91).

A portrait of the geographic dissemination of the Clostridium difficile North American pulsed-field type 1 strain and the epidemiology of C. difficile-associated disease in Québec.

BACKGROUND: An increase in the incidence and severity of Clostridium difficile-associated disease in Québec and the United States has been associated with a hypervirulent strain referred to as North American pulsed-field type 1 (NAP1)/027. METHODS: In 2005, a prospective study was conducted in 88 Québec hospitals, and 478 consecutive nosocomial isolates of C. difficile were obtained. The isolates were subjected to pulsed-field gel electrophoresis (PFGE) typing, antimicrobial susceptibility testing, and detection of binary toxin genes and tcdC gene deletion. Data on patient age and occurrence of complications were collected. RESULTS: PFGE typing of 478 isolates of C. difficile yielded 61 PFGE profiles. Pulsovars A (57%), B (10%), and B1 (8%) were predominant. The PFGE profile of pulsovar A was identical to that of strain NAP1. It showed 67% relatedness with 15 other PFGE patterns, among which 11 had both binary toxin genes and a partial tcdC deletion but different antibiotic susceptibility profiles. Pulsovars B and B1 were identical to strain NAP2/ribotype 001. In hospitals showing a predominant clonal A or B-B1 PFGE pattern, incidence of C. difficile-associated disease was 2 and 1.3 times higher, respectively, than in hospitals without any predominant clonal PFGE pattern. Severe disease was twice as frequent among patients with strains possessing binary toxin genes and tcdC deletion than among patients with strains lacking these virulence factors. CONCLUSIONS: This study helped to quantify the impact of strain NAP1 on the incidence and severity of C. difficile-associated disease in Québec in 2005. The identification of the geographic dissemination of this predominant strain may help to focus regional infection-control efforts.

A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality.

BACKGROUND: In March 2003, several hospitals in Quebec, Canada, noted a marked increase in the incidence of Clostridium difficile-associated diarrhea. METHODS: In 2004 we conducted a prospective study at 12 Quebec hospitals to determine the incidence of nosocomial C. difficile-associated diarrhea and its complications and a case-control study to identify risk factors for the disease. Isolates of C. difficile were typed by pulsed-field gel electrophoresis and analyzed for binary toxin genes and partial deletions in the toxin A and B repressor gene tcdC. Antimicrobial susceptibility was evaluated in a subgroup of isolates. RESULTS: A total of 1703 patients with 1719 episodes of nosocomial C. difficile-associated diarrhea were identified. The incidence was 22.5 per 1000 admissions. The 30-day attributable mortality rate was 6.9 percent. Case patients were more likely than matched controls to have received fluoroquinolones (odds ratio, 3.9; 95 percent confidence interval, 2.3 to 6.6) or cephalosporins (odds ratio, 3.8; 95 percent confidence interval, 2.2 to 6.6). A predominant strain, resistant to fluoroquinolones, was found in 129 of 157 isolates (82.2 percent), and the binary toxin genes and partial deletions in the tcdC gene were present in 132 isolates (84.1 percent). CONCLUSIONS: A strain of C. difficile that was resistant to fluoroquinolones and had binary toxin and a partial deletion of the tcdC gene was responsible for this outbreak of C. difficile-associated diarrhea. Exposure to fluoroquinolones or cephalosporins was a risk factor.