A Blast From the Past: Abdominal Wall Amyloidosis Due to Enfuvirtide Injections

Enfuvirtide was the first marketed fusion inhibitor that worked by binding to glycoprotein 41 of the HIV envelope, preventing the conformational changes required for HIV fusion with CD4+ T cells. Due to its novel mechanisms of action, it was frequently used in the past as part of regimens for the indication of multi-class-resistant HIV until newer oral agents emerged. Here, we describe the case of a 40-year-old man who used enfuvirtide injections from 2012 to 2017 inclusive for multi-class-resistant HIV until he presented in 2021 with an abscess overlying a right lower quadrant mass requiring drainage via pigtail. Congo red stain of the tissue showed positive apple green birefringence on amorphous material after polarization, enabling the diagnosis of enfuvirtide-induced amyloidosis. The patient experienced significant improvement following surgical excision of the cysts and nodules. This case demonstrates that sequelae of injection site reactions can persist for many years following the cessation of enfuvirtide injections.

Clostridium difficile: Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing

Background

Whole genome sequencing (WGS) studies can enhance our understanding of the role of patients with asymptomatic Clostridium difficile colonization in transmission.

Methods

Isolates obtained from patients with Clostridium difficile infection (CDI) and colonization identified in a study conducted during 2006-2007 at 6 Canadian hospitals underwent typing by pulsed-field gel electrophoresis, multilocus sequence typing, and WGS. Isolates from incident CDI cases not in the initial study were also sequenced where possible. Ward movement and typing data were combined to identify plausible donors for each CDI case, as defined by shared time and space within predefined limits. Proportions of plausible donors for CDI cases that were colonized, infected, or both were examined.

Results

Five hundred fifty-four isolates were sequenced successfully, 353 from colonized patients and 201 from CDI cases. The NAP1/027/ST1 strain was the most common strain, found in 124 (62%) of infected and 92 (26%) of colonized patients. A donor with a plausible ward link was found for 81 CDI cases (40%) using WGS with a threshold of ≤2 single nucleotide polymorphisms to determine relatedness. Sixty-five (32%) CDI cases could be linked to both infected and colonized donors. Exclusive linkages to infected and colonized donors were found for 28 (14%) and 12 (6%) CDI cases, respectively.

Conclusions

Colonized patients contribute to transmission, but CDI cases are more likely linked to other infected patients than colonized patients in this cohort with high rates of the NAP1/027/ST1 strain, highlighting the importance of local prevalence of virulent strains in determining transmission dynamics.

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

Background

The identification of genomic biomarkers is a key step towards improving diagnostic tests and therapies. We present a reference-free method for this task that relies on a k-mer representation of genomes and a machine learning algorithm that produces intelligible models. The method is computationally scalable and well-suited for whole genome sequencing studies.

Results

The method was validated by generating models that predict the antibiotic resistance of C. difficile, M. tuberculosis, P. aeruginosa, and S. pneumoniae for 17 antibiotics. The obtained models are accurate, faithful to the biological pathways targeted by the antibiotics, and they provide insight into the process of resistance acquisition. Moreover, a theoretical analysis of the method revealed tight statistical guarantees on the accuracy of the obtained models, supporting its relevance for genomic biomarker discovery.

Conclusions

Our method allows the generation of accurate and interpretable predictive models of phenotypes, which rely on a small set of genomic variations. The method is not limited to predicting antibiotic resistance in bacteria and is applicable to a variety of organisms and phenotypes. Kover, an efficient implementation of our method, is open-source and should guide biological efforts to understand a plethora of phenotypes (http://github.com/aldro61/kover/).

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2889-6) contains supplementary material, which is available to authorized users.

Carbapenem non-susceptible enterobacteriaceae in Quebec, Canada: results of a laboratory surveillance program (2010-2012)

The emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE) represent a major public health concern because these bacteria are usually extensively resistant to most antibiotics. In order to evaluate their dissemination in Quebec, a surveillance program was introduced in 2010. We report the molecular and epidemiological profiles of CPE isolates collected. Between August 2010 and December 2012, a total of 742 non-duplicate isolates non-susceptible to carbapenems were analysed. AmpC β-lactamase and metallo-β-lactamase production were detected by Etest and carbapenemase production by the modified Hodge test (MHT). Antibiotic susceptibility profiles were determined using broth microdilution or Etest. Clonality of Klebsiella pneumoniae carbapenemase (KPC) strains was analyzed by pulsed-field gel electrophoresis (PFGE). The presence of genes encoding carbapenemases as well as other β-lactamases was detected using PCR. Of the 742 isolates tested, 169 (22.8%) were CPE. Of these 169 isolates, 151 (89.3%) harboured a bla_KPC gene while the remaining isolates carried bla_SME (n = 9), bla_OXA-48 (n = 5), bla_NDM (n = 3), and bla_NMC (n = 1) genes. Among the 93 KPC strains presenting with a unique pattern (unique PFGE pattern and/or unique antibiotics susceptibility profile), 99% were resistant to ertapenem, 95% to imipenem, 87% to meropenem, 97% to aztreonam, 31% to colistin and 2% to tigecycline. In 19 patients, 2 to 5 KPC strains from different species or with a different PFGE pattern were isolated. CPE strains were present in the province of Quebec with the majority of strains harbouring KPC. Alternately, SME, OXA-48 and NMC containing strains were rarely found.

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.

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.).

vanA-containing Enterococcus faecium susceptible to vancomycin and teicoplanin because of major nucleotide deletions in Tn1546

OBJECTIVES

During the course of routine screening for vancomycin-resistant enterococci (VRE), we found six Enterococcus faecium isolates positive for vanA by PCR, but susceptible to vancomycin and teicoplanin by phenotypic testing. The aim of this study was to characterize the genetic composition of the Tn1546 vanA gene cluster of these isolates.

METHODS

The E. faecium isolates were characterized by antibiotic susceptibility, PFGE and structural analysis of the Tn1546 elements. Plasmids extracted from these isolates were used to determine the presence of the Tn1546 vanA gene cluster by PCR and the genomic organization of the deleted Tn1546 element by primer walking DNA sequencing.

RESULTS

The vancomycin-susceptible vanA-positive E. faecium isolates showed three PFGE patterns, and were missing the vanR and vanS genes that are responsible for the activation of transcription of resistance genes. Primer walking sequencing revealed that these genes were completely deleted and that interruptions in the vanA cluster were in the vicinity of insertion sequence elements.

CONCLUSIONS

The presence of vancomycin-susceptible vanA-positive E. faecium in clinical samples results from major deletions in the Tn1546 vanA operon. Our findings support the essential role of vanR and vanS for the expression of resistance to vancomycin in enterococci.

Epidemic of group A Streptococcus M/emm59 causing invasive disease in Canada

BACKGROUND

The incidence of invasive group A Streptococcus (GAS) disease can vary over time and geographic region, possibly reflecting the population's susceptibility to particular strains but also variation in the predominant M/emm types. Canadian surveillance documented an epidemic of an uncommon M/emm59 type from 2006 to 2009.

METHODS

Invasive GAS isolates are submitted by Public Health Laboratories in Canada to the National Centre for Streptococcus for M/emm typing. Patient age, sex, geographic location, and the anatomical source of isolate are provided with the isolate. When it was recognized that M/emm59 strains were increasing in prevalence, clinical information was collected on M/emm59 cases captured in Alberta and compared with cases of other M/emm types occurring in this province.

RESULTS

From January 2006 through December 2009, 539 (13.0%) of 4150 invasive GAS cases were identified as M/emm59: 164 from British Columbia, 146 from Alberta, 62 from Saskatchewan, 82 from Manitoba, 68 from Ontario, 14 from Quebec, 1 from New Brunswick, 1 from Newfoundland, 1 from Yukon, and 1 from Nunavut. The predominant clinical presentation was bacteremia (45.0%) followed by cellulitis (41.4%). Compared with concurrent cases of invasive GAS disease caused by all other M/emm types, identified risk factors for M/emm59 disease were alcohol abuse (odds ratio [OR], 2.3; 95% confidence interval [CI], 1.4-3.8), homelessness (OR, 2.0; 95% CI, 1.2-3.4), hepatitis C virus infection (OR, 2.0; 95% CI, 1.1-3.5), and illicit drug use (OR, 1.7; 95% CI, 1.0-3.0).

CONCLUSIONS

Western Canada has witnessed the rapid emergence of a rare GAS strain causing invasive disease predominately in a select population of disadvantaged persons.

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.

In vitro susceptibility of Clostridium difficile clinical isolates from a multi-institutional outbreak in Southern Québec, Canada

Clostridium difficile isolates from a 2004 outbreak in Québec, Canada, were all found to be susceptible to metronidazole, vancomycin, rifampin, and meropenem but resistant to bacitracin, cefotaxime, ciprofloxacin, and levofloxacin, and most (>80%) were resistant to ceftriaxone, clarithromycin, gatifloxacin, and moxifloxacin. The predominant NAP1 isolates were susceptible to clindamycin, while the NAP2 isolates were resistant.

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.

Characterization of 2 influenza A(H3N2) clinical isolates with reduced susceptibility to neuraminidase inhibitors due to mutations in the hemagglutinin gene

Previous studies have shown that amino acid changes in the hemagglutinin (HA) gene of influenza viruses may result in decreased susceptibility to neuraminidase inhibitors (NAIs) in vitro. However, the emergence and characteristics of such HA variants in the clinical setting remain poorly studied. Herein, we report 2 influenza A(H3N2) isolates, from untreated patients, harboring an Arg229-->Ile substitution in the HA1 gene. The Ile229 variants were as sensitive as the Arg229 viruses to zanamivir and oseltamivir in neuroaminidase inhibition assays but were significantly less susceptible (by 60-140-fold) in cell-based assays. Although the Ile229 variants adsorbed less efficiently to Madin-Darby canine kidney (MDCK) cells in kinetic binding assays, they remained very sensitive to zanamivir in ferrets. Our study shows the importance of the HA1 229 residue in virus binding to MDCK cells and confirms the unreliability of cell-based assays in predicting the in vivo susceptibility of HA variants to NAIs.

An unusual case of hepatic abscess

A case of recurring primary hepatic actinomycosis is reported. A 50-year-old man presented with fever, weight loss and multiple hepatic masses. A diagnosis was obtained by cytological examination of a biopsy sample taken from the largest hepatic mass, which revealed the presence of Actinomyces species. The patient was treated with penicillin for 12 months and did well. Seven years later, he presented with similar symptoms but with a single large liver mass and a pulmonary infiltrate in the right lower lobe. Liver biopsy showed an inflammatory pseudotumour, and lung biopsy showed the presence of Actinomyces species. Again, the patient was treated with penicillin. Five months later, the patient was doing well, and a follow-up computed tomography scan showed partial regression of the hepatic pseudotumour. This case indicates that hepatic actinomycosis can recur several years after an appropriate treatment and stresses the need for careful follow-up in such patients.

Prevalence and antifungal susceptibility of 442 Candida isolates from blood and other normally sterile sites: results of a 2-year (1996 to 1998) multicenter surveillance study in Quebec, Canada

During a 2-year surveillance program (1996 to 1998) in Quebec, Canada, 442 strains of Candida species were isolated from 415 patients in 51 hospitals. The distribution of species was as follows: Candida albicans, 54%; C. glabrata, 15%; C. parapsilosis, 12%; C. tropicalis, 9%; C. lusitaniae, 3%; C. krusei, 3%; and Candida spp., 3%. These data, compared to those of a 1985 survey, indicate variations in species distribution, with the proportions of C. glabrata and C. parapsilosis increasing by 9 and 4%, respectively, and those of C. albicans and C. tropicalis decreasing by 10 and 7%, respectively. However, these differences are statistically significant for C. glabrata and C. tropicalis only. MICs of amphotericin B were > or =4 microg/ml for 3% of isolates, all of which were non-C. albicans species. Three percent of C. albicans isolates were resistant to flucytosine (> or =32 microg/ml). Resistance to itraconazole (> or =1 microg/ml) and fluconazole (> or =64 microg/ml) was observed, respectively, in 1 and 1% of C. albicans, 14 and 9% of C. glabrata, 5 and 0% of C. tropicalis, and 0% of C. parapsilosis and C. lusitaniae isolates. Clinical data were obtained for 343 patients. The overall crude mortality rate was 38%, reflecting the multiple serious underlying illnesses found in these patients. Bloodstream infections were documented for 249 patients (73%). Overall, systemic triazoles had been administered to 10% of patients before the onset of candidiasis. The frequency of isolation of non-C. albicans species was significantly higher in this group of patients. Overall, only two C. albicans isolates were found to be resistant to fluconazole. These were obtained from an AIDS patient and a leukemia patient, both of whom had a history of previous exposure to fluconazole. At present, it appears that resistance to fluconazole in Quebec is rare and is restricted to patients with prior prolonged azole treatment.

Epidemiology of enterococcal bacteremia in a referral center for hepatobiliary diseases

BACKGROUND

Enterococcus faecium (EFM) and Enterococcus faecalis (EFL) account for most infections which predominantly originate in the abdomen or the urinary tract. The objectives of this study were to compare the risk factors associated with EFM and EFL bacteremia Patients and Method: Retrospective study of 64 EFL and 27 EFM bacteremia cases that occurred between January 1993 and December 1996 in a referral center for hepatobiliary diseases.

RESULTS

Univariate predictors of EFM bacteremia, compared to EFL, were an orthoptic liver transplantation (OLT), use of steroids, admission in the hepatology service, a central vascular catheter and an abdominal source. Forward regression models identified OLT as the only independent risk factor for EFM bacteremia (odds ratio, OR = 4.320; p = 0.0064), and septic shock as the only predictor of a fatal enterococcal bacteremia (OR = 13.152; p = 0.0003). Molecular typing of EFM isolates identified four small nosocomial clusters (of two to seven patients each) of EFM bacteremia, involving primarily patients admitted to the intensive care unit or on the hepatology ward.

CONCLUSION

Strategies are needed to prevent enterococcal bacteremia in patients with severe liver disease, especially those undergoing OLT.

Trends in antimicrobial resistance among clinical isolates of the Bacteroides fragilis group from 1992 to 1997 in Montreal, Canada

The objective of the present study was to analyze the susceptibility profiles of 911 clinical strains of the Bacteroides fragilis group isolated from 1992 to 1997 in our institution in order to monitor susceptibility changes over time. Whereas the rates of resistance to metronidazole, imipenem, piperacillin-tazobactam, ticarcillin-clavulanic acid, penicillin, piperacillin, and cefoxitin remained essentially unchanged, there was a significant increase in the rates of resistance to clindamycin, which rose from 8.2% in 1992 to 19.7% in 1997 (P < 0.0004).

Should all stool specimens be routinely tested for Clostridium difficile?

OBJECTIVE: To determine the frequency with which Clostridium difficile was detected in stool specimens from outpatients and patients hospitalized for less than 4 days to assess the usefulness of routine laboratory screening for detecting this enteric pathogen. METHODS: Seven hundred and forty-one specimens from 398 patients were cultured over a 6-month period for Salmonella, Shigella, Yersinia, Escherichia coli O157:H7, Campylobacter and Clostridium difficile. Clostridium difficile culture-positive samples were further tested for cytotoxin production. RESULTS: Campylobacter, Salmonella, Shigella and E. coli O157:H7 were isolated in 50 (6.7%) specimens from 35 (8.8%) patients. Clostridium difficile was cultured from 88 (11.9%) specimens from 35 (8.8%) patients and its cytotoxin detected in 35 (4.7%) specimens of 12 (3%) patients. Clostridium difficile was the second most frequent enteric pathogen after Campylobacter. Of 178 (24%) specimens submitted with a specific request for Clostridium difficile testing, 13 (7.3%) were cytotoxin positive (three patients); of 563 specimens for which Clostridium difficile was not requested, 22 (3.9%) were cytotoxin positive (nine patients). CONCLUSIONS: Nine of 12 patients with cytotoxin-positive specimens would have gone undiagnosed in the laboratory had all stool samples submitted not been tested. These results suggest that Clostridium difficile disease is under-recognized and that testing all stool samples for Clostridium difficile may be warranted in our community of patients.

Multicenter evaluation of the fully automated COBAS AMPLICOR PCR test for detection of Chlamydia trachomatis in urogenital specimens

The fully automated COBAS AMPLICOR CT/NG test for the detection of Chlamydia trachomatis was evaluated in a multicenter trial. Test performance was evaluated for 2,014 endocervical swab and 1,278 urine specimens obtained from women and for 373 urethral swab and 254 urine specimens obtained from men. Culture served as the reference test. Culture-negative, COBAS AMPLICOR-positive specimens that tested positive in a confirmatory PCR test for an alternative target sequence within the C. trachomatis major outer membrane protein gene were resolved as true positives. The overall prevalence of chlamydia was 4.3% in cervical swabs and 11.0% in urethral swabs from men. When the results for each specimen type were considered separately, the resolved sensitivities were 96.5% (83 of 86) for endocervical swab specimens, 95.1% (39 of 41) for urine specimens from women, 100.0% (41 of 41) for urethral swab specimens from men, and 94.4% (17 of 18) for urine specimens from men; the resolved specificities were 99.4% (1,912 of 1,924) for endocervical swab specimens, 99.8% (1,204 of 1,207) for urine specimens from women, 98. 5% (325 of 330) for urethral swab specimens from men, and 100.0% (236 of 236) for urine specimens from men. For the subset of patients from whom both swab and urine specimens were collected, the combined results for both specimen types were used to identify all infected patients. Using these combined reslts as criteria, the resolved sensitivities for the COBAS AMPLICOR test were 82.6% (38 of 46) for endocervical swab specimens, 84.4% (38 of 45) for urine specimens from women, 84.2% (16 of 19) for urethral swab specimens from men, and 89.5% (17 of 19) for urine specimens from men. In comparison, the sensitivity of culture was only 56.5% (26 of 46) for endocervical specimens and 63.2% (12 of 19) for urethral specimens from men. The internal control provided in the COBAS AMPLICOR test revealed that 2.9% of specimens were inhibitory when they were initially tested. Nevertheless, valid results were obtained for 99. 1% of specimens because 68.7% of the inhibitory specimens were not inhibitory when a second aliquot of the original sample was tested. Two additional COBAS AMPLICOR-positive specimens were detected by retesting inhibitory specimens. The COBAS AMPLICOR CT/NG test for the detection of C. trachomatis exhibited equally high sensitivities and specificities with both urogenital swab and urine specimens and, thus, is well-suited for use in screening.

Invasive fungal infections in Canada from 1992 to 1994

PURPOSE

To describe the frequency, characteristics and impact of invasive fungal infection in Canada.

METHODS

Nominal case reporting with standardized data collection from selected sites across Canada. Cases were found primarily through laboratory review with supplementation by record review and clinical surveillance at some sites.

RESULTS

The frequency of invasive fungal infection varied from 3.54 to 6.64/100,000 population per year. Candida species were responsible for 66% of all reports; 80% of candidal infections were bloodstream isolates. Crytococcus neoformans, Aspergillus species and Histoplasma capsulatum each accounted for 5% to 10% of cases, and all other organisms less than 5% each. Human immunodeficiency virus infection was an important comorbidity for cryptococcus and histoplasma infections, and was associated with increased mortality for only histoplasma infections. Geographical variation of histoplasma, blastomyces and coccidioidomyces infection was confirmed. Case fatality was high for all invasive fungal infections, except coccidioidomycosis, blastomycosis and sporotrichosis.

CONCLUSIONS

Candida species infections are the major pathogens in invasive fungal infections in Canada; all other species occur relatively infrequently. The potential for therapeutic intervention to limit mortality requires further assessment.

Multicenter evaluation of the COBAS AMPLICOR HCV assay, an integrated PCR system for rapid detection of hepatitis C virus RNA in the diagnostic laboratory

The benefits shown by the recent introduction of PCR for the in vitro diagnosis of hepatitis C virus (HCV) infection has prompted the development of standardized, ready-to-use assays that can be implemented in routine clinical laboratories. We have evaluated the clinical performance of COBAS AMPLICOR HCV (COBAS), the first instrument system that allows the automation of HCV RNA amplification and detection, to determine its performance in the routine laboratory setting. More than 2,000 specimens collected at five centers were analyzed in parallel by the COBAS and the manual AMPLICOR HCV (AMPLICOR) tests, and the results were compared with the results for biochemical and serological markers of HCV. In this study the two PCR systems showed the same accuracy, with a concordance rate of 99.8%. As expected, the correlation between serology and PCR was not absolute because the presence of anti-HCV antibodies may be associated with a latent or past infection. On the other hand, if the presence of confirmed anti-HCV antibodies and elevated alanine aminotransferase levels are taken as the "gold standard," indicating an active, ongoing infection, the COBAS and AMPLICOR tests show high and comparable sensitivities (100%) and specificities (98%), with positive and negative predictive values of 100 and 97%, respectively. During the study no false-positive reactions were detected. The use of an internal control allowed the identification of inhibitory substances that prevented amplification for 0.3 and 0.4% of samples tested by the COBAS and AMPLICOR tests, respectively. Compared to the manual system, the COBAS system allowed a significant reduction of hands-on time and could improve the overall laboratory work flow. In conclusion, these results support the use of the COBAS and AMPLICOR tests for the molecular diagnosis of active HCV infections.

Risk factors for early recurrent Clostridium difficile-associated diarrhea

Recurrence is a common sequela of Clostridium difficile-associated diarrhea (CDD) and may increase morbidity, costs, and treatment-related antimicrobial resistance. Because recurrent CDD (RCDD) frequently occurs very soon after an initial episode, our goal was to determine the risk factors for early RCDD (occurring < or = 45 days after the initial episode). We conducted a case-control study, comparing 13 patients with early RCDD (case patients) with 46 patients who had only one CDD episode (control patients) at Centre Hospitalier Angrignon (Québec) during January 1993 through November 1994. Risk factors for early RCDD included a history of chronic renal insufficiency, a white blood cell count of > or = 15 x 10(3)/mm3, and community-acquired diarrhea with the first CDD episode. For seven of eight case patients, C. difficile strains from the first and second CDD episodes were identical, suggesting that relapse is more common than reinfection. These results suggest that treatments should be directed at preventing relapses in patients at high risk for early RCDD.

Update on Pan-American activities in the field of anaerobes: Canada

During the past 15 years, important contributions have been made to the field of anaerobes in Canada. Studies on the importance of the intestinal flora as a source of vitamin K for humans, investigations of the mechanisms of synergy in polymicrobial infections, and extensive research on the field of immunocompetence of surgical patients have provided interesting and valuable information. Several clinical and epidemiological studies of anaerobic infections have been carried out. Rapid methods have been developed for the identification and susceptibility testing of clinical isolates. National and regional surveys have been conducted on the susceptibility patterns of the Bacteroides fragilis group. Studies on the mechanism of action of metronidazole and on the mechanisms of resistance of Bacteroides species have also been carried out. The Canadian Infectious. Disease Society has published position papers on therapy with cefotetan, ceftizoxime, and imipenem and on antimicrobial prophylaxis in surgical patients.

Clindamycin resistance in the Bacteroides fragilis group: association with hospital-acquired infections

A retrospective study was conducted to assess the relationships between clindamycin resistance in members of the Bacteroides fragilis group, previous antimicrobial therapy, and the context for the development of infection, whether in the community or during hospitalization. Eighty-five clindamycin-resistant clinical strains (one isolate per patient) isolated from January 1988 to October 1994 were matched (one to one) with clindamycin-susceptible isolates recovered during the same period, and the charts of the patients from whom the isolates were recovered were reviewed retrospectively. Of the clindamycin-resistant strains, 65% were recovered from patients with hospital-acquired infections compared with 40% of the clindamycin-susceptible strains (odds ratio [OR], 2.75; 95% confidence interval [CI], 1.41-5.38; P = .002). Prior antimicrobial therapy for > or = 48 hours was also associated with clindamycin resistance (OR, 2.33; 95% CI, 1.16-4.70; P = .02). However, clindamycin resistance remained associated with hospital-acquired infections independent of prior antimicrobial therapy (Mantel-Haenszel weighted average OR, 2.22; 95% CI, 1.03-4.89; P = .04). Clinicians should consider the risks for clindamycin resistance when treating hospital-acquired infections caused by members of the B. fragilis group.

Survey of Bacteroides fragilis group susceptibility patterns in Canada

The in vitro activities of penicillin, clindamycin, chloramphenicol, metronidazole, piperacillin, piperacillin-tazobactam, ticarcillin, ticarcillin-clavulanate, ampicillin-sulbactam, cefoxitin, ceftizoxime, cefotetan, moxalactam, and imipenem against 348 Bacteroides fragilis group isolates collected from six Canadian cities during 1990 were determined by the National Committee for Clinical Laboratory Standards (NCCLS) agar dilution technique. All isolates were susceptible to chloramphenicol, metronidazole, piperacillin-tazobactam, and imipenem. For the other antibiotics tested, the following resistance rates were observed: penicillin, 97%; clindamycin, 9%; piperacillin, 19%; ticarcillin, 31%; ticarcillin-clavulanate, 0.28%; ampicillin-sulbactam, 0.85%; cefoxitin, 26%; ceftizoxime, 15%; cefotetan, 53%; and moxalactam, 17%. Susceptibility profiles to beta-lactam antibiotics varied among the different species tested: B. fragilis and Bacteroides vulgatus demonstrated lower resistance rates than Bacteroides distasonis and indole-positive Bacteroides thetaiotaomicron and Bacteroides ovatus. Ceftizoxime results should be interpreted cautiously, because the MICs obtained with the recommended NCCLS control strain were lower than expected.

Thiamine deficiency and Wernicke's encephalopathy in AIDS

Several neuropathological reports in the last 5 years have described brain lesions characteristic of Wernicke's Encephalopathy in patients with AIDS. Using the erythrocyte transketolase activation assay, we now report biochemical evidence of thiamine deficiency in 9/39 (23%) of patients with AIDS or AIDS-related complex. In no cases was there history of alcohol abuse nor were there clinical signs of Wernicke's Encephalopathy. Thiamine deficiency in these patients most likely results from the cachexia and catabolic state characteristic of AIDS. In view of (i) the confirmed neuropathological evidence of Wernicke's Encephalopathy in AIDS patients, (ii) the significant thiamine deficiency in these patients and (iii) the difficulties of clinical diagnosis of Wernicke's Encephalopathy, it is recommended that dietary thiamine supplementation be initiated in all newly diagnosed cases of AIDS or AIDS-related complex.

Usefulness of semi-quantitative cultures in the diagnosis of Clostridium difficile associated disease

Semi-quantitative stool cultures on CCFA were compared to cytotoxic assays for the diagnosis of Clostridium difficile associated disease (CAD). There was a significant correlation between the amount of Clostridium difficile growth on CCFA, the presence of cytotoxin and a clinical diagnosis of CAD in the 541 initial stool specimens tested.

Ghost mycobacteria on Gram stain

The Gram stain is a key tool in diagnostic microbiology. Its usefulness with respect to mycobacteria is undefined. The neutrality of mycobacteria other than Mycobacterium tuberculosis on Gram staining of various clinical specimens is described.

Multilaboratory evaluation of an agar diffusion disk susceptibility test for rapidly growing anaerobic bacteria

A multilaboratory collaborative study was undertaken to determine whether the anaerobic disk diffusion test of Horn et al. could be performed reproducibly and accurately. Tests with nine different antimicrobial disks were evaluated. Reproducibility of the agar diffusion disk method was similar to that of the reference agar dilution test procedure. The anaerobic disk diffusion procedure was found to be a potentially useful method for testing some antimicrobial agents against rapidly growing anaerobes belonging to the Bacteroides fragilis group. These promising results warrant further investigations and validations.

Evaluation of the KOH test and the antibiotic disk test in routine clinical anaerobic bacteriology

We have evaluated the KOH test, the antibiotic disk identification test, and the Gram stain reaction for the preliminary grouping of gram-positive and gram-negative anaerobes and have assessed the value of erythromycin 60-micrograms-disk resistance as a predictive index of clindamycin resistance among anaerobes. By testing 931 clinical isolates, 281 gram positive and 650 gram negative, with the KOH test and vancomycin 5-micrograms-disk test, we obtained the following parameters: sensitivity, 89.7 and 97.1%; specificity, 97.5 and 98.3%; positive predictive value, 80.4 and 98.7%; and efficiency, 92.1 and 98% for the KOH test and the vancomycin test, respectively. The KOH reaction incorrectly grouped 42 of 97 Bacteroides bivius and 12 of 50 pigmented Bacteroides strains. The vancomycin test correctly identified 63 of 67 gram-negative strains that had given a negative KOH reaction. The erythromycin disk result correctly predicted clindamycin resistance in gram-negative isolates but had a sensitivity of 85.7%, a specificity of 92.4%, and a positive predictive value of 42.8% for gram-positive isolates. Therefore, the use of these preliminary identification tests can assist in the correct grouping of anaerobes and accurately predict significant clindamycin resistance in gram-negative anaerobic bacteria.

Disk diffusion susceptibility testing of the Bacteroides fragilis group

The susceptibilities of 225 isolates of the Bacteroides fragilis group to six antibiotics were determined by a new disk diffusion test in Wilkins-Chalgren agar and by the standard agar dilution method. For disk diffusion, the bacteria were directly suspended in saline and immediately swabbed onto 15-cm agar plates. Disks of cefoxitin (30 micrograms), chloramphenicol (30 micrograms), clindamycin (2 micrograms), moxalactam (30 micrograms), imipenem (10 micrograms), and ticarcillin (75 micrograms) were applied, and the plates were incubated at 37 degrees C in an anaerobic atmosphere. Zone sizes were measured at 24 h. The results of disk diffusion and agar dilution were compared by regression analysis by the method of least squares and by the error rate-bounded method. Zones were easily measured for 216 strains (96%). The correlation between the MICs and diameters of inhibition for cefoxitin, clindamycin, moxalactam, and ticarcillin was generally good. A correlation could not be established for chloramphenicol and imipenem, as there were too few resistant strains. With the recommended resistance breakpoints, the following susceptible and resistant zone diameter breakpoints could be established: cefoxitin, less than or equal to 19 and greater than or equal to 21 mm; clindamycin, less than or equal to 14 and greater than or equal to 18 mm; moxalactam, less than or equal to 21 and greater than or equal to 25 mm; and ticarcillin, less than or equal to 15 and greater than or equal to 16 mm. By applying these zone criteria, the percentage of false-susceptible strains was less than 1% and of false-resistant strains was less than 4% for the drugs tested.

Comparison of agar disk diffusion, microdilution broth, and agar dilution for testing antimicrobial susceptibility of coagulase-negative staphylococci

A collection of 120 oxacillin-susceptible and 120 oxacillin-resistant coagulase-negative staphylococci (CNS) from six tertiary care hospital laboratories were tested by agar disk diffusion, three microdilution broth systems (Sensititre, Dynatech, and Alpkem), and the Vitek AutoMicrobic system for comparison with reference agar dilution results. The antimicrobial agents tested were oxacillin, cefazolin, cefotaxime, cefuroxime, cefamandole, fusidic acid, rifampin, and vancomycin. Incubation was at 30 or 35 degrees C for 24, 48, and 72 h. The broth media were supplemented with 2% NaCl for some antimicrobial agents, and the agar dilution method was used with and without the addition of 4% NaCl. The CNS were identified to species by the method of Kloos and Schleifer. The results showed a lack of concordance between two hospitals with respect to oxacillin susceptibility testing by agar dilution with no NaCl supplement. The reasons are not clear but may be related to variations in media. The 4% NaCl supplement or extended incubation to 48 h eliminated this difference. The cefazolin and cefotaxime susceptibility results in the agar disk diffusion test were unreliable if accepted at face value. Cefamandole testing correlated well with the reference method regardless of the method used, and salt supplementation is not recommended. Most of the oxacillin-resistant CNS were resistant to the other beta-lactam drugs except cefamandole. Of 22 CNS resistant to cefamandole, 21 were S. haemolyticus.

Survey of anaerobic susceptibility patterns in Canada

The in vitro activity of penicillin, cefoxitin, moxalactam, ticarcillin, clindamycin, chloramphenicol, and metronidazole against 590 anaerobic isolates collected from five Canadian hospitals during 1984 was determined by an agar dilution technique. Cefoxitin, clindamycin, chloramphenicol, and metronidazole were very active against most of the isolates. No major regional differences in the susceptibility patterns were observed.

In-vitro activity of amoxycillin and ticarcillin in combination with clavulanic acid compared with that of new beta-lactam agents against species of the Bacteroides fragilis group

One hundred and one isolates representing five species of the Bacteroides fragilis group were examined for their susceptibility to amoxycillin and ticarcillin alone or in combination with clavulanic acid, as well as to cefoxitin, latamoxef (moxalactam), ceftizoxime, imipenem, chloramphenicol, clindamycin and metronidazole by the proposed NCCLS agar dilution method. Bactericidal activity of amoxycillin, ticarcillin, combinations of amoxycillin-clavulanic acid and ticarcillin-clavulanic acid, cefoxitin and latamoxef against 54 strains was further assessed by a dilution test in broth. The most active agents were imipenem and the combinations of amoxycillin-clavulanic acid and ticarcillin-clavulanic acid. MIC results indicated that Bacteroides fragilis and B. vulgatus were more susceptible to beta-lactams than were B. distasonis, B. ovatus and B. thetaiotaomicron. Clavulanic acid greatly potentiated the activity of amoxycillin and ticarcillin against the 94 beta-lactamase positive strains but had no effect on the seven B. distasonis isolates that were beta-lactamase negative. Synergistic bactericidal activities could be observed by the amoxycillin-clavulanic and ticarcillin-clavulanic combinations.

Comparison of anaerobic susceptibility results obtained by two methods of inoculum preparation

We evaluated the use of inocula prepared directly from blood agar plates in agar dilution susceptibility tests of anaerobic bacteria and compared the results with susceptibility results obtained from the National Committee for Clinical Laboratory Standards proposed thioglycolate broth cultures. The objectives were to evaluate the reproducibility of each of the two methods of inoculum preparation and to compare the MICs obtained by each method. The reproducibility studies were conducted on 14 stock strains. The mode MICs obtained by the direct agar method were identical to those obtained by the reference broth method 74% of the time and within +/- 1 log2 dilution 100% of the time. The degree of reproducibility of each of the two methods was identical (93% +/- 1 log2 dilution). MIC results obtained by the direct agar method agreed with the MICs obtained by the reference broth culture method in 92.9% of 1,125 MIC data pair determinations performed on stock cultures. The reproducibility of the direct agar method within +/- 1 log2 dilution step for 115 fresh clinical isolates was 93%, including 93.4% of the results with the Bacteroides fragilis group. Only two very major discrepancies (false-susceptible by the agar method) were identified among the 708 MIC data pairs on these clinical isolates. Preparation of inocula directly from growth on agar plates provides a rapid and reproducible method for agar dilution susceptibility testing of anaerobes.

Antimicrobial susceptibilities of coagulase-negative staphylococci isolated from urinary infections

The susceptibilities of 107 urinary isolates of coagulase-negative staphylococci to 19 antibiotics was determined by an agar dilution technique. Major differences in the antimicrobial susceptibilities of species of coagulase-negative staphylococci were observed. Staphylococcus epidermidis was more resistant to a wider spectrum of antibiotics than was Staphylococcus saprophyticus.

Anaerobic septic arthritis

During a 3 1/2 year period anaerobic septic arthritis was diagnosed in 43 patients (46 joints). The hip and knee accounted for 83% of the infected joints. Anaerobic infections complicated elective musculoskeletal surgery in 23 patients, including 21 with total joint arthroplasties. An additional 12 patients developed septic arthritis following surgical treatment of traumatic injuries of an extremity. Gram-positive cocci were the anaerobes most commonly found in these two groups of surgical patients, accounting for 64% of the isolates; Peptococcus magnus was the most common organism. In contrast, gram-negative bacilli (especially Bacteroides fragilis) comprised 63% of the anaerobes isolated from eight patients with chronic debilitating diseases who had not had prior surgery. Only anaerobes were recovered from approximately half of all the patients with septic arthritis while mixed aerobic-anaerobic cultures accounted for the remainder. Adequate treatment required aggressive surgery and prolonged (minimum of three weeks) antimicrobial therapy. Infected total joint arthroplasties had to be removed. Loss of joint function occurred in six patients with posttraumatic infections when surgery was delayed or antimicrobials were inadequate. Outcome was poorest in the patients with chronic debilitating diseases, four of whom died.

Emergence of rifampin-resistant Haemophilus influenzae

Rifampin susceptibility of nasopharyngeal Haemophilus influenzae strains was determined before and after community-wide chemoprophylaxis with rifampin (children) and sequential minocycline-rifampin (adults). All strains were rifampin susceptible before prophylaxis, but 10.3% of the strains at 1 week and 7.5% of the strains at 9 weeks after prophylaxis were rifampin resistant.

Chemoprophylaxis for Neisseria meningitidis in an isolated Arctic community

Community chemoprophylaxis with a regimen of sequential minocycline/rifampin (adults) or rifampin alone (children [less than 12 years of age]) was undertaken in a remote Arctic community one year after an outbreak of meningitis due to Neisseria meningitidis serogroup B. Nasopharyngeal carriage rates of N. meningitidis before prophylaxis were 32.4% in Inuit (Eskimos) and 6% in Caucasians, with maximal carriage (44.8%) in adolescents. Serogroup B accounted for 63.9% of all isolates before prophylaxis. One week after prophylaxis, the nasopharyngeal carriage rates were 0.8% in Inuit who had received prophylaxis and 33.3% in those who had not received prophylaxis (P less than 0.005). This reduction persisted at nine weeks after prophylaxis, when carriage rates were 1.2% in those who had received prophylaxis and 22.6% in individuals who had not received prophylaxis. Of the strains obtained before prophylaxis, 7.8% were sulfadiazine-resistant, whereas 35% of all isolates obtained from prophylaxis were sulfadiazine-resistant. Rifampin- or minocycline-resistant strains were not identified either before or after prophylaxis.

Trimethoprim-rifampin, a new combination agent: efficacy in localized urinary infection and influence on microflora

Twenty women with recurrent or persistent urinary tract infections were treated with a fixed combination of trimethoprim-rifampin (TMP-RAM). The site of infection was established by the antibody-coated bacteria test. Sixteen women had upper tract infections (antibody-coated bacteria tests positive); eight were cured, three failed, and five relapsed. All four women with lower tract infections (antibody-coated bacteria tests negative) were cured. Three of five patients with structural abnormalities failed. The 12 cures and 5 relapses were associated with organisms susceptible to either TMP (minimal inhibitory concentration, less than or = to 7 micrograms/ml) or RAM (minimal inhibitory concentration, less than or = to 32 micrograms/ml). In contrast, two of the three failures were associated with organisms resistant to both TMP and RAM. In one patient, RAM resistance emerged during treatment. During therapy, urinary strains were eradicated from the periurethral and anal-canal areas in all but 3 fo 16 patients. Adverse reactions, noted in 16 women, included nausea (10), dizziness (6), headaches (2), rash (1), an blurred vision (1). Antimicrobial susceptibility data on 246 isolated from urinary, periurethral, and anal-canal specimens are included. Our findings suggest that TMP-RAM is effective in urinary infections and may prevent the emergence of RAM-resistant strains.

Peptococcus magnus: a significant human pathogen

Peptococcus magnus was recovered from 10% of anaerobic cultures collected from suspected clinical infections over a 3.5-year period. It was the commonest species of anaerobic gram-positive cocci isolated (30%). To evaluate the clinical significance of this organism, we retrospectively reviewed the charts of 222 patients from whom P. magnus was isolated. Twenty-five patients had no evidence of infection, 151 had mixed infections, and 32 had infections from which only P. magnus was isolated (pure cultures). Mixed infections involved the following sites: bone and joint (32 cases), soft tissue (57 cases), foot ulcers (29 cases), abdominal cavity (16 cases), and miscellaneous (17 cases). The average number of organisms was four (2.5 facultatives and 1.5 anaerobes). Eighteen patients with pure cultures of P. magnus had bone or joint infections, and foreign bodies were present in 15 of these. Other pure cultures of P magnus infections included 12 soft tissue, one vascular graft, and one infected sternotomy with persistent bacteremia. Pure culture infections were usually chronic, and serious sequelae often resulted. Peptococcus magnus is frequently isolated from significant infections and seems particularly pathogenic in infections of bones and joints or in association with the presence of foreign bodies, or both.