Comparison of commercial assays and laboratory developed tests for detection of SARS-CoV-2.

The global COVID-19 pandemic has led to the rapid development of tests for detection of SARS-CoV-2. Studies are required to assess the relative performance of different assays. Here, we compared the performance of two commercial assays, the cobas® SARS-CoV-2 (Roche Diagnostics) and Xpert® Xpress SARS-CoV-2 (Cepheid®) tests, and a laboratory developed RT-PCR test adapted for use on the Hologic® Panther Fusion® (Hologic®) instrument as well as Bio-Rad and QIAGEN real-time PCR detection systems. Performance characteristics for each test were determined by testing clinical specimens and reference material. All assays detect the pan-Sarbecovirus E (envelope structural protein) gene plus a SARS-CoV-2-specific target. The limit of detection for the E gene target varied from ∼2 copies/reaction to >30 copies/reaction. Due to assay-specific differences in sample processing and nucleic acid extraction, the overall analytical sensitivity ranged from 24 copies/mL specimen to 574 copies/mL specimen. Despite these differences, there was 100 % agreement between the commercial and laboratory developed tests. No false-negative or false-positive SARS-CoV-2 results were observed and there was no cross-reactivity with common respiratory viruses, including endemic coronaviruses.

Antimicrobial susceptibility of Clostridioides difficile isolated from diarrhoeal stool specimens of Canadian patients: summary of results from the Canadian Clostridioides difficile (CAN-DIFF) surveillance study from 2013 to 2017.

OBJECTIVES: To summarize data generated by the Canadian Clostridioides difficile (CAN-DIFF) surveillance study from 2013 to 2017. METHODS: Isolates of C. difficile (n = 2158) were cultured from toxin-positive diarrhoeal stool specimens submitted by eight hospital laboratories to a coordinating laboratory. Antimicrobial susceptibility testing was performed according to the CLSI agar dilution method (M11, 2018). Isolate ribotypes were determined using an international, standardized, high-resolution capillary gel-based electrophoresis protocol. RESULTS: Of the 2158 isolates of C. difficile, 2133 (98.8%) had vancomycin MICs ≤2 mg/L [i.e. were vancomycin susceptible (EUCAST breakpoint tables, v 9.0, 2019) or WT (CLSI M100, 29th edition, 2019)]. Fidaxomicin MICs were lower than those of all other agents tested (MIC90, 0.5 mg/L); however, one isolate with a fidaxomicin MIC of >8 mg/L was identified. Metronidazole MICs ranged from 0.12 to 4 mg/L; all isolates were metronidazole susceptible by the CLSI breakpoint (≤8 mg/L) compared with 96.8% susceptible by the EUCAST breakpoint (≤2 mg/L). In total, 182 different ribotypes were identified from 2013 to 2017. The most common ribotypes identified were 027 (19.3% of isolates) and 106 (8.2%). Ribotype 027 isolates were frequently moxifloxacin resistant (87.3% of isolates) and MDR (48.6%), associated with vancomycin (10/25, 40.0%) and metronidazole (58/69, 84.1%) resistance and from patients aged ≥80 years. The prevalence of ribotype 027 decreased significantly (P < 0.0001) from 2013 (27.5%) to 2017 (9.0%) and was replaced by increases in ribotype 106 (P = 0.0003) and multiple less common ribotypes. CONCLUSIONS: Periodic surveillance is required to monitor clinical isolates of C. difficile for changes to in vitro susceptibility testing profiles and ribotype evolution.

Antimicrobial susceptibility testing of invasive isolates of Streptococcus pneumoniae from Canadian patients: the SAVE study, 2011-15.

Objectives: To assess antimicrobial susceptibility for 14 agents tested against 6001 invasive isolates of Streptococcus pneumoniae cultured from invasive patient samples from 2011 to 2015 as a part of the annual SAVE study. Methods: Isolates of S. pneumoniae were tested using the standard CLSI broth microdilution method (M07-A10, 2015) with MICs interpreted by CLSI M100 27th Edition (2017) MIC breakpoints. Results: From 2011 to 2015, small but significant increases (P ≤ 0.05) in the percentage susceptibility for penicillin (interpreted by all three CLSI MIC breakpoint criteria) (increase of 1.7%-3.2%), clindamycin (3.1%) and ceftriaxone (interpreted by non-meningitis and meningitis CLSI MIC breakpoint criteria) (1.1%-1.5%) were observed. Susceptibility rates for clarithromycin and other commonly tested antimicrobial agents remained unchanged (P > 0.05) over the 5 year period. Isolates with an MDR phenotype (resistance to three or more antimicrobial agent classes) decreased significantly (P < 0.001) from 8.5% in 2011 to 5.6% in 2015. Antimicrobial susceptibility rates were not generally associated (P > 0.05) with patient gender (exception: clarithromycin) but were associated (P ≤ 0.05) with patient age (chloramphenicol and clindamycin) or specimen source (penicillin, doxycycline, trimethoprim/sulfamethoxazole and clindamycin), as well as geographic location in Canada and concurrent resistance to penicillin or clarithromycin. Conclusions: The in vitro susceptibility of invasive isolates of S. pneumoniae in Canada to penicillin, clindamycin and ceftriaxone increased from 2011 to 2015, coincident with a significant decrease in MDR phenotypes.

Analysis of multidrug resistance in the predominant Streptococcus pneumoniae serotypes in Canada: the SAVE study, 2011-15.

Objectives: This study assessed MDR invasive isolates of Streptococcus pneumoniae, in relation to serotype evolution in Canada between 2011 and 2015 as part of the annual SAVE study. Methods: As part of a collaboration between the Canadian Antimicrobial Resistance Alliance and Public Health Agency of Canada-National Microbiology Laboratory, 6207 invasive isolates of S. pneumoniae were evaluated. All isolates were serotyped and had antimicrobial susceptibility testing performed, in accordance with CLSI guidelines (M07-A10, 2015). Complete susceptibility profiles were available for 6001 isolates. MDR was defined as resistance to three or more classes of antimicrobial agents (with penicillin MIC ≥2 mg/L defined as resistant). Results: The overall rate of MDR S. pneumoniae was 6.2% (372/6001) in SAVE, decreasing significantly from 8.5% in 2011 to 5.6% in 2015 (P = 0.0041). MDR was observed in 32 serotypes, with serotypes 15A and 19A predominating (26.6% and 41.7% of the MDR isolates, respectively). The overall proportion of serotypes 19A, 7F and 33A decreased significantly (P < 0.0001) throughout the study. The annual proportion of serotypes 7C, 8, 9N, 10A, 20, 24F, 29, 31, 33F, 35B and 38 increased throughout the study; however, among these increasing serotypes, MDR was only notable (>5%) for 24F and 33F. Conclusions: In 2015, 56.3% of invasive MDR S. pneumoniae were serotypes included in the PCV-13 vaccine. PCV-13 includes the most commonly identified serotype, 19A; however, other increasingly important MDR serotypes, such as 15A, 24F and 33F, are notably not in the currently used vaccines.

PCR ribotyping and antimicrobial susceptibility testing of isolates of Clostridium difficile cultured from toxin-positive diarrheal stools of patients receiving medical care in Canadian hospitals: the Canadian Clostridium difficile Surveillance Study (CAN-DIFF) 2013-2015.

Clostridium difficile toxin-positive diarrheal stool specimens submitted to eight Canadian hospital laboratories from 2013 to 2015 were cultured. Polymerase chain reaction ribotyping of isolates was performed using an internationally standardized, high-resolution capillary gel-based electrophoresis protocol and antimicrobial susceptibility testing conducted by CLSI-defined agar dilution (M11-A8, 2012). Among the 1310 isolates of C. difficile cultured, 141 different ribotypes were identified; the most common ribotypes were 027 (24.5% of isolates), 014 (7.7%), 020 (6.6%), 106 (6.1%), and 002 (4.6%). Ribotype 027 was the commonest ribotype in all geographic regions of Canada and was more frequently isolated from patients aged ≥80 years (40.6%) than younger patients (P<0.00001). Ribotype 027 isolates were frequently moxifloxacin-resistant (92.2% of isolates) and multidrug-resistant (49.5%). Fidaxomicin demonstrated the greatest in vitro potency (lowest MIC90, 0.5 µg/mL; lowest maximum MIC, 2 µg/mL) of eight antimicrobial agents tested and was the most active agent against each of the five commonest ribotypes (MIC90, 0.25-1 µg/mL).

Telavancin: mechanisms of action, in vitro activity, and mechanisms of resistance.

Telavancin is a semisynthetic lipoglycopeptide derivative of vancomycin. Telavancin has a dual mechanism of antibacterial action, disrupting peptidoglycan synthesis and cell membrane function. In 2014, the Clinical and Laboratory Standards Institute (CLSI) revised the antimicrobial susceptibility testing method for telavancin, resulting in minimum inhibitory concentration (MIC) determinations that are more accurate and reproducible and demonstrate greater in vitro potency than shown with the previous testing method. The CLSI testing method changes coincided with revised telavancin MIC interpretive break point criteria for susceptibility approved by the US Food and Drug Administration for Staphylococcus aureus (≤0.12 µg/mL), Streptococcus pyogenes (≤0.12 µg/mL), Streptococcus agalactiae (≤0.12 µg/mL), Streptococcus anginosus group (≤0.06 µg/mL), and Enterococcus faecalis (vancomycin susceptible, ≤0.25 µg/mL). Telavancin is equally potent against methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). It demonstrates activity against isolates of heterogeneous vancomycin-intermediate S. aureus and vancomycin-intermediate S. aureus but is poorly active against vancomycin-resistant S. aureus. It also demonstrates potent activity against Staphylococcus epidermidis and Streptococcus spp. (MIC90 ≤0.03 µg/mL). Thus far, it has not been possible to select for high-level telavancin resistance in the laboratory using serially passaged clinical isolates of MRSA and MSSA.

Evaluation of five chromogenic agar media and the Rosco Rapid Carb screen kit for detection and confirmation of carbapenemase production in Gram-negative bacilli.

An efficient workflow to screen for and confirm the presence of carbapenemase-producing Gram-negative bacilli was developed by evaluating five chromogenic screening agar media and two confirmatory assays, the Rapid Carb screen test (Rosco Diagnostica A/S, Taastrup, Denmark) and the modified Hodge test. A panel of 150 isolates was used, including 49 carbapenemase-producing isolates representing a variety of ß-lactamase enzyme classes. An evaluation of analytical performance, assay cost, and turnaround time indicated that the preferred workflow (screening test followed by confirmatory testing) was the chromID Carba agar medium (bioMérieux, Marcy l'Étoile, France), followed by the Rapid Carb screen test, yielding a combined sensitivity of 89.8% and a specificity of 100%. As an optional component of the workflow, a determination of carbapenemase gene class via molecular means could be performed subsequent to confirmatory testing.

An unusual case of Streptococcus anginosus group pyomyositis diagnosed using direct 16S ribosomal DNA sequencing.

Bacteria belonging to the Streptococcus anginosus group (Streptococcus intermedius, Streptococcus constellatus and Streptococcus anginosus) are capable of causing serious pyogenic infections, with a tendency for abscess formation. The present article reports a case of S anginosus group pyomyositis in a 47-year-old man. The pathogen was recovered from one of two blood cultures obtained from the patient, but speciation was initially not performed because the organism was considered to be a contaminant (viridans streptococci group). The diagnosis was ultimately confirmed using 16S ribosomal DNA sequencing of purulent fluid obtained from a muscle abscess aspirate. The present case serves to emphasize that finding even a single positive blood culture of an organism belonging to the S anginosus group should prompt careful evaluation of the patient for a pyogenic focus of infection. It also highlights the potential utility of 16S ribosomal DNA amplification and sequencing in direct pathogen detection from aspirated fluid in cases of pyomyositis in which antimicrobial therapy was initiated before specimen collection.

Les bactéries qui appartiennent au groupe Streptococcus anginosus (streptocoques intermedius, constellatus et anginosus) peuvent causer de graves infections à pyogènes qui ont tendance à former des abcès. Le présent article contient un cas de pyomyosite du groupe S anginosus chez un homme de 47 ans. Le pathogène a été décelé récupéré dans une des deux cultures sanguines prélevées sur le patient, mais au départ, la spéciation n'a pas été effectuée parce que l'organisme était considéré comme un contaminant (groupe de streptocoques viridians). Le diagnostic a finalement été confirmé au moyen du séquençage de l'ADN ribosomal 16S du fluide purulent obtenu dans l'aspirat d'un abcès musculaire. Le présent cas fait ressortir le fait que la détection d'une seule culture sanguine positive dans un organisme appartenant au groupe S anginosus devrait susciter une évaluation attentive du patient afin de trouver un foyer d'infection à pyogènes. Il fait également ressortir l'utilité potentielle de l'amplification et du séquençage de l'ADN ribosomal 16S pour la détection directe d'un pathogène dans le fluide aspiré en cas de pyomyosite lorsque le traitement aux antibiotiques a commencé à être administré avant le prélèvement.

Evolution and molecular characterization of macrolide-resistant Streptococcus pneumoniae in Canada between 1998 and 2008.

OBJECTIVES: Studies were performed to assess resistance mechanisms, multidrug resistance (MDR), genetic relatedness, serotype distribution, heptavalent pneumococcal conjugate vaccine (PCV7) coverage and pili virulence factors among macrolide-resistant Streptococcus pneumoniae (MRSP) isolated from respiratory samples submitted to hospital laboratories across Canada from 1998 to 2008. METHODS: Isolates of MRSP (n = 1518) collected by the national surveillance studies CROSS (Canadian Respiratory Organism Susceptibility Study; 1998-2006) and CANWARD (Canadian Ward Surveillance Study; 2007-08) were tested using the CLSI broth microdilution method to establish antimicrobial susceptibilities. PCR was used to detect macrolide resistance genes [mef(A) and erm(B)] and pili virulence factors (type 1 pili and type 2 pili), the Quellung reaction was used to identify serotypes and PFGE was used to determine genetic relatedness. RESULTS: The prevalence of MRSP increased from 8% in 1998 to 22% in 2008 (P = 0.0001). MRSP were 51% mef(A) positive, 36% erm(B) positive, 8% dual mef(A) and erm(B) positive and 5% mef(A) and erm(B) negative. Dual mef(A)- and erm(B)-positive isolates increased in prevalence from 3% in 1998 to 19% in 2008 (P = 0.001). The prevalence of PCV7 serotypes (4, 6B, 9V, 14, 18C, 19F and 23F) decreased from 67% in 1998 to 31% in 2008 (P = 0.0072). The prevalence of serotype 19A, a non-PCV7 serotype, increased by 15% from 1998 to 2008; isolates of serotype 19A were MDR, dual mef(A) and erm(B) positive, genetically related by PFGE and associated with the presence of pili virulence factors. CONCLUSIONS: From 1998 to 2008, respiratory isolates of MRSP in Canada increased significantly due primarily to the emergence and spread of serotypes 6A, 19A and other non-PCV7 serotypes.

Hypermucoviscous Klebsiella syndrome without liver abscess in a patient with immunoglobulin g2 immune deficiency.

BACKGROUND: Hypermucoviscous Klebsiella pneumoniae (HMVKP) emerged as a cause of invasive infections in South-East (SE) Asia. It has become the most common cause of liver abscess in that region, and it is a significant causative organism in endogenous endophthalmitis and meningitis. During the past decade, cases of this uniquely virulent organism have been reported outside of SE Asia, with a propensity to affect individuals of SE Asian descent. Cases have been reported from North America including Canada. METHODS: We report a case of a patient of Filipino descent living in Canada who presented with recurrent HMVKP bacteremia in the absence of pyogenic liver abscess or other localized metastatic Klebsiella infection. RESULTS: Investigations identified an immunoglobulin (Ig)G2 deficiency and low IgM indicating potential common variable immunodeficiency, and administration of intravenous immunoglobulins was associated with prevention of further recurrences. CONCLUSIONS: To our knowledge, this is the first report of HMVKP associated with predisposing antibody deficiency.

Assessment of the activity of ceftaroline against clinical isolates of penicillin-intermediate and penicillin-resistant Streptococcus pneumoniae with elevated MICs of ceftaroline using an in vitro pharmacodynamic model.

OBJECTIVES: This study assessed the pharmacodynamics of ceftaroline against penicillin-intermediate and penicillin-resistant Streptococcus pneumoniae with elevated MICs of ceftaroline using an in vitro pharmacodynamic model. METHODS: Nine isolates of S. pneumoniae, including one penicillin-susceptible isolate, one penicillin-intermediate isolate and seven penicillin-resistant isolates, were tested. The pharmacodynamic model was inoculated with a concentration of 1 × 10(6) cfu/mL and ceftaroline was dosed twice daily (at 0 and 12 h) to simulate the fC(max) (maximum free concentration in serum) and t(1/2) (half-life in serum) obtained after 600 mg intravenous doses every 12 h (fC(max), 16 mg/L; t(1/2), 2.6 h). Ceftaroline was compared with ceftriaxone dosed once daily to simulate the fC(max) and t(1/2) obtained after a 1 g dose (fC(max), 18 mg/L; t(1/2), 8.0 h). Samples were collected over 24 h to assess viable growth and possible changes in ceftaroline MICs over time. RESULTS: Ceftaroline fT(>MIC) (time of free serum concentration over the MIC) of 100% (ceftaroline MICs, ≤ 0.5 mg/L) was bactericidal (≥ 3 log(10) killing) against all isolates at 6 h and completely eradicated all organisms at 12 and 24 h. No bacterial regrowth occurred over the study period and no changes in ceftaroline MICs were observed. Upon ceftriaxone exposure, S. pneumoniae isolates with ceftriaxone MICs of 0.12 and 0.25 mg/L were eradicated, but isolates with ceftriaxone MICs of 1-8 mg/L resulted in initial bacterial reduction at 6 h with organism regrowth at 12 h and no reduction in organism concentration, relative to the starting inoculum, at 24 h. CONCLUSIONS: Ceftaroline fT(>MIC) of 100% (ceftaroline MICs, ≤ 0.5 mg/L) was bactericidal (≥ 3 log(10) killing) and eradicated all S. pneumoniae at 12 and 24 h with no regrowth.

Caulobacter species as a cause of postneurosurgical bacterial meningitis in a pediatric patient.

Caulobacter species have been rarely found to be a cause of human infection. A case of probable Caulobacter species meningitis occurring postneurosurgery in a pediatric patient is reported in the present article. Gram stain and colony morphology of the isolate were not consistent with the identification provided by commercial phenotypic identification systems. The present case illustrates the need to reconcile conflicting phenotypic test results using 16S ribosomal DNA sequencing.Caulobacter species have been rarely found to be a cause of human infection. A case of probable Caulobacter species meningitis occurring postneurosurgery in a pediatric patient is reported in the present article. Gram stain and colony morphology of the isolate were not consistent with the identification provided by commercial phenotypic identification systems. The present case illustrates the need to reconcile conflicting phenotypic test results using 16S ribosomal DNA sequencing.

Les espèces de Caulobacter sont rarement responsables d'infections chez les humains. Les auteurs rendent compte d'un cas probable de méningite à espèces de Caulobacter après une neurochirurgie chez un patient d'âge pédiatrique. La coloration de Gram et la morphologie des colonies de l'isolat ne correspondaient pas aux résultats obtenus par les systèmes de repérage phénotypiques commerciaux. Le présent cas démontre la nécessité de réconcilier les résultats des tests phénotypiques conflictuels au moyen du séquençage d'ADN ribosomique 16S.

Ceftaroline pharmacodynamic activity versus community-associated and healthcare-associated methicillin-resistant Staphylococcus aureus, heteroresistant vancomycin-intermediate S. aureus, vancomycin-intermediate S. aureus and vancomycin-resistant S. aureus using an in vitro model.

BACKGROUND: This study assessed the pharmacodynamics of ceftaroline against methicillin-resistant Staphylococcus aureus (MRSA), heteroresistant (h) vancomycin-intermediate S. aureus (hVISA), VISA and vancomycin-resistant S. aureus (VRSA) using an in vitro model. METHODS: Two methicillin-susceptible S. aureus (MSSA), one community-associated (CA)-MRSA, one healthcare-associated (HA)-MRSA, one hVISA, three VISA and two VRSA were studied. The pharmacodynamic model was inoculated with a concentration of 1 × 106 cfu/mL and ceftaroline dosed every 12 h (at 0 and 12 h) to simulate the ƒC(max) and t(½) obtained after administering 600 mg intravenously every 12 h (ƒC(max), 16 mg/L; t(½), 2.6 h). Samples were collected over 24 h to assess viable growth and changes in ceftaroline MIC over time. RESULTS: Ceftaroline ƒT(> MIC) of ≥ 92% (ceftaroline MICs, ≤ 1 mg/L) was bactericidal (≥ 3 log10 killing) against MSSA, CA-MRSA, HA-MRSA, hVISA, VISA and VRSA at 12 and 24 h. No bacterial regrowth occurred over the study period and no change in ceftaroline MIC was observed. CONCLUSIONS: Ceftaroline ƒT(> MIC) of ≥ 92% (ceftaroline MICs, ≤ 1 mg/L) was bactericidal (≥ 3 log10 killing) against MSSA, CA-MRSA, HA-MRSA, hVISA, VISA and VRSA at 12 and 24 h.

Pharmacodynamic activity of ceftobiprole compared with vancomycin versus methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate Staphylococcus aureus (VISA) and vancomycin-resistant Staphylococcus aureus (VRSA) using an in vitro model.

BACKGROUND: This study compared the pharmacodynamics of ceftobiprole and vancomycin against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate S. aureus (VISA) and vancomycin-resistant S. aureus (VRSA) using an in vitro model. METHODS: Two methicillin-susceptible S. aureus (MSSA), two community-associated (CA)-MRSA, one healthcare-associated (HA)-MRSA, three VISA and two VRSA were studied. The pharmacodynamic model was inoculated with a concentration of 1 x 10(6) cfu/mL and ceftobiprole dosed every 8 h (at 0, 8 and 16 h) to simulate the fC(max) and t(1/2) obtained after 500 mg intravenous (iv) every 8 h dosing (fC(max,) 30 mg/L; t(1/2,) 3.5 h). Vancomycin was dosed every 12 h (at 0 and 12 h) to simulate fC(max) and t(1/2) obtained after 1 g iv every 12 h dosing (fC(max), 20 mg/L; t(1/2), 8 h). Samples were collected over 24 h to assess viable growth. RESULTS: Ceftobiprole T > MIC of > or =100% (ceftobiprole MICs, < or =2 mg/L) was bactericidal (> or =3 log(10) killing) against MSSA, CA-MRSA, HA-MRSA, VISA and VRSA at 16 and 24 h. Vancomycin fAUC(24)/MIC of 340 (vancomycin MIC, 1 mg/L for MSSA and MRSA) resulted in a 1.8-2.6 log(10) reduction in colony count at 24 h. Vancomycin fAUC(24)/MIC of 85-170 (vancomycin MIC, 2-4 mg/L for VISA) resulted in a 0.4-0.7 log(10) reduction at 24 h. Vancomycin fAUC(24)/MIC of 5.3 (vancomycin MIC, 64 mg/L for VRSA) resulted in a limited effect. CONCLUSIONS: Ceftobiprole T > MIC of > or =100% (ceftobiprole MICs, < or =2 mg/L) was bactericidal (> or =3 log(10) killing) against MSSA, CA-MRSA, HA-MRSA, VISA and VRSA at 16 and 24 h. Vancomycin was bacteriostatic against MSSA, MRSA and VISA, while demonstrating no activity against VRSA.

Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002 to 2004.

The extent to which clonal spread contributes to emerging antimicrobial resistance in Escherichia coli is incompletely defined. To address this question within a recent, nationally representative strain collection, three established drug-resistant E. coli clonal groups (i.e., clonal group A, E. coli O15:K52:H1, and sequence type 131 [ST131]) were sought among 199 E. coli urine isolates recovered from across Canada from 2002 to 2004, with stratification by resistance to trimethoprim-sulfamethoxazole (TS) and fluoroquinolones (FQs). The isolates' clonal backgrounds, virulence genotypes, and macrorestriction profiles were assessed. The three clonal groups were found to account for 37.2% of isolates overall, but accounted for 0% of TS-susceptible (TS-S) and FQ-susceptible (FQ-S) isolates, 20% of TS-resistant (TS-R) and FQ-S isolates, 60% of TS-S and FQ-R isolates, and 68% of TS-R and FQ-R isolates (P < 0.001). E. coli ST131, the most prevalent clonal group, accounted for 23.1% of isolates overall and for 44% of the FQ-R isolates. Nearly all ST131 isolates were FQ-R (96%) but, notably, cephalosporin susceptible (98%). Although the distinctive virulence profiles of the FQ-R clonal group isolates were less extensive than those of the susceptible isolates, they were significantly more extensive than those of the other FQ-R isolates. These findings indicate that among the E. coli urine isolates studied, resistance to TS and FQs has a prominent clonal component, with the O15:K52:H1 clonal group and especially E. coli ST131 being the major contributors. These clonal groups appear to be more virulent than comparably resistant isolates, possibly contributing to their success as emerging multi-drug-resistant pathogens.

Mechanisms of resistance and mobility among multidrug-resistant CTX-M-producing Escherichia coli from Canadian intensive care units: the 1st report of QepA in North America.

We studied the molecular mechanisms of resistance and mobility of 18 multidrug-resistant CTX-M-producing Escherichia coli isolates isolated from patients in Canadian intensive care units. Fluoroquinolone-resistant isolates (83.3%) had mutations in gyrA and parC. Plasmid-mediated quinolone resistance genes qnr (A, B, and S), qepA, and aac(6')-Ib-cr were detected in 0%, 5.6%, and 44.4%, respectively. Sulfamethoxazole/trimethoprim-resistant isolates (61.1%) carried a dfr gene, and 10 (90.9%) of the 11 carried 1 or more sul genes. Gentamicin-resistant isolates (27.8%) carried the aac(3')-II gene, and doxycycline-resistant isolates (33.3%) carried 1 or more tet efflux genes. Both genetically related and unrelated groups of E. coli harboring extended-spectrum beta-lactamases were observed. The bla(CTX-M) genes were primarily located on diverse IncF plasmids of multiple replicon types downstream of the ISEcp1 element. The spread of the bla(CTX-M) genes among E. coli in Canada occurs through a diversity of different mechanisms and does not correspond to a single CTX-M determinant, or a single clone, or a single plasmid but rather through the combination of clonal spread of virulent strains and acquisition of diverse CTX-M-bearing plasmids. We report the 1st qepA-producing E. coli in North America.

Antimicrobial susceptibility of 3931 organisms isolated from intensive care units in Canada: Canadian National Intensive Care Unit Study, 2005/2006.

We tested the in vitro activity of 15 antimicrobials against Gram-positive cocci and 12 antimicrobials against Gram-negative bacilli versus 3931 isolates (20 most common organisms) obtained between September 1, 2005, and June 30, 2006, from 19 intensive care units (ICUs) across Canada. The most active (based upon MIC only) agents against methicillin-resistant Staphylococcus aureus and methicillin-resistant Staphylococcus epidermidis were dalbavancin, daptomycin, linezolid, tigecycline, and vancomycin with MIC(90) (microg/mL) of 0.06 and < or =0.03, 0.25 and 0.12, 2 and 1, 0.5 and 0.5, and 1 and 2, respectively. The most active agents against vancomycin-resistant enterococci were daptomycin, linezolid, and tigecycline with MIC(90) (microg/mL) of 1, 4, and 0.12, respectively. The most active agents against Escherichia coli were amikacin, cefepime, meropenem, piperacillin/tazobactam, and tigecycline with MIC(90) (microg/mL) of 4, < or =1, < or =0.12, 8, and 0.5, respectively. The most active agents against extended-spectrum beta-lactamase-producing E. coli were meropenem and tigecycline with MIC(90) (microg/mL) of < or =0.12 and 1, respectively. The most active agents against Pseudomonas aeruginosa were amikacin, cefepime, meropenem, and piperacillin/tazobactam with MIC(90) (microg/mL) of 16, 32, 16, and 64, respectively. The most active agents against Stenotrophomonas maltophilia were tigecycline and trimethoprim/sulfamethoxazole with MIC(90) (microg/mL) of 4 and 4, respectively. The most active agents against Acinetobacter baumannii were fluoroquinolones (e.g., levofloxacin), meropenem, and tigecycline with MIC(90) (microg/mL) of 0.5, 1, and 2, respectively. In conclusion, the most active agents versus Gram-positive cocci and Gram-negative bacilli obtained from Canadian ICUs were daptomycin, linezolid, tigecycline, dalbavancin and amikacin, cefepime, meropenem, piperacillin/tazobactam, and tigecycline (not P. aeruginosa), respectively.