CRE were defined according to current CDC guidelines, applied in local clinical microbiology laboratories.10 Briefly, CDC-defined CRE were Enterobacteriaceae that tested resistant to any of the carbapenems (i.e., minimum inhibitory concentrations [MIC] of ≥ 4 μg/mL for doripenem, meropenem, or imipenem, OR ≥ 2 μg/mL for ertapenem) or were documented to harbor a gene encoding a carbapenemase or were positive for carbapenemase production. For Enterobacteriaceae that exhibit intrinsic imipenem non-susceptibility (i.e. Morganella morganii, Proteus species, Providencia species), resistance to carbapenems other than imipenem was required. Eligibility was based on antimicrobial susceptibility testing performed in local contributing clinical microbiology laboratories. Bacterial identification and carbapenem susceptibility testing were performed in these laboratories using MicroScan (Beckman Coulter, Atlanta, GA), Vitek 2, Etest (both bioMérieux, Durham, NC), BD Phoenix, BBL disks (both Becton Dickinson, Durham, NC), Sensititre (Thermo Fisher, Waltham, MA), disc diffusion, or in-house agar dilution. Central carbapenem susceptibility testing was performed in two independent central research laboratories using Etest and MicroScan (Beckman Coulter, Atlanta, GA).
Microscan
Manufactured by Beckman Coulter
Sourced in United States, France, Spain
The MicroScan is a diagnostic instrument used for the identification and antimicrobial susceptibility testing of microorganisms. It utilizes a microdilution technique to determine the minimal inhibitory concentration of various antimicrobial agents against isolated bacterial and fungal species.
Automatically generated - may contain errors
Lab products found in correlation
Vitek 2, by bioMérieux (9 mentions)
Etest, by bioMérieux (5 mentions)
Bactec fx, by BD (5 mentions)
Vitek 2 system, by bioMérieux (4 mentions)
Co2 incubator, by Thermo Fisher Scientific (3 mentions)
Maldi tof ms, by Bruker (2 mentions)
Vitek ms, by bioMérieux (2 mentions)
Imipenem, by Merck Group (2 mentions)
Bactec 9240, by BD (2 mentions)
Mic test strip, by Liofilchem (1 mentions)
Chromoid esbl, by bioMérieux (1 mentions)
Venturi transystem, by Copan (1 mentions)
Sensititre yeastone, by Thermo Fisher Scientific (1 mentions)
Meropenem, by Merck Group (1 mentions)
Aztreonam, by Bristol-Myers Squibb (1 mentions)
Phe arg β naphthylamide paβn, by Merck Group (1 mentions)
Meropenem, by AstraZeneca (1 mentions)
Id 32c system, by bioMérieux (1 mentions)
Bactec plus aerobic, by BD (1 mentions)
Etest strips, by bioMérieux (1 mentions)
41 protocols using microscan
1
Carbapenem-Resistant Enterobacteriaceae Identification
2
Bacterial Isolation and Identification from ICU Samples
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The ICU samples were handled by the King Faisal Hospital Microbiology Laboratory in accordance with the established protocols for bacterial isolation and identification. Blood culture bottles were incubated with Biomeieux BACT/ALERT. Once the machine indicated growth, the samples were cultured in blood, MacConkey, and chocolate agar. Grown-on blood, MacConkey, or CLED agar were urine sample samples. They spent the next five to seven days incubating. Preliminary identification of certain isolates was made using colony morphology, Gram stain, and typical rapid biochemical assays such as catalase, indole, and oxidase tests. According to the procedures of the hospital where the strain originated, gram-negative bacteria were found using Pos Breakpoint Combo Panel Type 50 in MicroScan (Beckman Coulter Inc., Brea, CA, USA) and gram-positive strains using Pos Breakpoint Combo Panel Type 28 in MicroScan (Beckman Coulter Inc., CA, USA).
3
ESBL-E Surveillance with Rectal Swabs
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Rectal swabs for ESBL-E surveillance cultures were collected on the day of admission or the following 2 days, once a week thereafter, and on the day of discharge or the prior and/or following 2 days. Swabs were processed at the local microbiological laboratories following a standardized protocol. Chromogenic agar plates were used for detection of ESBL-E (bioMérieux, Marcy l’Etoile, France). Disk diffusion, Vitek2 (bioMérieux), or MicroScan (Beckman Coulter, Brea, CA) was used to confirm ESBL-E production. Swab results were reported back to the wards as part of routine laboratory notification procedures.10 (link)
4
Antimicrobial Susceptibility Testing Protocol
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Susceptibilities to ampicillin, azithromycin, clindamycin, cefoxitin, ciprofloxacin, daptomycin, erythromycin, gentamicin, linezolid, mupirocin, oxacillin, penicillin, rifampicin, quinupristin-dalfopristin, trimethoprim-sulfamethoxazole, teicoplanin, and vancomycin were tested using microdilution panels (MicroScan, Beckman Coulter Inc., Brea, CA, USA). Ceftaroline and telavancin MIC values were determined using the MIC test strip (Liofilchem, Roseto degli Abruzzi, Italy) and the Oxoid M.I.C.Evaluator™ (M.I.C.E™; Thermo Fisher Scientific, Basingstoke, England), respectively. The plates were incubated at 35 °C and read after 48 h. Population analysis was performed according to a reported method (Saito et al. 2014 (link)). Briefly, about 107–108 colony-forming units (CFU) of the overnight culture of each strain were inoculated on TSA plates containing various concentrations of vancomycin. The numbers of colonies formed after 48 h incubation at 35 °C were counted and plotted in a semilogarithmic graph.
5
Phenotypic and Genotypic Characterization of ESBL and Carbapenemase-Producing Bacteria
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The samples were seeded on ChromoID-ESBL and Chromo-ID CARBA/OXA-48 (BioMérieux, France) selective chromogenic agar plates. Bacterial identification was performed using the MALDI-TOF-MS (Bruker-Daltonics, Germany) mass spectrometry. ESBL and carbapenemase (CP) production were phenotypically confirmed by the double-disk diffusion test, Hodge test and KPC/MBL/OXA-48 Confirm and ESBL AmpC screen kits (Rosco Diagnostica, Germany). Antimicrobial susceptibility was studied with microdilution (MicroScan, Beckman, CA) and gradient strips (Etests, BioMérieux, France). Genes codifying ESBL (blaSHV, blaTEM, blaCTX-M) and CP (blaVIM, blaKPC, blaNDM, blaOXA-48) were characterised by PCR and sequencing.
6
Skin Infection: Microbial Identification and Antibiotic Susceptibility
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Skin swab cultures (sterile transport swab on Stuart agar gel medium, Copan Venturi Transystem®; Copan, Murrieta, CA, USA) were performed at suspected sites of skin infection and then inoculated on blood agar plates followed by McConkey agar plates. They were subsequently incubated in a carbon dioxide (CO2) incubator set at 35℃ and 5% CO2 for 1 day (Thermo Scientific Inc., Waltham, MA, USA). Gram staining was performed in the presence of colonies on inoculated culture medium. Gram-positive bacteria were judged to be S. aureus when their catalase and coagulase tests were positive, and CoNS was determined according to negative catalase and coagulase results. Subsequently, the specimens were inoculated on Mueller-Hinton agar and tested for susceptibility to antibiotics by disk diffusion method.
For other species, automation equipment, including VITEK 2 (bioMerieux Inc., Hazelwood, MO, USA) and MicroScan (Beckman Coulter Inc., Brea, CA, USA), was used for microbial identification and antibiotic susceptibility tests.
For other species, automation equipment, including VITEK 2 (bioMerieux Inc., Hazelwood, MO, USA) and MicroScan (Beckman Coulter Inc., Brea, CA, USA), was used for microbial identification and antibiotic susceptibility tests.
7
Diagnosis of Bacteremia and Antibiotic Susceptibility
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Two sets of blood cultures were collected for each bacteremia episode using BD BACTEC PLUS Aerobic/F plus Anaerobic/F or Lytic/10 Anaerobic/F mediums. The samples were processed in a BD BACTEC FX blood culture system (Becton Dickinson, Barcelona, Spain).
Urine samples were plated on CLED agar following standard procedures. S. aureus was identified by classical methods (latex agglutination and DNase production) or by MALDI-TOF (since 2013).
Antimicrobial susceptibility was determined according to the EUCAST guidelines by either disk diffusion method (urine samples) or microdilution (blood samples) using commercially available panels (MicroScan, Beckman Coulter, Barcelona, Spain) [19 ].
Urine samples were plated on CLED agar following standard procedures. S. aureus was identified by classical methods (latex agglutination and DNase production) or by MALDI-TOF (since 2013).
Antimicrobial susceptibility was determined according to the EUCAST guidelines by either disk diffusion method (urine samples) or microdilution (blood samples) using commercially available panels (MicroScan, Beckman Coulter, Barcelona, Spain) [19 ].
8
Carbapenem-Resistant Enterobacteriaceae Characterization
9
Rapid Pathogen Identification and Antibiotic Susceptibility for COVID-19 Patients
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When a positive blood culture result was notified, medical staff treating COVID-19 patients could request a dRAST with MALDI-TOF or MALDI-TOF only, based on individual judgment. They evaluated the need for obtaining results earlier on basis of clinical factors such as patients’ severity. If requested by the primary medical team, blood culture samples were subjected to MALDI-TOF mass spectrometry (Biotyper and Sepsityper kits; Bruker Daltonik GmbH, Bremen, Germany) [25 (link)]. Then if ordered, rapid phenotypic AST was performed using the QMAC-dRAST (QuantaMatrix, Inc., Korea), a method based on microscopic image analysis with microfluidic chip technology [22 (link)]. Along with MALDI-TOF, dRAST can determine minimal inhibitory concentrations (MIC) and antimicrobial susceptibility within 6 h after Gram staining. MIC results were interpreted according to the Clinical and Laboratory Standards Institute M100-Ed30, 2020 [26 ]. Conventional AST used the Micro-Scan (Beckman Coulter, Inc., Atlanta, GA, USA) for Gram-positive bacteria and the VITEK2 system (bioMerieux, Inc., Durham, NC, USA) for Gram-negative bacteria.
10
Antimicrobial Susceptibility Testing of S. aureus
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As part of the daily practice, S. aureus isolates were identified by conventional methods (Mannitol agar, DNase and coagulase test) and, since 2012, by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF). Antimicrobial susceptibility testing was performed by disk diffusion (1990–1998) and/or microdilution (from 1999 onwards) using commercial panels (MicroScan, Beckman Coulter, Brea, CA, USA) and following the recommendations and criteria of the Clinical and Laboratory Standards Institute (CLSI) for each period [25 ]. Susceptibility to 14 antimicrobials (ciprofloxacin, clindamycin, co-trimoxazole, erythromycin, fosfomycin, fusidic acid, gentamicin, linezolid, oxacillin, penicillin, rifampicin, tetracycline, tobramycin, and vancomycin) was routinely tested in all isolates. Susceptibility to ceftaroline, daptomycin, and mupirocin was additionally tested by microdilution and chloramphenicol by disk diffusion in all isolates selected for WGS. Isolates were classified as MDR if they were resistant to ≥3 antimicrobial categories [26 (link)].
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