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51 protocols using chromid esbl

1

Environmental Microbiome Sampling Protocols

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Sewage Samples. After homogenization, 1 ml of each sample was taken and added to 9 ml of sterile distilled water contained in a screw tube for the preparation of 10−1 dilution. Successive decimal dilutions were made up to 10−3and 100 μl of each dilution was then inoculated on McConkey and ChromID ESBL solid media (Biomerieux, France).
Solid Samples. Previously, all food samples were ground in a sterile mortar. 9 ml of sterile distilled water was added to 1 g of each solid sample (sediment/sludge, animal feces, and crushed food item) contained in a screw tube (stock solution). After homogenization through a vortex, 1 ml of the stock solution (10−1 dilution) was added again to 9 ml of distilled water (10−2 dilution). Successive decimal dilutions were made up to 10−4. The last three dilutions (10−2, 10−3, and 10−4) were then seeded on McConkey solid media and ChromID ESBL (Biomerieux, France).
Community Kitchen Samples. Each community kitchen sample swab was cultured on McConkey and ChromID ESBL solid media by streaking with sterile loop (Biomerieux, France).
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2

Isolation and Identification of ESBL-Producing Bacteria

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Samples were inoculated on Brain–Heart Infusion (BHI) broth and incubated at 37 °C for 24 h. All suspensions were then inoculated on a selective chromogenic agar (chromID® ESBL, bioMérieux, Linda-a-Velha, Portugal) and incubated at 37 °C for 24 h, to isolate the ESBL-positive bacteria. After incubation, the color of colonies was recorded, and bacteria were isolated in BHI agar before further testing.
Isolates were characterized considering their macroscopic morphology on ChromID®ESBL according to the manufacturer’s instructions (bioMérieux, Linda-a-Velha, Portugal), Gram staining, lactose-fermentation capability on MacConkey agar (Oxoid, Hampshire, UK), and oxidase production. Biochemical identification was performed by IMViC testing [97 (link)] or, in case of inconclusive result by IMViC, API 20E (bioMérieux, Linda-a-Velha, Portugal) galleries were used according to manufacturer’s instructions.
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3

Comparative Evaluation of ESBL Detection Protocols

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This study implemented three potential one-step AMR testing protocols. These protocols, labeled as Protocol A, Protocol B, and Protocol C, were based on the following agar media: ChromID ESBL (bioMe´rieux), MacConkey agar containing 16 µg/ml of ceftazidime, and MacConkey agar containing 4 µg/ml of cefotaxime, respectively. ChromID ESBL served as an agar designed for isolating and detecting ESBL production. It featured a rich nutrient capacity and an antibiotic, cefpodoxime, known for inhibiting the growth of Gram-positive bacteria and yeast53 (link). MacConkey agar, on the other hand, was designed to differentiate between fermenting and non-fermenting Gram-negative bacteria. It contained inhibitors for Gram-positive bacteria, crystal violet dye, and bile salts54 (link). The antibiotics cefpodoxime, cefotaxime, and ceftazidime were recognized indicators of ESBL production (CLSI, version 2021). Antibiotic concentrations followed CLSI guidelines (version 2021). All agars were prepared in-house, except for ChromID ESBL, which was sourced directly from the manufacturer (bioMe´rieux). Subsequently, samples were inoculated onto the three agars and incubated at 37 °C under aerobic conditions for 18 h in accordance with CLSI (version, 2021) recommendations. This approach enabled the assessment of the three protocols’ capability to detect ESBL production within clinical samples.
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4

Clonal Relatedness and Resistome Analysis

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The isolates HKP0018, HKP0064 and HKP0067 were recovered in 2015 from throat and rectal swabs of three patients on admission to a university hospital in northern Germany (Table 3). The isolates were collected as part of the CONTAIN multicentre cohort study of the German Centre for Infection Research (DZIF) on the efficiency of infection control measures to prevent the transmission of ESBL producing Enterobacterales in haematology/oncology units [36 (link)]. The selection of the three isolates for further investigation was based on their clonal relatedness, ST, and acquired resistome. The surveillance swabs were plated on selective media (chromID® ESBL; bioMérieux, Nürtingen, Germany) and incubated for 18–24 h. The species identification was performed with MALDI-TOF mass spectrometry. Additionally, plasmid DNA was extracted from the isolate HKP0018 with the PureYield Plasmid Midiprep System (Promega, Madison, WI, USA) and then used to transform One Shot MAX Efficiency DH5α-T1R Competent Cells (Thermo Fisher Scientific, Waltham MA, USA). Selection of transformants was performed using ampicillin (40 mg/L) and tetracycline (30 mg/L) and was confirmed by PCR (Supplementary data).
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5

Rapid Pathogen Screening in Hospitals

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Simple nasal, throat, and rectal/perirectal screening swabs were collected either immediately or during the first 24 hours of admission and sent to the microbiology laboratory. These specimens were processed according to microbiology laboratory standard operating procedures by plating on screening mediums. Nasal and throat swabs were plated on ChromID MRSA while rectal/perirectal swabs were plated on ChromID VRE and ChromID ESBL (bioMérieux, La Balme-les-Grottes, France) for 18–24 hours at 37°C. Bacterial colonies grown on screening mediums were further identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (Biotyper, Bruker Daltonics GmbH & Co, Bremen, Germany).
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6

Detecting ESBL-Producing Enterobacteriaceae from Boot Swabs

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Sterisox® boot swabs were incubated 20 ± 4 h at room temperature with 100 ml of physiological water and 900 µL of Brain-Heart Infusion broth (BioMérieux SA, Marcy l’Etoile, France). Ten µL of the enriched suspension was directly streaked onto selective chromogenic agar plates (ChromID-ESBL, Biomérieux, Marcy l’Etoile, France) and incubated overnight at 37 °C under aerobic condition. Presumptive ESBL-producers were sub-cultured individually on Drigalski lactose agar and bacterial species identification performed using MALDI-TOF mass spectrometry (Bruker Daltonics, Breme, Germany). All Enterobacteriacae isolates identified, one or more by positive farms, were considered ESBL-E if confirmed by the combination disc test according to the European Committee on Antimicrobial Susceptibility Testing guidelines [19 ]. Thus, Muller Hinton agar with cefotaxime, ceftazidime, cefixime and cefepime disks with and without clavulanic acid allowed testing. The result was considered positive if the inhibition zone diameter was ≥5 mm larger with clavulanic acid than without for at least on cephalosporin tested.
If ESBL-E were identified, antibiograms were performed on isolates with ertapenem (ETP), nalidixic acid (NA), ofloxacin (OFL), gentamicin (GEN), Amikacin (AMK), trimethoprim/sulfamethoxazole (SXT) and tetracycline (TCN) tested.
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7

ESBL-producing Enterobacterales Characterization

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As described earlier,3 (link) ESBL-PE were isolated and characterized using established methods with culture on chromID ESBL (BioMérieux, Marcy-l’étoile, France), followed by double-disk synergy (Oxoid, Thermo Fisher Scientific, Hampshire, UK) test for cefotaxime, ceftazidime and cefpodoxime (30 μg each), alone or with clavulanic acid (10 μg), and species identification by Vitek GN (BioMérieux). Susceptibility testing for ciprofloxacin, cotrimoxazole, nitrofurantoin, tobramycin, ertapenem, imipenem and meropenem was conducted with E-test (BioMérieux) according to criteria set by the European Committee on Antimicrobial Susceptibility Testing EUCAST 5.0 (2018; www.eucast.org). Finally, beta-lactamase genes (TEM, OXA, SHV, CTX-M) and plasmid-mediated AmpC beta-lactamase genes (DHA, CIT) were identified by multiplex PCR.41 (link) The co-resistance rates,42 (link) prevalence of beta-lactamase genes,3 (link) and phylogroup characterization43 of the ESBL-PE strains have been reported in our previous papers.
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8

Enrichment and Identification of Multidrug-Resistant Bacteria

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MRSA, MRSP, MRCoNS and MR Macrococcus spp. were cultured using a two-step enrichment procedure and selected on chromogenic selective MRSA agar plates (BBL CHROMagar MRSA II, Becton Dickinson GmbH, Heidelberg, Germany) [31 (link)].
COL-R, 3rd generation cephalosporin-resistant and carbapenem-resistant Enterobacterales including E. coli and Klebsiella spp. were isolated after overnight enrichment in Luria-Bertani broth on specific selective plates including ChromID ESBL, ChromID CARBA SMART (bioMérieux, Suisse S.A., Geneva, Switzerland), and CHROMAgar plates supplemented with Colistin (bioMérieux). Colonies were purified onto MacConkey II Agar (Becton Dickinson GmbH) and identified to the species level by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis (Microflex LT, Bruker Daltonics GmbH, Bremen, Germany).
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9

Surveillance of P. aeruginosa Antimicrobial Resistance

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Perianal surveillance swabs and tap drain samples were grown on selected chromogenic media (CHROMID®CARBA SMART, bioMérieux, Marcy-l’Étoile, France; and CHROMID® ESBL, bioMérieux, Marcy-l’Étoile, France). Isolates suggestive of P. aeruginosa were identified with a MALDI-TOF analysis (MALDI Biotyper, Bruker Daltonics, Bremen, Germany). Antimicrobial susceptibility tests were performed by disk diffusion tests according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines (“Breakpoint tables for interpretation of MICs and zone diameters”. Version 9.0, 2019. http://www.eucast.org (accessed on 3 January 2020)). P. aeruginosa isolates were classified into non-resistant and multidrug-resistant (MDR) according to their antimicrobial susceptibility pattern and according to previously described criteria [11 (link)].
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10

Detecting Antibiotic-Resistant Enterobacterales and Acinetobacter baumannii

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Local microbiology laboratories used standard microbiological techniques for bacteria identification and susceptibility testing. Patients recruited at 3 hospitals were asked to participate in an exploratory substudy of rectal carriage by ceftriaxone-resistant or carbapenem-resistant Enterobacterales or Acinetobacter baumannii, using McConkey agar with cefotaxime (2 mg/L) or ChromID-ESBL (BioMérieux). Rectal swabs were taken at days 0, 3, or 4 and at end of treatment. All study isolates were sent to Hospital Universitario Virgen Macarena, where identification and antimicrobial susceptibility were confirmed using matrix-assisted laser desorption and ionization time of flight and microdilution, respectively. European Committee on Antimicrobial Susceptibility Testing recommendations16 were used. ESBL and carbapenemase genes were characterized by polymerase chain reaction and sequencing, and clonality of isolates was studied by PFGE.
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