Direct Urine Resistance Detection Using VITEK 2

Eva Torres-Sangiao; Brais Lamas Rodriguez; María Cea Pájaro; Raquel Carracedo Montero; Noelia Parajó Pazos; Carlos García-Riestra

doi:10.3390/antibiotics11050663

Direct Urine Resistance Detection Using VITEK 2

Antibiotics (Basel). 2022 May 15;11(5):663. doi: 10.3390/antibiotics11050663.

Authors

Eva Torres-Sangiao^{1

2

3}, Brais Lamas Rodriguez⁴, María Cea Pájaro⁵, Raquel Carracedo Montero⁵, Noelia Parajó Pazos⁵, Carlos García-Riestra^{1

4

5}

Affiliations

¹ Grupo Escherichia coli, Fundación Instituto de InvestigaciónSanitaria (FIDIS), Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain.
² Clinical Microbiology Lab, University Hospital Marqués de Valdecilla, 39008 Santander, Spain.
³ Instituto de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain.
⁴ Dto Microbiology at Medical School, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain.
⁵ Clinical Microbiology Lab, Hospital Clínico Universitario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain.

Abstract

Urinary tract infections (UTIs) are the most common infectious diseases in both communities and hospitals. With non-anatomical or functional abnormalities, UTIs are usually self-limiting, though women suffer more reinfections throughout their lives. Certainly, antibiotic treatment leads to a more rapid resolution of symptoms, but also it selects resistant uropathogens and adversely affects the gut and vaginal microbiota. As uropathogens are increasingly becoming resistant to currently available antibiotics, it could be time to explore alternative strategies for managing UTIs. Rapid identification and antimicrobial susceptibility testing (AST) allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and the VITEK 2 system for the direct analysis of urine samples. First, we selected positive urine samples by flow cytometry using UF5000, establishing the cut-off for positive at 150 bacteria/mL. After confirming the identification using MALDI-TOF MS and filtering the urine samples for Escherichia coli, we directly tested the AST N388 card using VITEK 2. We tested a total of 211 E. coli from urine samples. Cefoxitin, ertapenem, imipenem, gentamicin, nalidixic acid, ciprofloxacin, fosfomycin, and nitrofurantoin had no major important errors (MIE), and ampicillin, cefuroxime, and tobramycin showed higher MIEs. Cefepime, imipenem, and tobramycin had no major errors (ME). Fosfomycin was the antibiotic with the most MEs. The antibiotic with the most minor errors (mE) was ceftazidime. The total categorical agreement (CA) was 97.4% with a 95% CI of (96.8-97.9)_95%. The direct AST from the urine samples proposed here was shorter by one day, without significant loss of sensibility regarding the standard diagnosis. Therefore, we hypothesize that this method is more realistic and better suited to human antibiotic concentrations.

Keywords: Escherichia coli; MALDI-TOF MS; carbapenemases; resistance; urinary tract infections.

Grants and funding

This work was supported by the Joint Programming Initiative-Antimicrobial Resistance (JPI634 AMR), the DARWIN Project [#7044-00004B], and ISCIII funding number AC16/00049. ETS was supported by a regional postdoctoral grant (Axudas de Apoio á Etapa De Formación Posdoutoral (Modalidade A), 2016-2019), GAIN, Xunta de Galicia (ES).