A method for the detection of antibiotic resistance markers in clinical strains of Escherichia coli using MALDI mass spectrometry

The commensal bacteria Escherichia coli causes several intestinal and extra-intestinal diseases, since it has virulence factors that interfere in important cellular processes. These bacteria also have a great capacity to spread the resistance genes, sometimes to phylogenetically distant bacteria, which poses an additional threat to public health worldwide. Here, we aimed to use the analytical potential of MALDI-TOF mass spectrometry (MS) to characterize E. coli isolates and identify proteins associated closely with antibiotic resistance. Thirty strains of extended-spectrum beta-lactamase producing E. coli were sampled from various animals. The phenotypes of antibiotic resistance were determined according to Clinical and Laboratory Standards Institute (CLSI) methods, and they showed that all bacterial isolates were multi-resistant to trimethoprim-sulfamethoxazole, tetracycline, and ampicillin. To identify peptides characteristic of resistance to particular antibiotics, each strain was grown in the presence or absence of the different antibiotics, and then proteins were extracted from the cells. The protein fingerprints of the samples were determined by MALDI-TOF MS in linear mode over a mass range of 2 to 20 kDa. The spectra obtained were compared by using the ClinProTools bioinformatics software, using three machine learning classification algorithms. A putative species biomarker was also detected at a peak m/z of 4528.00.

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Evaluation of the presence of AmpC (FOX) beta-lactamase gene in clinical strains of Escherichia coli isolated from hospitalized patients in Tabriz, Iran

Journal of Experimental and Clinical Medicine ◽

10.52142/omujecm.38.3.17 ◽

2021 ◽

Vol 38 (3) ◽

pp. 301-304

Author(s):

Zahra SADEGHI DEYLAMDEH ◽

Abolfazl JAFARI SALES

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Hospitalized Patients ◽

Disk Diffusion ◽

Beta Lactamase ◽

Beta Lactam ◽

Beta Lactamases ◽

Clinical Strains ◽

Beta Lactam Antibiotics ◽

Lactamase Gene

Beta-lactamases are the most common cause of bacterial resistance to beta-lactam antibiotics. AmpC-type beta-lactamases hydrolyze cephalosporins, penicillins, and cephamycins. Therefore, the study aims was to determine antibiotic resistance and to investigate the presence of AmpC beta-lactamase gene in clinical strains of Escherichia coli isolated from hospitalized patients in Tabriz. In this cross-sectional descriptive study, 289 E. coli specimens were collected from clinical specimens. Disk diffusion method and combined disk method were used to determine the phenotype of extended spectrum β-Lactamase producing (ESBLs) strains. Then PCR was used to evaluate the presence of AmpC (FOX) beta-lactamase gene in the strains confirmed in phenotypic tests. Antibiotic resistance was also determined using disk diffusion by the Kibry-Bauer method. A total of 121 isolates were identified as generators of beta-lactamase genes. 72 (59.5 %) isolates producing ESBL and 49 (40.5 %) isolates were identified as AmpC generators. In the PCR test, 31 isolates contained the FOX gene. The highest resistance was related to the antibiotics amoxicillin (76.12%), ceftazidime (70.24%) and nalidixic acid (65.05%). The results indicate an increase in the prevalence of beta-lactamase genes and increased resistance to beta-lactam antibiotics, which can be the result of improper use of antibiotics and not using antibiotic susceptibility tests before starting treatment. Also, using phenotypic and molecular diagnostic methods such as PCR together can be very useful.

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Antibiotic resistance features in Klebsiella pneumoniae and Escherichia coli strains isolated from hospital and community acquired urinary tract infections

ROMANIAN BIOTECHNOLOGICAL LETTERS ◽

10.25083/rbl/26.1/2244.2248 ◽

2021 ◽

Vol 26 (1) ◽

pp. 2244-2248

Author(s):

AL SHAIKHLI NAWFAL HAITHAM ◽

VIOLETA CORINA CRISTEA ◽

IRINA GHEORGHE ◽

SAJJAD MOHSIN IRRAYIF ◽

HAMZAH BASIL MOHAMMED ◽

...

Keyword(s):

Mass Spectrometry ◽

Escherichia Coli ◽

Antibiotic Resistance ◽

Pcr Amplification ◽

Tetracycline Resistance ◽

Tetracycline Resistance Gene ◽

E Coli ◽

Maldi Biotyper ◽

Tract Infections ◽

Automated Methods

A total number of 35 strains (n=23 of K. pneumoniae and n=12 of E.coli) were isolated in May 2017 from patients with UTI, hospitalized in the National Institute for Cardiovascular Diseases Prof. C.C. Iliescu and from community infections (CA) diagnosed in Central Reference Synevo-Medicover Laboratory from Bucharest. The hospital strains were identified by BD Phoenix and the CA ones by mass spectrometry using MALDI Biotyper. The antibiotic susceptibility was determined by agar disk diffusion (CLSI, 2017) and automated methods (BD Phoenix and Vitek II system). For molecular characterization, all strains were analyzed be using PCR amplification. The investigated strains revealed the presence of tetracycline resistance gene, i.e. tet(A) (67% in E. coli and 45% of K. pneumoniae strains), tet(D) (8% of E. coli and 5% of K. pneumoniae strains), carbapenemase genes (blaOXA-48 in 40% of the K. pneumoniae strains); blaTEM (25% of E. coli strains and 10% of K. pneumoniae strains).

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Determination of sensitivity of microorganisms of the Klebsiella genus to antimicrobial drugs by the MALDI-TOF MS method

Bacteriology ◽

10.20953/2500-1027-2020-3-8-13 ◽

2020 ◽

Vol 5 (3) ◽

pp. 8-13

Author(s):

A.A. Samoilova ◽

◽

I.V. Likhachev ◽

E.V. Zueva ◽

E.V. Rogacheva ◽

...

Keyword(s):

Mass Spectrometry ◽

Antibiotic Resistance ◽

Mass Spectra ◽

Antimicrobial Agents ◽

Antimicrobial Drugs ◽

Maldi Tof Mass Spectrometry ◽

Maldi Tof ◽

Resistance Markers ◽

Klebsiella Spp

Actual microbiological diagnostics of infections caused by Klebsiella spp. should include isolation of the strain, its identification and fastest possible determination of the pathogen susceptibility to antimicrobial agents. We evaluated the prospects of using MALDI-TOF mass spectrometry to determine the susceptibility of Klebsiella spp. strains to antimicrobial agents. According to the results of mass spectrometry Klebsiella spp. strains analysis, we carried out cluster analysis by the UPGMA method based on mass spectra and data on the susceptibility of the studied strains to antimicrobial agents, and then studied the obtained dendrograms. We identified the areas with the highest probability of the location of antibiotic resistance markers by comparing the mass spectra of susceptible and resistant microorganisms at different concentrations of antimicrobial agents. Thus, using MALDI-TOF mass spectrometry, a new direction in assessing the susceptibility of Klebsiella spp. to antimicrobial agents can be formed. Key words: antibiotic resistance, Klebsiella spp., MALDI-TOF mass spectrometry

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Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

Gut Pathogens ◽

10.1186/s13099-017-0206-9 ◽

2017 ◽

Vol 9 (1) ◽

Cited By ~ 28

Author(s):

Amira A. Moawad ◽

Helmut Hotzel ◽

Omnia Awad ◽

Herbert Tomaso ◽

Heinrich Neubauer ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Salmonella Enterica ◽

Beef Meat ◽

Northern Egypt ◽

Resistance Markers

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Diversity of P1 phage-like elements in multidrug resistant Escherichia coli

Scientific Reports ◽

10.1038/s41598-019-54895-4 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 12

Author(s):

Carola Venturini ◽

Tiziana Zingali ◽

Ethan R. Wyrsch ◽

Bethany Bowring ◽

Jonathan Iredell ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Multidrug Resistance ◽

Clinical Isolate ◽

Insertion Sequence ◽

Virulence Genes ◽

Multidrug Resistant ◽

Antibiotic Resistant ◽

E Coli ◽

Resistance Markers

AbstractThe spread of multidrug resistance via mobile genetic elements is a major clinical and veterinary concern. Pathogenic Escherichia coli harbour antibiotic resistance and virulence genes mainly on plasmids, but also bacteriophages and hybrid phage-like plasmids. In this study, the genomes of three E. coli phage-like plasmids, pJIE250-3 from a human E. coli clinical isolate, pSvP1 from a porcine ETEC O157 isolate, and pTZ20_1P from a porcine commensal E. coli, were sequenced (PacBio RSII), annotated and compared. All three elements are coliphage P1 variants, each with unique adaptations. pJIE250-3 is a P1-derivative that has lost lytic functions and contains no accessory genes. In pTZ20_1P and pSvP1, a core P1-like genome is associated with insertion sequence-mediated acquisition of plasmid modules encoding multidrug resistance and virulence, respectively. The transfer ability of pTZ20_1P, carrying antibiotic resistance markers, was also tested and, although this element was not able to transfer by conjugation, it was able to lysogenize a commensal E. coli strain with consequent transfer of resistance. The incidence of P1-like plasmids (~7%) in our E. coli collections correlated well with that in public databases. This study highlights the need to investigate the contribution of phage-like plasmids to the successful spread of antibiotic resistant pathotypes.

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