Data on antibiograms and resistance genes of Enterobacterales isolated from ready-to-eat street food of Ambato, Ecuador.

Foodborne pathogens represent a significant cause of negative impacts on human health and the economy worldwide. Unfortunately, information about epidemiological insights in Latin American countries is scarce. The consumption of ready-to-eat street food in Ecuador is extensive, and information about the presence of foodborne pathogens, their virulence factors, and antimicrobial resistance is negligible. This data includes the occurrence, phenotypic antibiotic resistance profiles, and antibiotic resistance genes of Enterobacterales isolated from ready-to-eat street food in Ambato, central Ecuador during 2020 and 2021. The most common genera detected were Escherichia coli, Klebsiella spp., and Cronobacter spp. Agar disk diffusion assays were performed to determine their phenotypic resistance. The presence of antibiotic resistance genes conferring resistance against colistin, β-Lactams, aminoglycosides, tetracyclines, sulfonamides, fluoroquinolones, and amphenicols was detected via polymerase chain reaction (PCR) amplification. Copyright:

Introduction

This data contributes information about the antibiotic resistance profiles of Enterobacterales strains isolated from street food that will facilitate pathogen surveillance in Ecuador and Latin America. This data is useful for the scientific community to determine the presence of pathogenic Escherichia coli isolates and antibiotic resistance genes, including mobile colistin resistance genes, carbapenemases, quinolone resistance genes, and extended-spectrum β-lactamases present on Enterobacterales strains isolated from street food. Researchers and policymakers involved with the work related to the One Health initiative could also benefit from this data for retrospective and comparative analysis or epidemiological surveillance projects. ,

Methods

Enterobacterales strains

Ready-to-eat street food was obtained in the streets of the city of Ambato, Ecuador, and processed the same day. A sharp sterile blade was used to cut the samples on sterile surfaces. 10 g of each sample was placed in sterile brain heart infusion broth (BHIB) (Merck, Darmstadt, Germany) in 90 ml, shaken on a rotator for 8-10 min, and incubated for 24 h at 37 °C. A large amount of broth was inoculated on MacConkey agar plates (Merck, Darmstadt, Germany), Cromocult Coliforms Agar (Merck KGaA, Darmstadt, Germany), and CHROMagar mSuperCARBA were incubated overnight at 37 °C under aerobic conditions. Further purification was performed on Macconkey agar.

The isolates were amplified by polymerase chain reaction (PCR), analysed using agarose gel electrophoresis and visualised with Sybr Safe DNA Gel Stain. For the identification of the isolated Enterobacterales, biochemical tests such as catalase, oxidase, TSI agar, Simmons citrate, lactose test, indole production, urea agar, methyl red test, and Voges-Proskauer were carried out and their interpretation was performed based on Bergey's manual. Additionally, the software for Automated Biometric Identification Systems (ABIS) was used to confirm the biochemical identification results.

Phenotypic antibiotic resistance profiles

Agar disk diffusion assays (Thermo Scientific Oxoid and Bioanalyse) on Mueller-Hinton Agar (Thermo Scientific Oxoid) were performed. Antibiograms tests were based on the measured diameter of the zones of inhibition and interpreted as sensible, intermediate or resistant by referring to CLSI breakpoints.

Detection of E. coli pathotypes and antibiotic resistance genes detection via PCR

The PCR test was performed according to the standardized protocol of the UTA RAM One Health research group , : 2.5 μL of DNA from each sample and 22.5 μL of PCR mix containing 12.5 μL DreamTaq PCR Master Mix (ThermoFisher Scientific, USA), 9 μL Nuclease-free water, 0.5 μL Primer 1 and 0.5 μL Primer 2 (final concentration of primers: 0.5 μM) were mixed to run PCR. The PCR conditions are reported in Supplementary Table S4. PCR products were analyzed by 1.2% agarose gel electrophoresis stained by Sybr Safe DNA Gel Stain (ThermoFisher Scientific, USA).

Hierarchical clustering

Hierarchical clustering was performed using the Euclidean correlation method and clustered by affinity. The MeV Multiexperiment Viewer software version 4.8.1 was used in this study.

Dataset validation

The data presented show the frequency of isolation of Enterobacterales in 151 samples of ready-to-eat street food in Ambato, Ecuador ( Figure 1). The specific characteristics (date of sampling, type of street food, location) of the samples were reported in Supplementary Table S1. A total of 145 isolates were analyzed, and the results of the biochemical tests were reported in Supplementary Table S2. Among them, 86 isolates corresponded to E. coli and 59 isolates to other Enterobacterales.

Figure 1.

Occurrence of Enterobacterales on 151 samples of ready-to-eat street food in Ambato, Ecuador.

To visualize the relative similarity of the antimicrobial resistance patterns of the isolates, a hierarchical cluster analysis was performed using the results of the antibiograms, where the phenotypes ‘resistant’, ‘intermediate’, and ‘susceptible’ were observed as red, white, and blue colors respectively. Dendrograms and clustered data were assembled using the complete linkage method through Pearson correlation and sample leaf organization. For this purpose, the MeV Multiexperiment Viewer software version 4.8.1 was used. Figures 2 and 3 represent the resistance profiles and the hierarchical clustering of E. coli and the rest of Enterobacterales, respectively. The complete information is shown in Supplementary Table S3.

Figure 2.

Profiles of antibiotic resistance and hierarchical tree of E. coli isolates.

Red: resistant, White: intermediate, Blue: sensitive.

Figure 3.

Profiles of antibiotic resistance and a hierarchical tree of other Enterobacterales isolates.

Red: resistant, White: intermediate, Blue: sensitive.

Abbreviations: TE: Tetracycline 30 μg, AM: Ampicilin 10 μg, KF: cephalotin 30 μg, C: chloramphenicol 30 μg, CIP: Ciprofloxacin 5 μg, CTX: Cefatoxime 30 μg, LEV: Levofloxacin 5 μg, FOX: Cefoxitin 30 μg, STX: Trimethoprim/sulphamethoxazole 25 μg, AMC: Amoxicyllin/ClavulanicAcid 30 μg, CN: Gentamicin 10 μg, CRO: Ceftriaxione 30 μg, FEP: Cefepime 30 μg, ATM: Aztreonam 30 μg, IPM: Imipenem 10 μg, TPZ: Piperacillin/Tazobactam 110 μg, ETP: Ertapenem 10 μg, MEM: Meropenem 10 μg, CAZ: Ceftazidime 30 μg.

The presence of diarrheagenic E. coli pathotypes present in ready-to-eat food was assessed in this study through the analysis of virulence genes related to the pathotypes. Only one isolate (C2.1c) was positive for the eae gene, suggesting the potential presence of enteropathogenic E. coli (EPEC) or enterohemorrhagic E. coli (EHEC). The β-lactamase resistance genes of Enterobacterales isolated in this study are reported in Table 1. Mobile colistin resistance genes or quinolone resistance genes were not found in the Enterobacterales isolates. The complete information about virulence genes and antibiotic resistance genes are available in Supplementary Table S5. The information about primers and PCR conditions were shown in Supplementary Table S4. The gel electrophoresis images are available at Supplementary figure S6. The disk difussion assays figures were shown at Supplementary figure S7.

Table 1.

Beta-lactamase resistance genes of Enterobacterales isolated from ready-to-eat food.

Ready-to-eat food samples	Bacteria	Sample ID	Date	Location market streets	Beta-lactamases
					bla tem	bla cmy
Cow stomach stew	E. coli	M1.1a	14/12/2020	Mayorista	+	-
Cane juice	E. coli	Jc5.2c1	08/03/2021	Modelo	+	-
Lupine ceviche	E. coli	ch5.1c2	08/03/2021	Modelo	+	-
Cow stomach stew	E. coli	Gap1a	20/04/2021	Sur	-	+
Boiled beans, ulluco and pork rind	E. coli	Hmm1a	10/05/2021	Artesanal	-	+
Chilli sauce	Klebsiella spp	D1.2a	07/12/2020	Mayorista	+	-
Sweet meringue (espumilla)	Salmonella spp	E2.2b	19/01/2021	Primera de Mayo	+	-
Salad from street food	E. coli	N1.2a	20/12/2020	Mayorista	+	-
Total Enterobacterales isolated					6(145)	2(145)

Data availability

Figshare project: https://figshare.com/projects/Data_on_antibiograms_and_resistance_genes_of_Enterobacterales_isolated_from_Ready-to-eat_street_food_of_Ambato_Ecuador/137014

This collection contains the following underlying data:

Figure 1. Occurrence of Enterobacterales on 151 samples of ready-to-eat street foods in Ambato, Ecuador. figshare. Figure. https://doi.org/10.6084/m9.figshare.19579087.v1

Table 1. Beta-lactamase resistance genes of Enterobacterales isolated from ready-to-eat food. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579099.v1

Figure 2 and 3. Antibiotic resistance profiles and hierarchical trees of Enterobacterales isolated from ready-to-eat street food in Ambato, Ecuador. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579267.v1

Extended data

This collection contains the following extended data:

Supplementary table S1. Characteristics (Sample type, date, treatment type, location, coordinates) of the ready-to-eat food samples. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579108.v1

Supplementary table S2. Biochemical tests performed on Enterobacterales isolates from Ready-to-eat Street Food in Ambato, Ecuador. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579177.v1

Supplementary table S3. Antibiogram of Enterobacterales isolated from ready-to-eat Street food of Ambato, Ecuador. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579189.v1

Supplementary table S4. Primers used in this study and PCR conditions. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579198.v1

Supplementary table S5. Antibiotic resistance genes and virulence genes harbored by Enterobacterales isolates from ready-to-eat street food in Ecuador. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19579207.v1

Supplementary figure S6. PCR results (positive electrophoresis images). figshare. Figure. https://doi.org/10.6084/m9.figshare.19729618.v1

Supplementary figure S7. Disk diffusion assay images-Antibiotic resistance evaluation of Enterobacterales isolated from ready-to-eat street food of Ambato, Ecuador. figshare. Figure. https://doi.org/10.6084/m9.figshare.19729630.v1

Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).

The data note by Tubón J et al. aims to give information about the antibiotic resistance profiles of Enterobacterales strains isolated from street food in Ecuador. The work is relevant because, usually in Latin American countries, street food consumption is typical, it has little sanitary regulation, and in some towns, potable water access is limited, which could favor the presence of resistant bacteria in foods. On the other hand, the research gives information about antibiotic resistance in settings different from hospitals and contributes information from Latin American countries where the data is limited. Another relevant point is that the work detects antibiotic resistance Enterobacterales strains in cooked food differently from other studies on lettuce and raw vegetables.

The manuscript is well structured and written. The protocols are appropriate and provide acceptable methods and details to allow replication.

I have provided comments/suggestions as follows:

I suggest to future reports, the author gives information about the bacteria typification, such as ERIC, PFGE, MLST, or WGS. This information could be help to understand what clones to type of strains are circulating in the region.

What is the resistance behavior in the Ambato hospitals where the project was carried out? The results could help to understand the resistance problem in the city?

Any limitations related to this manuscript and/or methods you want to bring up to the reader?

In the profiles of antibiotic resistance, there are Enterobacterales isolates resistant to carbapenems, and you did not detect carbapenemases. Could you give information about the reason to this resistance, for example, intrinsic mechanisms or other beta-lactamases not detected?

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Bacterial Antibiotic Resistance, Molecular Microbiology, Molecular Epidemiology, Medical Microbiology.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

In Latin American countries the consumption of street food represents in the majority the alimentary base, due to the conditions that present the most countries belonging to Latin American, for this reason, the information generated by Turbón et al., could facilitate the epidemiology surveillance and allow action before the emergence of foodborne pathogens outbreak.

The authors carry out a complete characterization of a significant number of strains (n=151), highlighting the distribution of pathogens, antibiotic resistance profiles, presence of antibiotic resistance genes.

I suggest reviewing next points: Both articles (that are referenced below) are related with the importance of a good epidemiological surveillance system in a possible outbreak of foodborne pathogens. These are closely related to the study presented by the authors, where they carry out the isolation and complete characterization, anticipating of the emergence of foodborne pathogens in an area such as Latin America where epidemiological data usually are limited.

The sentence that refers to " The isolates were amplified by polymerase chain reaction (PCR)" confuses a bit since later it is specified that the identification is carried out with conventional biochemicals, just to clarify well, why PCR was used in this section.

Add information about how to DNA was obtained for PCR assays.

Was there any pathogen that predominated in the sampling areas? If so, the results could show a strain that is already distributed in the community with outbreak potential.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

antibiotic resistance, microbiology, phages

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

In this data note article, Turbón and colleagues examined the antibiograms and resistance genes profiles of Enterobacterales order strains isolated in ready-to-eat street food in Ecuador. A larger number of samples and types of food have been selected, resulting in a solid database of Enterobacterales strains (n=151).

I suggested a few points to be clarified.

Methods

Enterobacterales strains- Section

“A larger amount of broth”. The authors can specify the volume used for the analysis.

Add the reference for the “software for Automated Biometric Identification Systems (ABIS)”.

Phenotypic antibiotic resistance profiles – Section.

Include the full reference for these companies (Thermo Scientific Oxoid and Bioanalyse) following the same style as the previous ones.

Detection of  E. coli pathotypes and antibiotic resistance genes detection via PCR - Section.

Include the method/kid used for the DNA extraction.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

water microbiology, food microbiology, microbial source tracking

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.