Shiga toxin-producing E. coli (STEC) isolated from wild mammals in Portugal

Background

Zoonoses are diseases common to humans and animals (livestock, wildlife, and pets). In 2018 about 360 000 zoonoses were reported in European Union. Shiga toxin-producing Escherichia coli (STEC) infections were among the most reported causes of these zoonotic diseases.

Methods

Faecal samples of mammal species (n=286) with distinct phenology (wild boar, red deer, otter, and red fox) were collected in Portugal. After the initial processing, the presence of STEC was screened by PCR, and suspicious samples were platted on CHROMagar STEC. STEC positive isolates were tested for antibiotic susceptibility. Thephylogenetic relationship of STEC strains was evaluated by PFGE. Of these, 20 representative strains were selected for whole genome sequencing with the Illumina NovaSeq 6000 system. For the assembly, annotation and genome characterization, multiple web-based bioinformatic tools were employed.

Results

Cultivable STEC (n=52) were recovered from 17% (n=49) of the samples collected from the four mammals. All the isolates were non-O157:H7 STEC encoding stx1 (n=2; 4%) and/or stx2 genes (n=51; 98%). Only one strain (2%) of red fox was resistant to ceftazidime, aztreonam and nalidixic acid. The 20 strains that were sequenced belong mainly to serotype O27:H30 (n=15), followed by O146:H28 (n=2), O146:H21 (n=1), O178:H19 (n=1) and O103:H2 (n=1). In addition to stx, all strains encode several virulence factors, mainly toxins, adhesins, fimbrae, secretion systems, among others. Additionally, several pathogenicity islands have been predicted for these strains.

Conclusions

Our results show that wild animals are reservoirs of STEC, potentially pathogenic to humans.

Pathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?

Shiga toxin-producing Escherichia coli (STEC) is one of the most frequent bacterial agents associated with food-borne outbreaks in Europe. In humans, the infection can lead to life-threatening diseases. Domestic and wild animals can harbor STEC, and ruminants are the main STEC reservoirs, although asymptomatic. In the present study we have characterized STEC from wildlife (wild boar (n = 56), red deer (n = 101), red fox (n = 37) and otter (n = 92)). Cultivable STEC (n = 52) were isolated from 17% (n = 49) of the faecal samples. All the isolates were non-O157 STEC encoding stx1 (n = 2; 4%) and/or stx2 genes (n = 51; 98%). Only one strain (2%) isolated from red fox had an antibiotic resistant phenotype. However, when the normalized resistance interpretation of epidemiological cutoffs (NRI ECOFFs) were used, 23% (n = 12) of the strains were non-wildtype to at least one of the antibiotics tested. After analysis by pulsed-field gel electrophoresis (PFGE), 20 strains were selected for whole genome sequencing and belonged to the following serotypes: O27:H30 (n = 15), O146:H28 (n = 2), O146:H21 (n = 1), O178:H19 (n = 1), and O103:H2 (n = 1). In addition to stx, all strains encode several virulence factors such as toxins, adhesins, fimbriae and secretion systems, among others. All sequenced genomes carried several mobile genetic elements (MGEs), such as prophages and/or plasmids. The core genome and the phylogenetic analysis showed close evolutionary relationships between some of the STEC recovered from wildlife and strains of clinical origin, highlighting their pathogenic potential. Overall, our results show the zoonotic potential of STEC strains originating from wildlife, highlighting the importance of monitoring their genomic characteristics following a One Health perspective, in which the health of humans is related to the health of animals, and the environment.

Genome analysis of two multidrug-resistant Escherichia coli O8:H9-ST48 strains isolated from lettuce

Vegetables may become contaminated with antibiotic-resistant bacteria from farm-to-fork. Here we report draft genome sequences of two multidrug-resistant Escherichia coli isolated from lettuce. Whole genomes of strains Y15 V.22 and Y15 V.54 were sequenced. Available tools were used to inspect for virulence factors (VF), metals tolerance, resistome and mobilome features. The predicted genome sizes were 5,4 Mb and 6,2 Mb for Y15 V.22 and Y15 V.54, respectively, both with 50.7% GC content, ST48 and serotype O8:H9. Resistome analysis showed genes encoding resistance to β-lactams, sulphonamides, trimethoprim, tetracyclines and macrolides. Cobalt, cadmium, zinc and copper tolerance determinants were identified in both. VF detected included genetic determinants related to toxin production, adherence and invasion. SNPs and VF content analysis showed a close relatedness to ETEC. Putative genomic islands, prophage and CRISPR sequences were predicted. The genome sequences here reported will aid in understanding antibiotic resistance transfer between vegetables consumed raw and humans.

Distribution of Beta-Lactamase Producing Gram-Negative Bacterial Isolates in Isabela River of Santo Domingo, Dominican Republic

Bacteria carrying antibiotic resistance genes (ARGs) are naturally prevalent in lotic ecosystems such as rivers. Their ability to spread in anthropogenic waters could lead to the emergence of multidrug-resistant bacteria of clinical importance. For this study, three regions of the Isabela river, an important urban river in the city of Santo Domingo, were evaluated for the presence of ARGs. The Isabela river is surrounded by communities that do not have access to proper sewage systems; furthermore, water from this river is consumed daily for many activities, including recreation and sanitation. To assess the state of antibiotic resistance dissemination in the Isabela river, nine samples were collected from these three bluedistinct sites in June 2019 and isolates obtained from these sites were selected based on resistance to beta-lactams. Physico-chemical and microbiological parameters were in accordance with the Dominican legislation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses of ribosomal protein composition revealed a total of 8 different genera. Most common genera were as follows: Acinetobacter (44.6%) and Escherichia (18%). Twenty clinically important bacterial isolates were identified from urban regions of the river; these belonged to genera Escherichia (n = 9), Acinetobacter (n = 8), Enterobacter (n = 2), and Klebsiella (n = 1). Clinically important multi-resistant isolates were not obtained from rural areas. Fifteen isolates were selected for genome sequencing and analysis. Most isolates were resistant to at least three different families of antibiotics. Among beta-lactamase genes encountered, we found the presence of blaTEM, blaOXA, blaSHV, and blaKPC through both deep sequencing and PCR amplification. Bacteria found from genus Klebsiella and Enterobacter demonstrated ample repertoire of antibiotic resistance genes, including resistance from a family of last resort antibiotics reserved for dire infections: carbapenems. Some of the alleles found were KPC-3, OXA-1, OXA-72, OXA-132, CTX-M-55, CTX-M-15, and TEM-1.

FunSys: Software for functional analysis of prokaryotic transcriptome and proteome

The vast amount of data produced by next-generation sequencing (NGS) has necessitated the development of computational tools to assist in understanding the myriad functions performed by the biological macromolecules involved in heredity. In this work, we developed the FunSys programme, a stand-alone tool with an user friendly interface that enables us to evaluate and correlate differential expression patterns from RNA sequencing and proteomics datasets. The FunSys generates charts and reports based on the results of the analysis of differential expression to aid the interpretation of the results.

AVAILABILITY

The database is available for free at https://sourceforge.net/projects/funsysufpa/