Antimicrobial resistance profiles of Shiga toxin-producing Escherichia coli O157 and Non-O157 recovered from domestic farm animals in rural communities in Northwestern Mexico

Antimicrobial Resistance in Diverse Escherichia coli Pathotypes from Nigeria

Escherichia coli is a gram-negative commensal bacterium living in human and animal intestines. Its pathogenic strains lead to high morbidity and mortality, which can adversely affect people by causing urinary tract infections, food poisoning, septic shock, or meningitis. Humans can contract E. coli by eating contaminated food-such as raw or undercooked raw milk, meat products, and fresh produce sold in open markets-as well as by coming into contact with contaminated settings like wastewater, municipal water, soil, and faeces. Some pathogenic strains identified in Nigeria, include Enterohemorrhagic (Verotoxigenic), Enterotoxigenic, Enteropathogenic, Enteroinvasive, and Enteroaggregative E. coli. This causes acute watery or bloody diarrhoea, stomach cramps, and vomiting. Apart from the virulence profile of E. coli, antibiotic resistance mechanisms such as the presence of blaCTX-M found in humans, animals, and environmental isolates are of great importance and require surveillance and monitoring for emerging threats in resource-limited countries. This review is aimed at understanding the underlying mechanisms of evolution and antibiotic resistance in E. coli in Nigeria and highlights the use of improving One Health approaches to combat the problem of emerging infectious diseases.

Antibiofilm activity of promethazine against ESBL-producing strains of Escherichia coli in urinary catheters

The bacterium Escherichia coli is one of the main causes of urinary tract infections. The formation of bacterial biofilms, especially associated with the use of urinary catheters, contributes to the establishment of recurrent infections and the development of resistance to treatment. Strains of E. coli that produce extended-spectrum beta-lactamases (ESBL) have a greater ability to form biofilms. In addition, there is a lack of drugs available in the market with antibiofilm activity. Promethazine (PMZ) is an antihistamine known to have antimicrobial activity against different pathogens, including in the form of biofilms, but there are still few studies of its activity against ESBL E. coli biofilms. The aim of this study was to evaluate the antimicrobial activity of PMZ against ESBL E. coli biofilms, as well as to assess the application of this drug as a biofilm prevention agent in urinary catheters. To this end, the minimum inhibitory concentration and minimum bactericidal concentration of PMZ in ESBL E. coli strains were determined using the broth microdilution assay and tolerance level measurement. The activity of PMZ against the cell viability of the in vitro biofilm formation of ESBL E. coli was analyzed by the MTT colorimetric assay and its ability to prevent biofilm formation when impregnated in a urinary catheter was investigated by counting colony-forming units (CFU) and confirmed by scanning electron microscopy (SEM). PMZ showed bactericidal activity and significantly reduced (p < 0.05) the viability of the biofilm being formed by ESBL E. coli at concentrations of 256 and 512 μg/ml, as well as preventing the formation of biofilm on urinary catheters at concentrations starting at 512 μg/ml by reducing the number of CFUs, as also observed by SEM. Thus, PMZ is a promising candidate to prevent the formation of ESBL E. coli biofilms on abiotic surfaces.

Antibiotic resistance profiles of sentinel bacteria isolated from aquaculture in Cambodia

The misuse of antibiotics and the emergence of antimicrobial resistance (AMR) is a concern in the aquaculture industry because it contributes to global health risks and impacts the environment. This study analyzed the AMR of sentinel bacteria associated with striped catfish (Pangasisanodon hypophthalmus) and giant snakehead (Channa micropeltes), the two main fish species reared in the pond culture in Cambodia. Phenotypic and genotypic characterization of the recovered isolates from fish, water, and sediment samples revealed the presence of bacteria, such as 22 species belonging to families Aeromonadaceae, Enterobacteriaceae, and Pseudomonadaceae. Among 48 isolates, Aeromonas caviae (n = 2), Aeromonas hydrophila (n = 2), Aeromonas ichthiosmia (n = 1), Aeromonas salmonicida (n = 4) were detected. A. salmonicida and A. hydrophilla are known as fish pathogens that occur worldwide in both fresh and marine water aquaculture. Antibiotic susceptibility testing revealed antibiotic resistance patterns of 24 (50 %) isolates among 48 isolates with higher multiple antibiotic resistance index (> 0.2). All the isolates of Enterobacteriaceae were susceptible to ciprofloxacin. Ciprofloxacin is a frontline antibiotic that is not recommended to use in aquaculture. Therefore, its use has to be strictly controlled. This study expands our knowledge of the AMR status in aquaculture farms which is very limited in Cambodia.

Antibiotic Resistance and Disinfectant Resistance Among Escherichia coli Isolated During Red Meat Production

Escherichia coli commonly found in the gastrointestinal tracts of food animals include Shiga toxin-producing E. coli (STEC, stx+, eae-), Enterohemorrhagic E. coli (EHEC, stx+, eae+), Enteropathogenic E. coli (EPEC, stx-, eae+), and "nondiarrheagenic" E. coli (NDEC, stx-, eae-). EHEC, EPEC, and STEC are associated with foodborne disease outbreaks. During meat processing, disinfectants are employed to control various bacteria, including human pathogens. Concerns exist that E. coli resistant to antibiotics are less susceptible to disinfectants used during meat processing. Since EHEC, EPEC, and STEC with reduced susceptibility to disinfectants are potential public health risks, the goal of this study was to evaluate the association of antibiotic resistant (ABR) E. coli with increased tolerance to 4% lactic acid (LA) and 150 ppm quaternary ammonium compounds (QACs). A pool of 3,367 E. coli isolated from beef cattle, veal calves, swine, and sheep at various processing stages was screened to identify ABR E. coli. Resistance to ≥1 of the six antibiotics examined was identified in 27.9%, 36.1%, 54.5%, and 28.7% among the NDEC (n = 579), EHEC (n = 693), EPEC (n = 787), and STEC (n = 1308) isolates evaluated, respectively. Disinfectant tolerance did not differ (P > 0.05) between ABR and antibiotic susceptible EHEC isolates. Comparable frequencies (P > 0.05) of biofilm formation or congo red binding were observed between ABR and antibiotic susceptible strains of E. coli. Understanding the frequencies of ABR and disinfectant tolerance among E. coli present in food-animal is a critically important component of meat safety.

Occurrence, molecular characterization, and antimicrobial susceptibility of sorbitol non-fermenting Escherichia coli in lake water, fish and humans in central Oromia, Ethiopia

Contaminated lake water and fish can be sources of bacterial pathogens of public health concern, including pathogenic E. coli. Within Ethiopia, specifically, Central Oromia, raw fish consumption is a common practice. Although there are few reports on occurrence of E. coli O157 in fish destined for human consumption and children under five years, information on the transmission pathways of E. coli O157 and other sorbitol non-fermenting (SN-F) E. coli from water-to-fish-to-human, and their virulence factors and antimicrobial resistant determinants along the fish supply chain is lacking. The study aimed to investigate the occurrence, molecular characteristics, and antimicrobial susceptibility of E. coli O157 and other SN-F E. coli strains in fish, lake water and humans in central Oromia, Ethiopia. A total of 750 samples (450 fish samples, 150 water samples, 150 human stool samples) were collected from five lakes and three health facilities. The samples were processed following the standard protocol recommended by European Food Safety Authority and Kirby-Bauer disc diffusion method for detection of the bacteria, and antimicrobial susceptibility tests, respectively. Molecular characterization of presumptive isolates was performed using Whole-Genome Sequencing (WGS) for serotyping, determination of virulence factors, antimicrobial resistance traits, and genetic linkage of the isolates. Overall, 3.9% (29/750) of the samples had SN-F E. coli; of which 6.7% (n = 10), 1.8% (n = 8) and 7.3% (n = 11) were retrieved from water, fish, and diarrheic human patients, respectively. The WGS confirmed that all the isolates were SN-F non-O157: H7 E. coli strains. We reported two new E. coli strains with unknown O-antigen from fish and human samples. All the strains have multiple virulence factors and one or more genes encoding for them. Genetic relatedness was observed among strains from the same sources (water, fish, and humans). Most isolates were resistant to ampicillin (100%), tetracycline (100%), cefotaxime (100%), ceftazidime (100%), meropenem (100%), nalidixic acid (93.1%) and sulfamethoxazole/trimethoprim (79.3%). Majority of the strains were resistant to chloramphenicol (58.6%) and ciprofloxacin (48.3%), while small fraction showed resistance to azithromycin (3.45%). Isolates had an overall MDR profile of 87.5%. Majority, (62.1%; n = 18) of the strains had acquired MDR traits. Genes encoding for mutational resistance and Extended-spectrum beta-lactamases (ESBL) were also detected. In conclusion, our study revealed the occurrence of virulent and MDR SN-F E. coli strains in water, fish, and humans. Although no genetic relatedness was observed among strains from various sources, the genomic clustering among strains from the same sources strongly suggests the potential risk of transmission along the supply chain at the human-fish-environment interface if strict hygienic fish production is not in place. Further robust genetic study of the new strains with unknown O-antigens, and the epidemiology of SN-F E. coli is required to elucidate the molecular profile and public health implications of the pathogens.

Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli

Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.

Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids

Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.

Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand

Background

Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern.

Objectives

To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS.

Methods

Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms.

Results

ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene.

Conclusions

This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism.

Multidrug-resistant Escherichia coli isolated from patients and surrounding hospital environments in Bangladesh: A molecular approach for the determination of pathogenicity and resistance

Extended spectrum β-lactamase producing Escherichia coli (ESBL E. coli) is a primary concern for hospital and community healthcare settings, often linked to an increased incidence of nosocomial infections. This study investigated the characteristics of ESBL E. coli isolated from hospital environments and clinical samples. In total, 117 ESBL E. coli isolates were obtained. The isolates were subjected to molecular analysis for the presence of resistance and virulence genes, antibiotic susceptibility testing, quantitative adherence assay, ERIC-PCR for phylogenetic analysis and whole genome sequencing of four highly drug resistant isolates. Out of the 117 isolates, 68.4% were positive for blaCTX-M, 39.3% for blaTEM, 30.8% for blaNDM-1, 13.7% for blaOXA and 1.7% for blaSHV gene. Upon screening for diarrheagenic genes, no isolates were found to harbour any of the tested genes. In the case of extraintestinal pathogenic E. coli (ExPEC) virulence factors, 7.6%, 11%, 5.9%, 4.3% and 21.2% of isolates harbored the focG, kpsMII, sfaS, afa and iutA genes, respectively. At a temperature of 25°C, 14.5% of isolates exhibited strong biofilm formation with 21.4% and 28.2% exhibiting moderate and weak biofilm formation respectively, whereas 35.9% were non-biofilm formers. On the other hand at 37°C, 2.6% of isolates showed strong biofilm formation with 3.4% and 31.6% showing moderate and weak biofilm formation respectively, whereas, 62.4% were non-biofilm formers. Regarding antibiotic susceptibility testing, all isolates were found to be multidrug-resistant (MDR), with 30 isolates being highly drug resistant. ERIC-PCR resulted in 12 clusters, with cluster E-10 containing the maximum number of isolates. Hierarchical clustering and correlation analysis revealed associations between environmental and clinical isolates, indicating likely transmission and dissemination from the hospital environment to the patients. The whole genome sequencing of four highly drug resistant ExPEC isolates showed the presence of various antimicrobial resistance genes, virulence factors and mobile genetic elements, with isolates harbouring the plasmid incompatibility group IncF (FII, FIB, FIA). The sequenced isolates were identified as human pathogens with a 93.3% average score. This study suggests that ESBL producing E. coli are prevalent in the healthcare settings of Bangladesh, acting as a potential reservoir for AMR bacteria. This information may have a profound effect on treatment, and improvements in public healthcare policies are a necessity to combat the increased incidences of hospital-acquired infections in the country.

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States.

Methods

In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed.

Results

We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated.

Discussion

This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.

Antibiotic expectation, behaviour, and receipt among patients presenting to emergency departments with uncomplicated upper respiratory tract infection during the COVID-19 pandemic

OBJECTIVES

Pre-COVID-19 pandemic, patients who attended the emergency department (ED) for upper respiratory tract infection (URTI) were more likely to receive antibiotics if they expected them. These expectations could have changed with the change in health-seeking behaviour during the pandemic. We assessed the factors associated with antibiotics expectation and receipt for uncomplicated URTI patients in four Singapore EDs during the COVID-19 pandemic.

METHODS

We conducted a cross-sectional study on adult patients with URTI from March 2021 to March 2022 in four Singapore EDs and assessed the determinants of antibiotics expectation and receipt using multivariable logistic regression models. We also assessed the reasons patients expect antibiotics during their ED visit.

RESULTS

Among 681 patients, 31.0% expected antibiotics while 8.7% received antibiotics during their ED visit. Factors (adjusted odds ratio [95% confidence interval]) that significantly influenced expectation for antibiotics include: 1) prior consultation for current illness with (6.56 [3.30-13.11]) or without (1.50 [1.01-2.23]) antibiotics prescribed; 2) anticipation for COVID-19 test (1.56 [1.01-2.41]); and 3) poor (2.16 [1.26-3.68]) to moderate (2.26 [1.33-3.84]) knowledge on antibiotics use and resistance. Patients expecting antibiotics were 10.6 times (10.64 [5.34-21.17]) more likely to receive antibiotics. Those with tertiary education were twice (2.20 [1.09-4.43]) as likely to receive antibiotics.

CONCLUSION

In conclusion, patients with URTI who expected antibiotics to be prescribed remained more likely to receive it during the COVID-19 pandemic. This highlights the need for more public education on the non-necessity for antibiotics for URTI and COVID-19 to address the problem of antibiotic resistance.

Can University Leaders Effectively Promote Research on Complex Societal Challenges? A Change-Agency Perspective

In recent years, new expectations have been placed on universities, demanding academic contributions towards solving large-scale, interdisciplinary challenges. This is in conflict with existing insights from university governance research, which emphasises that scientific communities focus on reproducing disciplinary practices that are unsuitable in addressing societal challenges, because the problems associated with them are usually large-scale, complex and interdisciplinary. In light of this seeming paradox, we revisit the question of how-and on which theoretical grounds-universities may still be able to develop suitable internal governance mechanisms that allow them to address complex societal challenges effectively. Because university leaders are usually unable to coerce individual researchers to address such challenges in their research simply through their bureaucratic powers, we will argue that university leaders can, however, leverage individual researchers' agency to deviate from routine and disciplinary practice by developing novel or legitimising existing interdisciplinary scripts necessary to deal with such societal problems. Specifically, we outline that university managements can create a dual role consisting of the communication of legitimising interdisciplinary research on societal challenges, as well as providing for the necessary degree of interdisciplinary coordination by convening researchers around these topics.

Enablers of Candida auris persistence on medical devices and their mode of eradication

Candida auris is an emerging pathogen predominantly isolated from immunocompromised patients, hospitalized for a long time. It inhabits the skin surfaces of patients causing ear, wound, and systemic infections; if not treated properly, it could lead to severe mortality. Apart from being a skin pathogen, C. auris colonizes the surfaces of medical devices. Medical devices are hospital tools and components often utilized for the diagnosis and treatment of diseases associated with human skin. The mechanism of survival and persistence of C. auris on medical devices has remained unclear and is a serious concern for clinicians. The persistence of C. auris on medical devices has deterred its effective elimination, hindered the treatment of infections, and increased its antifungal resistance. Evidence has shown that a few surface molecules on the cell wall of C. auris and the extracellular matrix of the biofilm are responsible for its persistence and exist as enablers. Due to the increased cases of ear, skin, and systemic infections as well as death resulting from the spread of C. auris in hospitals, there is a need to study these enablers. This review focused on the identification of the enablers and aimed to evaluate them in relation to their ability to induce persistence in C. auris. In order to reduce the spread of or completely eliminate C. auris and its enablers in hospitals, the efficacy of disinfection and sterilization methods were compared.

Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective

Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.

Genomic Analysis of Shiga Toxin-Producing E. coli O157 Cattle and Clinical Isolates from Alberta, Canada

Shiga toxin (stx) is the principal virulence factor of the foodborne pathogen, Shiga toxin-producing Escherichia coli (STEC) O157:H7 and is associated with various lambdoid bacterio (phages). A comparative genomic analysis was performed on STEC O157 isolates from cattle (n = 125) and clinical (n = 127) samples to characterize virulence genes, stx-phage insertion sites and antimicrobial resistance genes that may segregate strains circulating in the same geographic region. In silico analyses revealed that O157 isolates harboured the toxin subtypes stx1a and stx2a. Most cattle (76.0%) and clinical (76.4%) isolates carried the virulence gene combination of stx1, stx2, eae and hlyA. Characterization of stx1 and stx2-carrying phages in assembled contigs revealed that they were associated with mlrA and wrbA insertion sites, respectively. In cattle isolates, mlrA and wrbA insertion sites were occupied more often (77% and 79% isolates respectively) than in clinical isolates (38% and 1.6% isolates, respectively). Profiling of antimicrobial resistance genes (ARGs) in the assembled contigs revealed that 8.8% of cattle (11/125) and 8.7% of clinical (11/127) isolates harboured ARGs. Eight antimicrobial resistance genes cassettes (ARCs) were identified in 14 isolates (cattle, n = 8 and clinical, n = 6) with streptomycin (aadA1, aadA2, ant(3'')-Ia and aph(3'')-Ib) being the most prevalent gene in ARCs. The profound disparity between the cattle and clinical strains in occupancy of the wrbA locus suggests that this trait may serve to differentiate cattle from human clinical STEC O157:H7. These findings are important for stx screening and stx-phage insertion site genotyping as well as monitoring ARGs in isolates from cattle and clinical samples.

Characterization of the Lytic Phage Flora With a Broad Host Range Against Multidrug-Resistant Escherichia coli and Evaluation of Its Efficacy Against E. coli Biofilm Formation

Escherichia coli is a gram-negative bacterium that is distributed widely throughout the world; it is mainly found in contaminated food, the poultry industry, and animal feces. The emergence of antibiotic-resistant E. coli poses a threat to human and animal health, which has led to renewed interest in phage-based therapy. E. coli biofilm control and prevention are of great importance. In this study, the isolated phages Flora and KM18 were found to belong to the family Myoviridae; the optimal preservation buffer was pH = 6~7, and the phage genome sizes were 168,909 (Flora) and 168,903 (KM18) bp. Phage Flora had a broader lytic spectrum than KM18. Phage Flora had a better antibiofilm effect than kanamycin sulfate in high-concentration E. coli cultures. A combination of the phage Flora and kanamycin sulfate showed better antibiofilm effects than Flora or kanamycin sulfate alone in low-concentration E. coli cultures. These characteristics can serve as a guideline for the selection of effective candidates for phage therapy, in this case antibiotic-resistant E. coli control in the poultry industry.

Shiga toxin-producing Escherichia coli O157 in piglets and food from backyard systems

Piglets suffer from diarrhea caused by the Shiga toxin-producing Escherichia coli (STEC) and can be carriers of the bacteria, with public health consequences in developing countries. The aim of the present study was to study the prevalence of STEC O157 in feces of 465 piglets and 54 food mixes from backyard systems, the antimicrobial susceptibility of STEC and the frequency of genes encoding extended-spectrum β-lactamases. The E. coli was isolated from 75.90 % of the evaluated feces. The STEC strains were identified in 33.11% of the sampled population and in 43.60% of the piglets carrying E. coli. Among STEC strains, the stx1 gene was the most frequent (22.30%). The rfbO157 gene was amplified in 47.40% of the STEC strains. High frequencies of STEC strains were not susceptible to ampicillin, carbenicillin and tetracycline. The blaTEM gene (52) was the most frequent among strains not susceptible to ampicillin. Class 1 integrons were the most frequent in those strains. Of the identified STEC strains, 48.70% were considered as multi-drug resistant and 1.90% were considered extensively drug resistant. In the supplied food, STEC O157 strains were identified in 25.00% of the STEC strains. We conclude that the piglets from backyard systems are carriers of STEC O157 strains not susceptible to common antibiotics, including penicillins and tetracyclines. In addition, supplied food is a source of this type of pathogenic bacteria. Through their direct contact with humans, the piglets and food represent a potential source of bacterial dissemination capable of producing gastrointestinal infections in humans.

Multi-drug resistant gram-negative bacterial pneumonia: etiology, risk factors, and drug resistance patterns

Bacterial pneumonia is one of the most serious public health issues owing to its medical and economic costs, which result in increased morbidity and mortality in people of all ages around the world. Furthermore, antimicrobial resistance has risen over time, and the advent of multi-drug resistance in GNB complicates therapy and has a detrimental impact on patient outcomes. The current review aimed to summarize bacterial pneumonia with an emphasis on gram-negative etiology, pathogenesis, risk factors, resistance mechanisms, treatment updates, and vaccine concerns to tackle the problem before it causes a serious consequence. In conclusion, the global prevalence of GNB in CAP was reported 49.7% to 83.1%, whereas in VAP patients ranged between 76.13% to 95.3%. The most commonly reported MDR-GNB causes of pneumonia were A. baumannii, K. pneumoniae, and P. aeruginosa, with A. baumannii isolated particularly in VAP patients and the elderly. In most studies, ampicillin, tetracyclines, amoxicillin-clavulanic acid, cephalosporins, and carbapenems were shown to be highly resistant. Prior MDR-GNB infection, older age, previous use of broad-spectrum antibiotics, high frequency of local antibiotic resistance, prolonged hospital stays, ICU admission, mechanical ventilation, and immunosuppression are associated with the MDR-GNB colonization. S. maltophilia was reported as a severe cause of HAP/VAP in patients with mechanically ventilated and having hematologic malignancy due to its ability of biofilm formation, site adhesion in respiratory devices, and its intrinsic and acquired drug resistance mechanisms. Effective combination therapies targeting PDR strains and drug-resistant genes, antibiofilm agents, gene-based vaccinations, and pathogen-specific lymphocytes should be developed in the future.

Prevalence, Antibiogram, and Multidrug-Resistant Profile of E. coli O157: H7 in Retail Raw Beef in Addis Ababa, Ethiopia

Escherichia coli O157:H7 is an emerging foodborne pathogen of public health importance. The objectives of this study were to estimate the prevalence and evaluate the antimicrobial susceptibility pattern and multidrug-resistant profile of E. coli O157:H7 isolated from raw beef sold in butcher shops in Addis Ababa, Ethiopia. A total of 384 raw beef samples were collected from randomly selected butcher shops across the 10 sub-cities of Addis Ababa. E. coli O157:H7 was isolated following ISO-16654:2001 standard, and isolates were tested for resistance to 13 antimicrobial agents using the Kirby–Bauer disk diffusion method. Out of the 384 retail raw beef samples examined, 14 (3.64%) (95% CI = 1.77–5.51%) carried E. coli O157:H7 serotype. Of the 14 E. coli O157:H7 isolates, 8 (57.14%) were found to be resistant to three or more antimicrobial categories. The frequency of resistant phenotype was more common for ampicillin (92.8%), nitrofurantoin (92.8%), and tetracycline (50%). Multidrug-resistant E. coli O157:H7 were present in raw beef sold in butcher shops in Addis Ababa. Thus, more stringent monitoring of antimicrobial use in both human and animal populations should be implemented. In addition, further studies should be conducted to understand the E. coli O157:H7 points of contamination and define appropriate risk mitigation strategies.

Antibiotic Susceptibility Profiles and Frequency of Resistance Genes in Clinical Shiga Toxin-Producing Escherichia coli Isolates from Michigan over a 14-Year Period

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that contributes to over 250,000 infections in the United States each year. Because antibiotics are not recommended for STEC infections, resistance in STEC has not been widely researched despite an increased likelihood for the transfer of resistance genes from STEC to opportunistic pathogens residing within the same microbial community. From 2001 to 2014, 969 STEC isolates were collected from Michigan patients. Antibiotic susceptibility profiles to clinically relevant antibiotics were determined using disc diffusion, while epidemiological data were used to identify factors associated with resistance. Whole-genome sequencing was used for serotyping, examining genetic relatedness, and identifying genetic determinants and mechanisms of resistance in the non-O157 isolates. Increasing frequencies of resistance to at least one antibiotic were observed over the 14 years (P = 0.01). While the non-O157 serogroups were more commonly resistant than O157 (odds ratio, 2.4; 95% confidence interval,1.43 to 4.05), the frequency of ampicillin resistance among O157 isolates was significantly higher in Michigan than the national average (P = 0.03). Genomic analysis of 321 non-O157 isolates uncovered 32 distinct antibiotic resistance genes (ARGs). Although mutations in genes encoding resistance to ciprofloxacin and ampicillin were detected in four isolates, most of the horizontally acquired ARGs conferred resistance to aminoglycosides, β-lactams, sulfonamides, and/or tetracycline. This study provides insight into the mechanisms of resistance in a large collection of clinical non-O157 STEC isolates and demonstrates that antibiotic resistance among all STEC serogroups has increased over time, prompting the need for enhanced surveillance.

Molecular surveillance of shiga toxigenic Escherichia coli in selected beef abattoirs in Osun State Nigeria

Shiga toxigenic strains of E. coli (STEC) known to be etiological agents for diarrhea were screened for their incidence/occurrence in selected abattoirs sources in Osogbo metropolis of Osun State, Nigeria using a randomized block design. Samples were plated directly on selective and differential media and E. coli isolates. Multiplex PCR analysis was used to screen for the presence of specific virulence factors. These were confirmed serologically as non-O157 STEC using latex agglutination serotyping kit. Sequence analysis of PCR products was performed on a representative isolate showing the highest combination of virulence genes using the 16S gene for identification purposes only. Results showed that the average cfu/cm2 was significantly lower in the samples collected at Sekona-2 slaughter slab compared with those collected at Al-maleek batch abattoir and Sekona-1 slaughter slab in ascending order at P = 0.03. Moreover, the average cfu/cm2 E. coli in samples collected from butchering knife was significantly lower when compared with that of the workers' hand (P = 0.047) and slaughtering floor (P = 0.047) but not with the slaughter table (P = 0.98) and effluent water from the abattoir house (P = 0.39). These data suggest that the abattoir type may not be as important in the prevalence and spread of STEC as the hygiene practices of the workers. Sequence analysis of a representative isolate showed 100% coverage and 96.46% percentage identity with Escherichia coli O113:H21 (GenBank Accession number: CP031892.1) strain from Canada. This sequence was subsequently submitted to GenBank with accession number MW463885. From evolutionary analyses, the strain from Nigeria, sequenced in this study, is evolutionarily distant when compared with the publicly available sequences from Nigeria. Although no case of E. coli O157 was found within the study area, percent occurrence of non-O157 STEC as high as 46.3% at some of the sampled sites is worrisome and requires regulatory interventions in ensuring hygienic practices at the abattoirs within the study area.

Role of Recent Therapeutic Applications and the Infection Strategies of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) is a global foodborne bacterial pathogen that is often accountable for colon disorder or distress. STEC commonly induces severe diarrhea in hosts but can cause critical illnesses due to the Shiga toxin virulence factors. To date, there have been a significant number of STEC serotypes have been evolved. STECs vary from nausea and hemorrhoid (HC) to possible lethal hemolytic-based uremic syndrome (HUS), thrombotic thrombocytopenic purpura (TTP). Inflammation-based STEC is usually a foodborne illness with Shiga toxins (Stx 1 and 2) thought to be pathogenesis. The STEC's pathogenicity depends significantly on developing one or more Shiga toxins, which can constrain host cell protein synthesis leading to cytotoxicity. In managing STEC infections, antimicrobial agents are generally avoided, as bacterial damage and discharge of accumulated toxins are thought the body. It has also been documented that certain antibiotics improve toxin production and the development of these species. Many different groups have attempted various therapies, including toxin-focused antibodies, toxin-based polymers, synbiotic agents, and secondary metabolites remedies. Besides, in recent years, antibiotics' efficacy in treating STEC infections has been reassessed with some encouraging methods. Nevertheless, the primary role of synbiotic effectiveness (probiotic and prebiotic) against pathogenic STEC and other enteropathogens is less recognized. Additional studies are required to understand the mechanisms of action of probiotic bacteria and yeast against STEC infection. Because of the consensus contraindication of antimicrobials for these bacterial pathogens, the examination was focused on alternative remedy strategies for STEC infections. The rise of novel STEC serotypes and approaches employed in its treatment are highlighted.

Multidrug Resistance of Escherichia coli Strains Isolated From Bovine Feces and Carcasses in Northeast Mexico

In this work, the antimicrobial resistance profile of Escherichia coli strains (n = 248) isolated from bovine feces and carcass samples from Tamaulipas, Mexico, was evaluated. Susceptibility to 12 antibiotics conventionally used in human and veterinary treatments was determined according to Clinical and Laboratory Standards Institute guidelines. Genes encoding resistance to tetracycline (tetA and tetB), streptomycin (strA), aminoglycoside (aadA), and β-lactamase (bla_TEM and bla_SHV) were investigated by PCR. Also, stx1, stx2, eae, bfp, and hlyA encoding virulence factors were determined. Of the isolates, 85.9% were confirmed as E. coli strains. Among the 213 E. coli isolates tested, 94.8% (202/213) showed resistance for at least one antimicrobial, mainly ampicillin (83.0%; 177/213), cephalothin (76.0%; 162/213), and tetracyclines (69.0%; 147/213). In all the other antibiotics tested, the resistance percentage was below 36%. A multidrug-resistant phenotype was found in 72.7% of the tested strains. The presence of the tet gene (tetA or tetB) was detected in 43.1% of the isolates, the strA gene in 17.3%, and aadA1 in 51.6%. The bla_TEM and bla_SHV genes were found in 10.3 and 0.4% of the isolates, respectively. stx1 was detected in 4.2% of isolates, stx2 in 7.0, and hlyA in 2.8%. The virulence genes, eae and bfp, were not detected in any strain. These results indicate that Tamaulipas food products of bovine origin can be a source of multiresistant E. coli strains for the environment and exposure for consumers.

Characterization of antimicrobial susceptibility, extended-spectrum β-lactamase genes and phylogenetic groups of Shigatoxin producing Escherichia coli isolated from patients with diarrhea in Iran

Background

Shiga toxin‐producing Escherichia coli (STEC) are among common foodborne bacterial pathogens and healthy livestock are the main source of this bacterium. Severe diseases attribute to two types of cytotoxin Stx1 and Stx2, which are also called Shiga toxin (Stx). Infection of humans with STEC may result in Acute diarrhea with or without bleeding, hemorrhagic colitis (HC) and the hemolytic uremic syndrome (HUS). As antibiotic resistance is increasingly being reported among STEC isolates obtained from livestock and patients worldwide, in this study the pattern of antibiotic resistance in clinical isolates was determined.

Methods

Stool samples were collected from patients with diarrhea. All samples were cultured and identified by biochemical and molecular tests. Antimicrobial susceptibility test and assessment of extended-spectrum β-lactamase (ESBL)-related genes were conducted. Moreover, phylogenetic groups were analyzed using quadruplex PCR, and DNA analysis assessed multi-locus sequence types (MLST).

Results

Out of 340 E. coli samples, 174 were identified as STEC by PCR. Antimicrobial susceptibility test results showed that, 99.4%, 96% and 93.1% of isolates were susceptible to imipenem/ertapenem, piperacillin–tazobactam and amikacin, respectively. The highest resistance was towards ampicillin (68.4%), followed by trimethoprim–sulfamethoxazole (59.8%), and tetracycline (57.5%). A total of 106 (60.9%) isolates were multidrug resistance (MDR) and 40.8% of isolates were determined to be extended spectrum β-lactamase producers. In 94.4% of isolates, genes responsible for ESBL production could be detected, and blaTEM was the most prevalent, followed by blaCTX-M9. Furthermore, phylogenetic grouping revealed that majority of STEC strains belonged to Group C, followed by Groups E, B2 and A. MLST unveiled diverse ST types.

Conclusion

A periodical surveillance studies and thorough understanding of antibiotic resistant profiles in STEC isolates could help select effective antibiotic treatment for patients and develop strategies to effectively manage food contamination and human infections.

Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape

Antibiotic resistance (AR) phenotypes and acquired resistance determinants (ARDs) detected by in silico analysis of genome sequences were examined in 55 Shiga toxin-producing Escherichia coli (STEC) isolates representing diverse serotypes recovered from surfaces waters and sediments in a mixed use urban/agricultural landscape in British Columbia, Canada. The isolates displayed decreased susceptibility to florfenicol (65.5%), chloramphenicol (7.3%), tetracycline (52.7%), ampicillin (49.1%), streptomycin (34.5%), kanamycin (20.0%), gentamycin (10.9%), amikacin (1.8%), amoxicillin/clavulanic acid (21.8%), ceftiofur (18.2%), ceftriaxone (3.6%), trimethoprim-sulfamethoxazole (12.7%), and cefoxitin (3.6%). All surface water and sediment isolates were susceptible to ciprofloxacin, nalidixic acid, ertapenem, imipenem and meropenem. Eight isolates (14.6%) were multidrug resistant. ARDs conferring resistance to phenicols (floR), trimethoprim (dfrA), sulfonamides (sul1/2), tetracyclines (tetA/B), and aminoglycosides (aadA and aph) were detected. Additionally, narrow-spectrum β-lactamase blaTEM-1b and extended-spectrum AmpC β-lactamase (cephalosporinase) blaCMY-2 were detected in the genomes, as were replicons from plasmid incompatibility groups IncFII, IncB/O/K/Z, IncQ1, IncX1, IncY and Col156. A comparison with surveillance data revealed that AR phenotypes and ARDs were comparable to those reported in generic E. coli from food animals. Aquatic environments in the region are potential reservoirs for the maintenance and transmission of antibiotic resistant STEC, associated ARDs and their plasmids.

Incidence of Shiga toxin-producing Escherichia coli in diarrheic calves and its susceptibility profile to antimicrobials and Eugenia uniflora L

The aim of this study was to evaluate the occurrence of Shiga toxin (stx)-producing Escherichia coli (STEC) in diarrheic newborn calves, as well as the resistance profile of this microorganism against antimicrobials routinely used in veterinary therapy. The antimicrobial profile of Eugenia uniflora against E. coli clinical isolates was also analyzed. Specimens from the recto-anal junction mucosa were investigated by using chromogenic medium and identification of E. coli was done using microbiological methods (Gram staining, indole test, methyl red test, Voges-Proskauer test, citrate test, urease test, and hydrogen sulfide test). The stx1 and stx2 genes corresponding to the STEC pathotype were evaluated by using polymerase chain reaction and electrophoresis. The susceptibility profile to antimicrobial agents commonly used in veterinary therapeutic practice and the antimicrobial effect of lyophilized hydroalcoholic extract of E. uniflora L. leaves against E. coli clinical isolates were evaluated by disk diffusion and microdilution methods. Shiga toxin-positive E. coli was identified in 45% of diarrheic newborn calves (stx1 = 23.2%, stx2 = 4.0%, stx1 + stx2 = 18.2%). The frequency of stx-positive E. coli in the bacterial population was equal to 17.0% (168/990 clinical isolates): 97 (9.8%) stx1-positive E. coli, 12 (1.2%) stx2-positive E. coli, and 59 (6.0%) stx1 + stx2-positive E. coli isolates. All stx-positive E. coli analyzed showed resistance to multiple drugs, that is, from 4 to 10 antimicrobials per clinical isolate (streptomycin, tetracycline, cephalothin, ampicillin, sulfamethoxazole + trimethoprim, nitrofurantoin and nalidixic acid, ciprofloxacin, gentamicin, and chloramphenicol). Effective management measures should be implemented, including clinical and laboratory monitoring, in order to promote animal and worker health and welfare, prevent and control the spread of diseases, and ensure effective treatment of infectious diseases. The E. uniflora L. leaves showed inhibition of microbial growth based on the diameter of halos, ranging from 7.9 to 8.0 mm and 9.9 to 10.1 mm for concentrations of 50 and 150 mg/mL, respectively. This plant displayed bacteriostatic action and a minimum inhibitory concentration of 12.5 mg/mL for all clinical isolates. Its clinical or synergistic effects with antimicrobial agents must be determined from clinical and preclinical trials.

Improving the Quality of Turkey Meat via Storage Temperature, Packaging Atmosphere, and Oregano (Origanum vulgare) Essential Oil Addition

The provision of plentiful good-quality food is a primary issue in the modern world. This work was planned to study the influence of packaging atmosphere and oregano (Origanum vulgare) essential oil addition [(vacuum packaging: T1 or modified atmosphere packaging or T2 (CO2/N2 = 4:6) or T3, T2 with oregano essential oil (T2 + EO)] under various storage temperatures (0, 5, 10, and 15 °C) on the control of survival of Escherichia coli O157:H7 and associated spoilage flora in sliced smoked turkey meat. The pathogen increased by only <1.0 log colony-forming unit (CFU)/g under all packaging and temperature combinations. Moreover, T1, T2, and T3 exerted practically similar inhibitory activity against the pathogen and dominating bacteria, with a relatively low growth of E. coli O157:H7 in sliced smoked turkey during the shelf life under all storage regimes compared to the control. However, the pathogen survival was highest on the sliced smoked turkey under T1, decreasing by only 0.67, 0.74, 0.63, and 1.30 log CFU/g within 37 days if kept at 0, 5, 10, and 15 °C, respectively. Under T2 and the same condition, E. coli O157:H7 in the product declined by only 0.31, 0.50, 0.72, and 1.10 log CFU/g within 37 days of storage, respectively. In the T3 samples, the pathogen was reduced by only 0.33, 0.67, 1.72, and 3.46 log CFU/g through 37 days of storage, respectively. Under T3 were E. coli O157:H7 populations in smoked turkey eliminated (negative by enrichment) under all conditions (after 129, 95, 95, and 43 days maintained at 0, 5, 10, and 15 °C, respectively) compared with other packaging temperature combinations. Thus, T3 contributed to developing ready-to-eat smoked turkey with enhanced product quality and eliminating the pathogen.

Bacteriophages to control Shiga toxin-producing E. coli - safety and regulatory challenges

Shiga toxin-producing Escherichia coli (STEC) are usually found on food products due to contamination from the fecal origin, as their main environmental reservoir is considered to be the gut of ruminants. While this pathogen is far from the incidence of other well-known foodborne bacteria, the severity of STEC infections in humans has triggered global concerns as far as its incidence and control are concerned. Major control strategies for foodborne pathogens in food-related settings usually involve traditional sterilization/disinfection techniques. However, there is an increasing need for the development of further strategies to enhance the antimicrobial outcome, either on food-contact surfaces or directly in food matrices. Phages are considered to be a good alternative to control foodborne pathogens, with some phage-based products already cleared by the Food and Drug Administration (FDA) to be used in the food industry. In European countries, phage-based food decontaminants have already been used. Nevertheless, its broad use in the European Union is not yet possible due to the lack of specific guidelines for the approval of these products. Furthermore, some safety concerns remain to be addressed so that the regulatory requirements can be met. In this review, we present an overview of the main virulence factors of STEC and introduce phages as promising biocontrol agents for STEC control. We further present the regulatory constraints on the approval of phages for food applications and discuss safety concerns that are still impairing their use.

Phenotypic and Genotypic Antimicrobial Resistance in Non-O157 Shiga Toxin-Producing Escherichia coli Isolated From Cattle and Swine in Chile

Non-O157 Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that causes bloody diarrhea and hemolytic-uremic syndrome in humans, and a major cause of foodborne disease. Despite antibiotic treatment of STEC infections in humans is not recommended, the presence of antimicrobial-resistant bacteria in animals and food constitutes a risk to public health, as the pool of genes from which pathogenic bacteria can acquire antibiotic resistance has increased. Additionally, in Chile there is no information on the antimicrobial resistance of this pathogen in livestock. Thus, the aim of this study was to characterize the phenotypic and genotypic antimicrobial resistance of STEC strains isolated from cattle and swine in the Metropolitan region, Chile, to contribute relevant data to antimicrobial resistance surveillance programs at national and international level. We assessed the minimal inhibitory concentration of 18 antimicrobials, and the distribution of 12 antimicrobial resistance genes and class 1 and 2 integrons in 54 STEC strains. All strains were phenotypically resistant to at least one antimicrobial drug, with a 100% of resistance to cefalexin, followed by colistin (81.5%), chloramphenicol (14.8%), ampicillin and enrofloxacin (5.6% each), doxycycline (3.7%), and cefovecin (1.9%). Most detected antibiotic resistance genes were dfrA1 and tetA (100%), followed by tetB (94.4%), bla_TEM−1 (90.7%), aac(6)-Ib (88.9%), bla_AmpC (81.5%), cat1 (61.1%), and aac(3)-IIa (11.1%). Integrons were detected only in strains of swine origin. Therefore, this study provides further evidence that non-O157 STEC strains present in livestock in the Metropolitan region of Chile exhibit phenotypic and genotypic resistance against antimicrobials that are critical for human and veterinary medicine, representing a major threat for public health. Additionally, these strains could have a competitive advantage in the presence of antimicrobial selective pressure, leading to an increase in food contamination. This study highlights the need for coordinated local and global actions regarding the use of antimicrobials in animal food production.

Supershed Escherichia coli O157:H7 Has Potential for Increased Persistence on the Rectoanal Junction Squamous Epithelial Cells and Antibiotic Resistance

Supershedding cattle shed Escherichia coli O157:H7 (O157) at ≥ 104 colony-forming units/g feces. We recently demonstrated that a supershed O157 (SS-O157) strain, SS-17, hyperadheres to the rectoanal junction (RAJ) squamous epithelial (RSE) cells which may contribute to SS-O157 persistence at this site in greater numbers, thereby increasing the fecal O157 load characterizing the supershedding phenomenon. In order to verify if this would be the signature adherence profile of any SS-O157, we tested additional SS-O157 isolates (n = 101; each from a different animal) in the RSE cell adherence assay. Similar to SS-17, all 101 SS-O157 exhibited aggregative adherence on RSE cells, with 56% attaching strongly (>10 bacteria/cell; hyperadherent) and 44% attaching moderately (1-10 bacteria/cells). Strain typing using Polymorphic Amplified Typing Sequences (PATS) analysis assigned the 101 SS-O157 into 5 major clades but not to any predominant genotype. Interestingly, 69% of SS-O157 isolates were identical to human O157 outbreak strains based on pulsed field gel electrophoresis profiles (CDC PulseNet Database), grouped into two clades by PATS distinguishing them from remaining SS-O157, and were hyperadherent on RSE cells. A subset of SS-O157 isolates (n = 53) representing different PATS and RSE cell adherence profiles were analyzed for antibiotic resistance (AR). Several SS-O157 (30/53) showed resistance to sulfisoxazole, and one isolate was resistant to both sulfisoxazole and tetracycline. Minimum inhibitory concentration (MIC) tests confirmed some of the resistance observed using the Kirby-Bauer disk diffusion test. Each SS-O157 isolate carried at least 10 genes associated with AR. However, genes directly associated with AR were rarely amplified: aac (3)-IV in 2 isolates, sul2 in 3 isolates, and tetB in one isolate. The integrase gene, int, linked with integron-based AR acquisition/transmission, was identified in 92% of SS-O157 isolates. Our results indicate that SS-O157 isolates could potentially persist longer at the bovine RAJ but exhibit limited resistance towards clinical antibiotics.

Captive Green Iguana Carries Diarrheagenic Escherichia coli Pathotypes

The green iguana appears to be a carrier for bacteria causing gastrointestinal infections in humans. The presence of diarrheagenic E. coli (DEC) pathotypes, however, has not been studied in this reptile. The aim of the current work was to investigate the prevalence of DEC in the intestines of 240 captive green iguanas, their phylogenetic groups, and the antibiotic susceptibility profile. E. coli strains were isolated from 41.7% (N = 100/240) of the intestinal content of green iguanas. DEC strains was identified in 25.9% of the screened population and were detected in the majority (62%, p = 0.009) of those reptiles carrying E. coli strains. Among DEC strains, STEC strains carrying the stx1 gene were the most prevalent pathotype isolated (38.7%), followed by EAEC and ETEC (27.4% each). Genetic markers of DEC strains belonging to the EHEC pathotype were not detected. More than a half of DEC strains were classified into the Clade I-II phylogroup (64.5%), followed by the phylogroup A (14.5%). The antibiotic susceptibility method demonstrated that a high proportion of DEC strains were resistance, or non-susceptible, to carbenicillin, amikacin, and ampicillin. We conclude that the green iguana kept in captivity is a carrier of DEC strains bearing resistance to first-line antibiotics, including penicillins. Given the increase presence of the green iguana in Latin American households, these reptiles represent a potential source of transmission to susceptible humans and therefore a potential source of gastrointestinal disease.

Molecular characterization of multidrug-resistant Shiga toxin-producing Escherichia coli harboring antimicrobial resistance genes obtained from a farmhouse

Shiga toxin-producing Escherichia coli (STEC) colonize the gastrointestinal tract of animals; however, STEC may also cause severe diarrheal diseases. Food-producing animals have been acting as reservoirs and disseminators of multidrug-resistant (MDR) bacteria and antimicrobial resistance genes (ARGs); however, there are few studies characterizing molecularly bacterial isolates from sheep. Therefore, this study aimed to characterize E. coli isolates obtained from feces of sheep in a Brazilian farmhouse. A total of 14 MDR E. coli isolates were obtained from 100 feces samples, six of which were classified as non-O157 STEC (stx1, stx2 and ehxA). MDR E. coli isolates presented different ARGs [bla_CTX-M-Gp9, bla_CMY, bla_SHV, qnrS, oqxB, aac(6')-Ib, tet(A), tet(B), tet(C), sul1, sul2, and cmlA] and plasmids (IncI1, IncF_repB, IncFIB, IncFIA, IncHI1, IncK, and ColE-like). In addition, mutations in the quinolone-resistance determining region of GyrA (Ser83Leu; Asp87Asn) and ParC (Glu84Asp) were detected. PFGE showed a high genetic diversity (30.9 to 83.9%) and thirteen STs were detected (ST25, ST48, ST155, ST162, ST642, ST1247, ST1518, ST1725, ST2107, ST2522, ST3270, ST5036, and ST7100). Subtyping of the fimH gene showed seven fimH-type (25, 32, 38, 41, 54, 61, and 366). The results found in the present study showed high genetic diversity among MDR ARGs-producing E. coli obtained from a farmhouse. This study reports for the first time, the presence of MDR STEC and non-STEC belonging to ST25, ST162, ST642, ST1247, ST1518, ST1725, ST2107, ST3270, ST5036, and ST7100 in sheep, and contributes to the surveillance studies associated with One Health concept.

Preharvest Transmission Routes of Fresh Produce Associated Bacterial Pathogens with Outbreak Potentials: A Review

Disease outbreaks caused by the ingestion of contaminated vegetables and fruits pose a significant problem to human health. The sources of contamination of these food products at the preharvest level of agricultural production, most importantly, agricultural soil and irrigation water, serve as potential reservoirs of some clinically significant foodborne pathogenic bacteria. These clinically important bacteria include: Klebsiella spp., Salmonella spp., Citrobacter spp., Shigella spp., Enterobacter spp., Listeria monocytogenes and pathogenic E. coli (and E. coli O157:H7) all of which have the potential to cause disease outbreaks. Most of these pathogens acquire antimicrobial resistance (AR) determinants due to AR selective pressure within the agroecosystem and become resistant against most available treatment options, further aggravating risks to human and environmental health, and food safety. This review critically outlines the following issues with regards to fresh produce; the global burden of fresh produce-related foodborne diseases, contamination between the continuum of farm to table, preharvest transmission routes, AR profiles, and possible interventions to minimize the preharvest contamination of fresh produce. This review reveals that the primary production niches of the agro-ecosystem play a significant role in the transmission of fresh produce associated pathogens as well as their resistant variants, thus detrimental to food safety and public health.

Characterization of non-O157 Shiga toxin-producing Escherichia coli (STEC) obtained from feces of sheep in Brazil

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens and may induce severe diarrheagenic diseases in humans and other animals. Non-O157 STEC have been emerging as important pathogens causing outbreaks worldwide. Bacterial resistance to antimicrobials has become a global public health problem, which involves different ecological spheres, including animals. This study aimed to characterize the resistance to antimicrobials, plasmids and virulence, as well as the serotypes and phylogenetic groups in E. coli isolated from sheep in Brazil. A total of 57 isolates were obtained and showed different antimicrobial resistance profiles. Nineteen isolates presented acquired antimicrobial resistance genes (ARGs) (bla_CTX-M-Gp9, qnrB, qnrS, oqxB, oqxA, tetA, tetB, tetC, sul1 and sul2) and plasmid families (F, FIA, FIB, I1, K, HI1 and ColE-like). The stx1, stx2 and ehxA virulence genes were detected by PCR, being 50 isolates (87.7%) classified as STEC. A great diversity of serotypes was detected, being O176:HNM the most predominant. Phylogenetic group E was the most prevalent, followed by B1, A and B2. To the best of our knowledge, this is the first report in the world of bla_CTX-M-Gp9 (O75, O114, O100, O128ac and O176 serogroups), qnrB and oqxB genes in non-O157 STEC in healthy sheep. The results obtained in the present study call attention to the monitoring of antimicrobial-resistant non-O157 STEC harboring acquired ARGs worldwide and indicate a zoonotic risk due to the profile of virulence, resistance and serotype found.

Molecular profiling and antimicrobial resistance of Shiga toxin-producing Escherichia coli O26, O45, O103, O121, O145 and O157 isolates from cattle on cow-calf operations in South Africa

In this study, 140 cattle STEC isolates belonging to serogroups O157, O26, O145, O121, O103 and O45 were characterized for 38 virulence-associated genes, antimicrobial resistance profiles and genotyped by PFGE. The majority of isolates carried both stx1 and stx2 concurrently, stx2c, and stx2d; plasmid-encoded genes ehxA, espP, subA and saa but lacked katP and etpD and eaeA. Possession of eaeA was significantly associated with the presence of nle genes, katP, etpD, ureC and terC. However, saa and subA, stx1c and stx1d were only detected in eaeA negative isolates. A complete OI-122 and most non-LEE effector genes were detected in only two eaeA positive serotypes, including STEC O157:H7 and O103:H2. The eaeA gene was detected in STEC serotypes that are commonly implicated in severe humans disease and outbreaks including STEC O157:H7, STEC O145:H28 and O103:H2. PFGE revealed that the isolates were highly diverse with very low rates of antimicrobial resistance. In conclusion, only a small number of cattle STEC serotypes that possessed eaeA, had the highest number of virulence-associated genes, indicative of their high virulence. Further characterization of STEC O157:H7, STEC O145:H28 and O103:H2 using whole genome sequencing will be needed to fully understand their virulence potential for humans.

The impact of the national action plan on the epidemiology of antibiotic resistance among 352,238 isolates in a teaching hospital in China from 2015 to 2018

Background

We sought to understand the epidemiology and characteristics of antimicrobial resistance (AMR) and the impact of the National Action Plan (NAP) on AMR. This information will be critical to develop interventions and strengthen antibiotic stewardship in hospital settings in China.

Methods

Cross-sectional data collection from the hospital information management system from 1 January 2015 to 30 August 2018. Variables included patient age, sex, diagnosis, hospital department and antibiotic sensitivity test. T-test for two samples method was applied to compare the results before and after NAP implementation. Multivariate analysis with binary logistic regression was conducted to examine the associations of risk factors for antimicrobial resistance.

Results

In total there were 352,238 isolates in the final analysis after excluding contamination strains and isolates with incomplete information. More than 50% of patients were > 66 years old. 62% were male. 40% of the total samples were sputum. Among the total sample, the total resistance rate was 42% among all isolates. The rate of resistance to all antibiotics declined by 5.3% (95% CI 4.96-5.64%, p < 0.0001) and culture positivity rate declined by 9.8% (95% CI 9.22-10.34%, p < 0.0001) after NAP. Logistical regression showed that the NAP had effect with an adjusted odds ratio of 0.76 (95% CI 0.71-0.81, p = 0.002). Being male, age > 65 years, ICU department, diagnosed with certain diseases were more likely to be associated with antimicrobial resistance.

Conclusions

Antibiotic resistance rates were high in this teaching hospital. However, the introduction of the China NAP since 2016 followed by hospital policy emphasis was associated with a declining AMR trend. Policies will need to incorporate antimicrobial stewardship with a focus on certain departments, with infection control practices and with increases in vaccination coverage among elderly.

Dynamics of antibiotic resistance with special reference to Shiga toxin-producing Escherichia coli infections

The discovery of antibiotics was paralleled by the evolution of antibiotic resistance which is probably the best example of contemporary evolution in action. The selection pressure, imposed by indiscriminate use of antibiotics, has changed the scale, mode and tempo of antibiotic resistance evolution. The presence of multidrug resistance, wide range of adaptability features and the infectivity make antibiotic resistance of Shiga toxin-producing Escherichia coli (STEC) more dangerous. The characterization, prevalence and the virulence factors of STEC have been profusely reported, whereas, the antibiotic resistance has been largely ignored because the antibiotic use in STEC infections is controversial. Thus, the current review has focussed on the source, evolution, persistence, mechanism, dissemination and control of antibiotic resistance viz-a-viz the STEC infections. The resistance development occurs by the inactivation of antibiotics, regulating the membrane permeability, modification of natural antibiotic targets or the use of efflux pumps against antibiotics. And, the dissemination of resistance genes occurs vertically by DNA replication and horizontally by conjugation, transduction and transformation. The prevention of development and dissemination of antibiotic resistance needs international public health bodies to rationalize the antibiotic use, prevent the flux of antibiotics into the environment, develop the rapid diagnostics tests, undertake proper surveillance of antibiotic resistance, promote the research on antibiotic resistance prevention, promote the research and development of novel alternative antibiotics, and encourage the widespread social awareness campaigns against the inappropriate antibiotic usage.

Escherichia coli O26 and O113:H21 on Carcasses and Beef from a Slaughterhouse Located in Mato Grosso, Brazil

Shiga toxin-producing Escherichia coli (STEC) is a group of emerging pathogens that can cause human diseases, including hemolytic uremic syndrome (HUS) and hemorrhagic colitis (HC). Monitoring slaughtering stages and checking contamination points are crucial for the production of safe food. In this context, the aim of this study was to verify contamination by STEC strains, to determine the contamination points and evaluate the resistance profile to 12 antimicrobials used in both veterinary and human medicine. A total of 80 samples were obtained from eight collection points (pen floor, rectum, hide, carcass swabs and esophagus, diaphragm, masseter, and retail beef tissue samples). The isolates were collected by dilution plating on MacConkey agar with sorbitol, cefixime, and tellurite and analyzed by multiplex polymerase chain reaction for virulence genes. Serotyping of non-O157 was performed, and testing for 12 antibiotics by disk diffusion was carried out. A total of 18 STEC strains were isolated, presenting different virulence profiles. Contamination by STEC was observed in the rectum (5/18), carcass surface (5/18), hide (3/18), diaphragm (2/18), retail beef (2/18), and masseter muscle (1/18). Pen floor swabs and esophagus tissues showed no STEC contamination. Moreover, three strains were identified as O26 and three as O113:H21 strains, which have been linked to HUS and HC outbreak cases in Brazil. All STEC isolates were susceptible to all evaluated antimicrobials, except streptomycin. The presence of STEC strains is a direct risk to the consumer, especially when isolated from retail beef, and contamination can occur during different slaughter stages. However, antimicrobial resistance profiles did not identify multidrug-resistant strains, limiting potential antimicrobial resistance transmission to other pathogens.

Antimicrobial Drug-Resistant Shiga Toxin-Producing Escherichia coli Infections, Michigan, USA

High frequencies of antimicrobial drug resistance were observed in O157 and non-O157 Shiga toxin–producing E. coli strains recovered from patients in Michigan during 2010–2014. Resistance was more common in non-O157 strains and independently associated with hospitalization, indicating that resistance could contribute to more severe disease outcomes.

Prevalence, identification of virulence factors, O-serogroups and antibiotic resistance properties of Shiga-toxin producing Escherichia coli strains isolated from raw milk and traditional dairy products

Background

Shiga-toxigenic Escherichia coli strains are one of the most important foodborne bacteria with an emergence of antibiotic resistance. Foodborne STEC strains are mainly associated with presence of certain virulence factors and O-seogroups. The present investigation was done to study the distribution of virulence factors, O-serogroups and antibiotic resistance properties of Shiga-toxigenic Escherichia coli isolated from milk and dairy products.

Methods

Six-hundred samples were randomly collected and immediately transferred to laboratory. All samples were cultured and E. coli strains were isolated. STEC strains were identified based on the presence of putative virulence factors and subtypes. STEC isolates were subjected to multiplex PCR and disk diffusion methods.

Results

One-hundred and eighty-one out of 600 samples (30.16%) harbored E. coli. Prevalence of STEC strains was 10.66%. O157 (43.75%) and O26 (37.50%) were the most frequently identified serogroups. Aac(3)-IV (100%), CITM (96.87%) and tetA (76.56%) were the most commonly detected antibiotic resistance genes. STEC strains had the highest prevalence of resistance against ampicillin (100%), gentamicin (100%) and tetracycline (96.87%).

Conclusions

Kashk and dough were negative for presence of E. coli strains. High prevalence of resistant-O157 strains and simultaneous presence of multiple virulence factors pose an important public health problem regarding the consumption of raw milk and dairy products.

Complete genome sequence of SRT8, a novel T1-like Escherichia coli bacteriophage

In this study, an Escherichia coli virulent phage, SRT8, was isolated from sewage sludge samples collected from Jinan, Shandong Province, China. The genome of phage SRT8 consists of 49,579 bp with 47.83% G+C content. The phage genome contains 84 putative protein-coding genes, and no rRNA or tRNA genes. Comparative genomics analysis showed that the E. coli phage SRT8 is a member of a new species and belongs to the subfamily Tunavirinae, which includes T1-like phages.