Genomics Characterization of Colistin Resistant Escherichia coli from Chicken Meat-the First Report in the United Arab Emirates.

Plasmid-mediated colistin resistance is an emerging One Health challenge at the human-food-environment interface. In this study, 12 colistin-resistant Escherichia coli carrying mcr-1.1 gene were characterized using whole-genome sequencing. This is the first report from locally produced chicken meat in the United Arab Emirates. The characterized isolates harbored virulence-associated factors ranging from 4 to 17 genes per isolate. The multilocus sequence type 1011 was identified in 5 (41.6%) isolates. Six (50.0%) of the isolates harbored blaCTX-M-55. All of the E. coli isolates contained Incl2 plasmids. This study highlights for the first time chicken meat as a potential reservoir of mcr-1.1 carrying E. coli in the UAE. This study has implications for food safety and underscores the need for comprehensive surveillance strategies to monitor the spread of colistin resistance. Results presented in this short communication address knowledge gaps on the epidemiology of plasmid-mediated colistin resistance in the Middle East food production chain.

Enumeration, Antimicrobial Resistance, and Virulence Genes Screening of Enterococcus spp. Isolated from Retail Chicken Carcasses in the United Arab Emirates.

Enterococci have recently emerged as nosocomial pathogens worldwide. Their ubiquitous nature determines their frequent finding in foods as contaminants. In this study, we aimed to determine the counts, species diversity, antimicrobial resistance profile, and to screen for a set of virulence genes among enterococci. Enterococcus were identified from 75.7% (125/165) of chilled chicken carcasses, belonging to seven companies, sampled from retail markets in Abu Dhabi Emirate, United Arab Emirates (U.A.E.). Overall, the samples, with a mean Enterococcus count of 2.58 log10 colony-forming unit (CFU)/g with a standard deviation of ±1.17 log10 CFU/g. Among the characterized Enterococcus isolates (n = 90), Enterococcus faecalis was the predominant species (51.1%), followed by Enterococcus faecium (37.8%). Using Vitek2 automated antimicrobial sensitivity panel, we found none of the E. faecalis nor E. faecium to be resistant to ampicillin, teicoplanin, vancomycin, or tigecycline. A third of the E. faecalis (28.3%) and E. faecium (35.3%) were resistant to high-level gentamicin. Over half of E. faecalis (54.3%) were resistant to ciprofloxacin, and the same was in about a third of E. faecium isolates (29.4%). Linezolid resistance was identified in 10 E. faecalis and 7 E. faecium isolates belonging to samples from three companies. All of the linezolid-resistant isolates harbored oxazolidinone resistance optrA gene. Virulence-associated genes (asa1 and gelE) were significantly (p < 0.05) more detected among E. faecalis compared to E. faecium isolates recovered in this study. Over half of the E. faecalis (25/46) and E. faecium (20/34) isolates were identified as multidrug-resistant. This study provides further insight into virulence genes and their association with the dissemination of multidrug-resistant E. faecalis and E. faecium in supermarket chicken meat in the U.A.E. This is probably the first description of the optrA gene in enterococci from supermarket chicken meat in the U.A.E. and from Arab countries. This study adds to the regional and global understanding of antimicrobial resistance spread in foods of animal origin.

Occurrence of antibiotic resistant C. jejuni and E. coli in wild birds, chickens, humans, and the environment in Malay villages, Kedah, Malaysia.

Foodborne pathogens have become a major concern not only due to the diseases they cause, but also because of the rise of antibiotic resistant strains in human and animals. The purposes of this study were to determine the occurrence of Campylobacter jejuni and Escherichia coli and their antibiotic resistance profiles in wild birds, chickens, humans, and the environment in Malay villages in Malaysia. Three Malay villages in Kota Setar, Kedah were chosen. Three hundred nine (309) samples were collected in this study including wild birds (38), chickens (71), humans (47), and the environment (153). Subsequently, the C. jejuni and E coli isolates were tested against antibiotics using the disc diffusion method. Campylobacter jejuni was found positive in 17 (37.8%) flies and 8 (11.3%) chickens. Also, E. coli was found positive in 89.4% of human, 47.4% of bird, 44 62% of chicken and in 71.2% of the environmental samples. Ten antibiotics were used to determine the susceptibility of the isolates. Eighty four percent (84%) of C. jejuni and 100% of E. coli isolates were found to show resistance towards at least one antibiotic. The isolates showed high resistance to cefpodoxime and tetracycline.

History and epidemiology of foot-and-mouth disease in Afghanistan: a retrospective study.

BACKGROUND: Foot and mouth disease (FMD) is endemic in Afghanistan with serotypes O, A and Asia 1 being prevalent. A retrospective study of data collected through passive surveillance of outbreaks of FMD in Afghanistan from 1995 to 2016 was undertaken to determine the temporal and spatial distribution of FMD in the country. RESULTS: A total of 4171 outbreaks were reported between 1995 and 2008 with a strong correlation between the number of outbreaks and the number of provinces (r = 0.85, s = 68.2, p < 0.001); and between the number of outbreaks and the number of districts containing infected animals (r = 0.68, s = 147.8, p = 0.008). Of 7558 samples collected from livestock originating from 34 provinces in 2009, 2011 and 2013-2015, 54.1% were test positive (FMDV 3ABC-trapping ELISA) and the prevalence varied significantly between years (χ2 = 263.98, df = 4, P < 0.001). Clinically suspected cases were reported in 2016 with a substantial positive correlation (r = 0.70, P < 0.001) between the number of districts with cases and the number of reported cases. Serotype O was the predominant serotype detected during the study period, although serotypes A and Asia1 were also detected. Cattle were involved in all outbreaks in the study period and infections were detected in all years of the study in Hirat province in the north-west (bordering Iran), Nangarhar province in the east (bordering Pakistan) and Kabul province in the centre of the country. CONCLUSIONS: The current paper was the first analysis of existing data focusing on the spatiotemporal distribution of FMD in Afghanistan. The findings from this study provide valuable direction for further research to understand the epidemiology of FMD and its control in Afghanistan.

A Baseline Quantitative Survey of Campylobacter spp. on Retail Chicken Portions and Carcasses in Metropolitan Perth, Western Australia.

INTRODUCTION: Limited baseline retail surveys have been published over the past 10 years on Campylobacter in Australian chicken meat. This study generates quantitative baseline data to assist in risk assessment and management strategies. METHODS: Raw poultry products (n = 315) were purchased for a year (2016-2017) from retail supermarkets in metropolitan Perth, Western Australia (WA). Campylobacter concentration was determined by a direct plating method in all samples, whereas in 58.7% (185/315) of the samples, testing was done using enrichment culture in conjunction with direct plating according to standard methods. RESULTS: Using direct plating, Campylobacter were recovered from 23.8% (75/315) of the samples, whereas 53.7% (100/186) of the samples were positive for Campylobacter using enrichment culture (∼1 g). Campylobacter counts revealed that 76.2% of the chicken portions and carcasses were contaminated with <1 log10 colony-forming units (CFU)/g, and 18.7% of the samples were contaminated with ≥2 log10 CFU/g. The average Campylobacter concentration among 315 tested chicken meat samples was 1.82 log10 CFU/g (±standard deviation (SD) 2.26 log10 CFU/g). The likelihood of Campylobacter recovery by direct plating from chicken products with skin on was significantly higher (odds ratio [OR] 4.4; p < 0.0001) than product forms with skin off. The highest counts of Campylobacter were associated with chicken wings (1.94 log10 CFU/g [±SD 2.26 log10 CFU/g]). There were some significant variations in Campylobacter counts based on the interaction between product forms and sourcing poultry processing establishment. CONCLUSIONS: This study provides the first published research on Campylobacter status in retail chicken meat in Australia since almost 10 years. Results from this study add to the knowledge on the assessment of microbial safety of the WA poultry chain, and can be used as an input for future development of quantitative risk assessment of Campylobacter.

Veterinary Drug Residues in the Food Chain as an Emerging Public Health Threat: Sources, Analytical Methods, Health Impacts, and Preventive Measures.

Veterinary medications are necessary for both contemporary animal husbandry and food production, but their residues can linger in foods obtained from animals and pose a dangerous human risk. In this review, we aim to highlight the sources, occurrence, human exposure pathways, and human health effects of drug residues in food-animal products. Following the usage of veterinary medications, pharmacologically active compounds known as drug residues can be found in food, the environment, or animals. They can cause major health concerns to people, including antibiotic resistance development, the development of cancer, teratogenic effects, hypersensitivity, and disruption of normal intestinal flora. Drug residues in animal products can originate from variety of sources, including water or food contamination, extra-label drug use, and ignoring drug withdrawal periods. This review also examines how humans can be exposed to drug residues through drinking water, food, air, and dust, and discusses various analytical techniques for identifying these residues in food. Furthermore, we suggest some potential solutions to prevent or reduce drug residues in animal products and human exposure pathways, such as implementing withdrawal periods, monitoring programs, education campaigns, and new technologies that are crucial for safeguarding public health. This review underscores the urgency of addressing veterinary drug residues as a significant and emerging public health threat, calling for collaborative efforts from researchers, policymakers, and industry stakeholders to develop sustainable solutions that ensure the safety of the global food supply chain.

High prevalence and genomic features of multidrug-resistant Salmonella enterica isolated from chilled broiler chicken on retail sale in the United Arab Emirates.

Non-typhoidal Salmonella represents a significant global concern for food safety and One Health. Despite the United Arab Emirates (UAE) being a leading consumer of chicken meat globally, there is a lack of comprehensive understanding regarding the prevalence and genomic characteristics of Salmonella within the country. This study aims to address this gap by conducting a thorough analysis of Salmonella prevalence, antimicrobial resistance, and genomic profiles of isolates obtained from whole broiler carcasses retailed under chilled conditions in the UAE. Our findings reveal that Salmonella was detected in 41.2 % (130/315) of the sampled chilled broiler carcasses, with notable variability observed among samples sourced from six different companies. Phenotypic antimicrobial resistance (AMR) testing, among 105 isolates, highlighted high resistance rates to tetracycline (97.1 %), nalidixic acid (93.3 %), ampicillin (92.4 %), azithromycin (75.2 %), ciprofloxacin (63.8 %), and ceftriaxone (54.3 %). Furthermore, a concerning 99 % (104/105) of the isolates exhibited multidrug resistance. Whole-genome sequencing (WGS) of 60 isolates identified five serovars, with S. infantis/Sequence Type (ST) 32 (55 %) and S. Minnesota/ST-458 (28.3 %) being the most prevalent. WGS analysis unveiled 34 genes associated with antimicrobial resistance, including mcr-1.1 (only in two isolates), conferring resistance to colistin. The two major serovars, Infantis and Minnesota, exhibited significant variation (P-values <0.001) in the distribution of major AMR genes (aadA1, blaCMY-2, blaSHV-12, qnrB19, qnrS1, sul1, and sul2). Notably, the gene qacEdelta, conferring resistance to quaternary ammonium compounds commonly found in disinfectants, was universally present in all S. Infantis isolates (n = 33), compared to only one S. Minnesota isolate. Additionally, all S. Infantis isolates harbored the IncFIB (pN55391) plasmid replicon type. Major serovars exhibited distinct distributions of antimicrobial resistance genes, underscoring the importance of serovar-specific surveillance. These findings emphasize the critical need for continuous surveillance and intervention measures to address Salmonella contamination risks in poultry products, providing valuable insights for public health and regulatory strategies not only in the UAE but also globally.

Pre-Harvest Food Safety Challenges in Food-Animal Production in Low- and Middle-Income Countries.

Food safety remains a significant global public health concern, with the risk of unsafe food varying worldwide. The economies of several low- and middle-income countries (LMICs) heavily rely on livestock, posing a challenge to ensuring the production of safe food. This review discusses our understanding of pre-harvest critical issues related to food safety in LMICs, specifically focusing on animal-derived food. In LMICs, food safety regulations are weak and inadequately enforced, primarily concentrating on the formal market despite a substantial portion of the food sector being dominated by informal markets. Key critical issues at the farm level include animal health, a low level of good agriculture practices, and the misuse of antimicrobials. Effectively addressing foodborne diseases requires a comprehensive One Health framework. Unfortunately, the application of the One Health approach to tackle food safety issues is notably limited in LMICs. In conclusion, considering that most animal-source foods from LMICs are marketed through informal channels, food safety legislation and policies need to account for this context. Interventions aimed at reducing foodborne bacterial pathogens at the farm level should be scalable, and there should be strong advocacy for the proper implementation of pre-harvest interventions through a One Health approach.

Staphylococcus spp. in Salad Vegetables: Biodiversity, Antimicrobial Resistance, and First Identification of Methicillin-Resistant Strains in the United Arab Emirates Food Supply.

Contamination of leafy greens with Staphylococcus spp. can occur at various supply chain stages, from farm to table. This study comprehensively analyzes the species diversity, antimicrobial resistance, and virulence factors of Staphylococci in salad vegetables from markets in the United Arab Emirates (UAE). A total of 343 salad items were sampled from three major cities in the UAE from May 2022 to February 2023 and tested for the presence of Staphylococcus spp. using standard culture-based methods. Species-level identification was achieved using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Antimicrobial susceptibility testing was conducted using the VITEK-2 system with AST-P592 cards. Additionally, whole genome sequencing (WGS) of ten selected isolates was performed to characterize antimicrobial resistance determinants and toxin-related virulence factors. Nine Staphylococcus species were identified in 37.6% (129/343) of the tested salad items, with coagulase-negative staphylococci (CoNS) dominating (87.6% [113/129]) and S. xylosus being the most prevalent (89.4% [101/113]). S. aureus was found in 4.6% (14/343) of the salad samples, averaging 1.7 log10 CFU/g. One isolate was confirmed as methicillin-resistant S. aureus, harboring the mecA gene. It belonged to multi-locus sequence type ST-672 and spa type t384 and was isolated from imported fresh dill. Among the characterized S. xylosus (n = 45), 13.3% tested positive in the cefoxitin screen test, and 6.6% were non-susceptible to oxacillin. WGS analysis revealed that the cytolysin gene (cylR2) was the only toxin-associated factor found in S. xylosus, while a methicillin-sensitive S. aureus isolate harbored the Panton-Valentine Leukocidin (LukSF/PVL) gene. This research is the first to document the presence of methicillin-resistant S. aureus in the UAE food chain. Furthermore, S. xylosus (a coagulase-negative staphylococcus not commonly screened in food) has demonstrated phenotypic resistance to clinically relevant antimicrobials. This underscores the need for vigilant monitoring of antimicrobial resistance in bacterial contaminants, whether pathogenic or commensal, at the human-food interface.

First Report of Colistin-Resistant Escherichia coli Carrying mcr-1 IncI2(delta) and IncX4 Plasmids from Camels (Camelus dromedarius) in the Gulf Region.

Addressing the emergence of antimicrobial resistance (AMR) poses a significant challenge in veterinary and public health. In this study, we focused on determining the presence, phenotypic background, and genetic epidemiology of plasmid-mediated colistin resistance (mcr) in Escherichia coli bacteria isolated from camels farmed in the United Arab Emirates (UAE). Fecal samples were collected from 50 camels at a Dubai-based farm in the UAE and colistin-resistant Gram-negative bacilli were isolated using selective culture. Subsequently, a multiplex PCR targeting a range of mcr-genes, plasmid profiling, and whole-genome sequencing (WGS) were conducted. Eleven of fifty camel fecal samples (22%) yielded colonies positive for E. coli isolates carrying the mcr-1 gene on mobile genetic elements. No other mcr-gene variants and no chromosomally located colistin resistance genes were detected. Following plasmid profiling and WGS, nine E. coli isolates from eight camels were selected for in-depth analysis. E. coli sequence types (STs) identified included ST7, ST21, ST24, ST399, ST649, ST999, and STdaa2. Seven IncI2(delta) and two IncX4 plasmids were found to be associated with mcr-1 carriage in these isolates. These findings represent the first identification of mcr-1-carrying plasmids associated with camels in the Gulf region. The presence of mcr-1 in camels from this region was previously unreported and serves as a novel finding in the field of AMR surveillance.

Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.

Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC ß-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.

Pathogenic E. coli in the Food Chain across the Arab Countries: A Descriptive Review.

Foodborne bacterial infections caused by pathogens are a widespread problem in the Middle East, leading to significant economic losses and negative impacts on public health. This review aims to offer insights into the recent literature regarding the occurrence of harmful E. coli bacteria in the food supply of Arab countries. Additionally, it aims to summarize existing information on health issues and the state of resistance to antibiotics. The reviewed evidence highlights a lack of a comprehensive understanding of the extent to which harmful E. coli genes are present in the food supply of Arab countries. Efforts to identify the source of harmful E. coli in the Arab world through molecular characterization are limited. The Gulf Cooperation Council (GCC) countries have conducted few surveys specifically targeting harmful E. coli in the food supply. Despite having qualitative data that indicate the presence or absence of harmful E. coli, there is a noticeable absence of quantitative data regarding the actual numbers of harmful E. coli in chicken meat supplies across all Arab countries. While reports about harmful E. coli in animal-derived foods are common, especially in North African Arab countries, the literature emphasized in this review underscores the ongoing challenge that harmful E. coli pose to food safety and public health in Arab countries.

Comparison of Antimicrobial Resistance among Commensal Escherichia coli Isolated from Retail Table Eggs Produced by Laying Hens from the Cage and Non-Cage Housing Systems in Western Australia.

Antimicrobial resistance (AMR) has become a global public health concern in recent decades. Although several investigations evaluated AMR in commensal and pathogenic bacteria from different foods of animal origin in Australia, there is a lack of studies that compared AMR in commensal E. coli isolated from retail table eggs obtained from different laying hen housing systems. This study aimed to determine AMR and differences in AMR patterns among E. coli isolates recovered from retail table eggs sourced from caged and non-caged housing systems in Western Australia. Commensal E. coli isolates were tested for susceptibility to 14 antimicrobials using a broth microdilution method. Clustering analyses and logistic regression models were applied to identify patterns and differences in AMR. Overall, there were moderate to high frequencies of resistance to the antimicrobials of lower importance used in Australian human medicine (tetracycline, ampicillin, trimethoprim, and sulfamethoxazole) in the isolates sourced from the eggs of two production systems. All E. coli isolates were susceptible to all critically important antimicrobials except the very low level of resistance to ciprofloxacin. E. coli isolates from eggs of non-caged systems had higher odds of resistance to tetracycline (OR = 5.76, p < 0.001) and ampicillin (OR = 3.42, p ≤ 0.01) compared to the isolates from eggs of caged systems. Moreover, the number of antimicrobials to which an E. coli isolate was resistant was significantly higher in table eggs from non-caged systems than isolates from caged systems' eggs. Considering the conservative approach in using antimicrobials in the Australian layer flocks, our findings highlight the potential role of the environment or human-related factors in the dissemination and emergence of AMR in commensal E. coli, particularly in retail table eggs of non-cage system origin. Further comprehensive epidemiological studies are required to better understand the role of different egg production systems in the emergence and dissemination of AMR in commensal E. coli.

Genomic characterization of molecular markers associated with antimicrobial resistance and virulence of the prevalent Campylobacter coli isolated from retail chicken meat in the United Arab Emirates.

Campylobacter is a major cause of gastroenteritis worldwide, with broiler meat accounting for most illnesses. Antimicrobial intervention is recommended in severe cases of campylobacteriosis. The emergence of antimicrobial resistance (AMR) in Campylobacter is a concerning food safety challenge, and monitoring the trends of AMR is vital for a better risk assessment. This study aimed to characterize the phenotypic profiles and molecular markers of AMR and virulence in the prevalent Campylobacter species contaminating chilled chicken carcasses sampled from supermarkets in the United Arab Emirates (UAE). Campylobacter was detected in 90 (28.6%) out of 315 tested samples, and up to five isolates from each were confirmed using multiplex PCR. The species C. coli was detected in 83% (75/90) of the positive samples. Whole-genome sequencing was used to characterize the determinants of AMR and potential virulence genes in 45 non-redundant C. coli isolates. We identified nine resistance genes, including four associated with resistance to aminoglycoside (aph(3')-III, ant(6)-Ia, aph(2″)-Ib, and aac(6')-Im), and three associated with Beta-lactam resistance (blaOXA-61, blaOXA-193, and blaOXA-489), and two linked to tetracycline resistance (tet(O/32/O), and tet(O)), as well as point mutations in gyrA (fluoroquinolones resistance), 23S rRNA (macrolides resistance), and rpsL (streptomycin resistance) genes. A mutation in gyrA 2 p.T86I, conferring resistance to fluoroquinolones, was detected in 93% (42/45) of the isolates and showed a perfect match with the phenotype results. The simultaneous presence of blaOXA-61 and blaOXA-193 genes was identified in 86.6% (39/45) of the isolates. In silico analysis identified 7 to 11 virulence factors per each C. coli isolate. Some of these factors were prevalent in all examined strains and were associated with adherence (cadF, and jlpA), colonization and immune evasion (capsule biosynthesis and transport, lipooligosaccharide), and invasion (ciaB). This study provides the first published evidence from the UAE characterizing Campylobacter virulence, antimicrobial resistance genotype, and phenotype analysis from retail chicken. The prevalent C. coli in the UAE retail chicken carries multiple virulence genes and antimicrobial resistance markers and exhibits frequent phenotype resistance to macrolides, quinolones, and tetracyclines. The present investigation adds to the current knowledge on molecular epidemiology and AMR development in non-jejuni Campylobacter species in the Middle East and globally.

Contamination Levels and Phenotypic and Genomic Characterization of Antimicrobial Resistance in Escherichia coli Isolated from Fresh Salad Vegetables in the United Arab Emirates.

Contaminated fresh produce has been identified as a vehicle for human foodborne illness. The present study investigated the counts, antimicrobial resistance profile, and genome-based characterization of Escherichia coli in 11 different types of fresh salad vegetable products (n = 400) sampled from retailers in Abu Dhabi and Dubai in the United Arab Emirates. E. coli was detected in 30% of the tested fresh salad vegetable items, with 26.5% of the samples having an unsatisfactory level (≥100 CFU/g) of E. coli, notably arugula and spinach. The study also assessed the effect of the variability in sample conditions on E. coli counts and found, based on negative binominal regression analysis, that samples from local produce had a significantly higher (p-value < 0.001) E. coli count than imported samples. The analysis also indicated that fresh salad vegetables from the soil-less farming system (e.g., hydroponic and aeroponic) had significantly (p-value < 0.001) fewer E. coli than those from traditional produce farming. The study also examined the antimicrobial resistance in E. coli (n = 145) recovered from fresh salad vegetables and found that isolates exhibited the highest phenotypic resistance toward ampicillin (20.68%), tetracycline (20%), and trimethoprim-sulfamethoxazole (10.35%). A total of 20 (13.79%) of the 145 E. coli isolates exhibited a multidrug-resistant phenotype, all from locally sourced leafy salad vegetables. The study further characterized 18 of the 20 multidrug-resistant E. coli isolates using whole-genome sequencing and found that the isolates had varying numbers of virulence-related genes, ranging from 8 to 25 per isolate. The frequently observed genes likely involved in extra-intestinal infection were CsgA, FimH, iss, and afaA. The ß-lactamases gene blaCTX-M-15 was prevalent in 50% (9/18) of the E. coli isolates identified from leafy salad vegetable samples. The study highlights the potential risk of foodborne illness and the likely spread of antimicrobial resistance and resistance genes associated with consuming leafy salad vegetables and emphasizes the importance of proper food safety practices, including proper storage and handling of fresh produce.

Genomic profiling of extended-spectrum ß-lactamase-producing Escherichia coli from Pets in the United Arab Emirates: Unveiling colistin resistance mediated by mcr-1.1 and its probable transmission from chicken meat - A One Health perspective.

BACKGROUND: The United Arab Emirates (UAE) has witnessed rapid urbanization and a surge in pet ownership, sparking concerns about the possible transfer of antimicrobial resistance (AMR) from pets to humans and the environment. This study delves into the whole-genome sequencing analysis of ESBL-producing E. coli strains from healthy cats and dogs in the UAE, which exhibit multidrug resistance (MDR). Additionally, it provides a genomic exploration of the mobile colistin resistance gene mcr-1.1, marking the first instance of its detection in Middle Eastern pets. METHODS: We investigate 17 ESBL-producing E. coli strains from healthy UAE pets using WGS and bioinformatics analysis to identify genes encoding virulence factors, assign diverse typing schemes to the isolates, and scrutinize the presence of AMR genes. Furthermore, we characterized plasmid contigs housing the mcr-1.1 gene and conducted phylogenomic analysis to evaluate their relatedness to previously identified UAE isolates. RESULTS: Our study unveiled a variety of virulence factor-encoding genes within the isolates, with fimH emerging as the most prevalent. Regarding ß-lactamase resistance genes, the blaCTX group 1 gene family predominated, with CTX-M-15 found in 52.9% (9/17) of the isolates, followed by CTX-M-55 in 29.4% (5/17). These isolates were categorized into multiple sequence types (STs), with the epidemic ST131 being the most frequent. The presence of the mcr-1.1 gene, linked to colistin resistance, was confirmed in two isolates. These isolates belonged to ST1011 and displayed distinct profiles of ß-lactamase resistance genes. Phylogenomic analysis revealed close connections between the isolates and those from chicken meat in the UAE. CONCLUSION: Our study underscores the presence of MDR ESBL-producing E. coli in UAE pets. The identification of mcr-1.1-carrying isolates warrants the urgency of comprehensive AMR surveillance and highlights the role of companion animals in AMR epidemiology. These findings underscore the significance of adopting a One Health approach to mitigate AMR transmission risks effectively.

Domestic Pets in the United Arab Emirates as Reservoirs for Antibiotic-Resistant Bacteria: A Comprehensive Analysis of Extended-Spectrum Beta-Lactamase Producing Escherichia coli Prevalence and Risk Factors.

Extended-spectrum ß-lactamases resistant (ESBL-R) Escherichia coli (E. coli) has been reported from healthy and sick pets. However, data from Middle Eastern countries, including the United Arab Emirates (UAE), are minimal. This study provides the first evidence of ESBL-R E. coli carriage among pets in the UAE. A total of 148 rectal swabs were collected from domestic cats (n = 122) and dogs (n = 26) attending five animal clinics in the UAE. Samples were cultured directly onto selective agar, and suspected colonies were confirmed as ESBL-producing using phenotypic and molecular methods. Confirmed isolates were screened for their phenotypic resistance to twelve antimicrobial agents using the Kirby Bauer method. The owners of the pets completed a questionnaire at the time of sampling, and the data were used to identify risk factors. ESBL-R E. coli was detected in rectal swabs of 35 out of 148 animals (23.65%) (95% confidence interval [CI]: 17.06-31.32). Multivariable logistic regression analysis identified cats and dogs with access to water in ditches and puddles as 3.71 (p-value = 0.020) times more likely to be positive to ESBL-R E. coli than those without access to open water sources. Ciprofloxacin resistance was evident in 57.14% (44/77) of the ESBL-R E. coli isolates. The percentage of resistance to azithromycin and cefepime was 12.99% (10/77) and 48.05% (37/77), respectively. The blaCTX-M gene was detected in 82% of the PCR-screened isolates (n = 50). Multidrug resistance (MDR) phenotypes were evident in 91% (70/77) of the isolates. In conclusion, ESBL-R E. coli was detected at a noticeable rate among healthy pet cats and dogs in the UAE, and the majority are MDR to clinically important antimicrobials such as fluoroquinolones and 3rd and 4th generation cephalosporins. Our results call for strengthening antimicrobial stewardship among companion animal veterinarians in the UAE to reduce the potential transmission of ESBL-R E. coli between pets, humans, and urban environments.

Enumeration, antimicrobial resistance and genomic characterization of extended-spectrum ß-lactamases producing Escherichia coli from supermarket chicken meat in the United Arab Emirates.

The occurrence and counts of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in retail chicken sold in the United Arab Emirates (UAE) were investigated in this study. Results indicated that 79.68 % of chicken carcasses (251/315) sampled from UAE supermarkets harbored ESBL-producing E. coli. About half (51.75 % [163/315]) of the tested samples had an ESBL-producing E. coli count range between ≥3 log10 and < 5 log10 CFU/g. The antimicrobial resistance profiles of a subset of 100 isolates showed high rates of non-susceptibility to clinically significant antibiotics, particularly ciprofloxacin (80 %) and cefepime (46 %). Moreover, 7 % of the isolates exhibited resistance to colistin, with PCR-based screening revealing the presence of the mcr-1 gene in all colistin-resistant isolates. Multiplex PCR screening identified blaCTX-M and blaTEM genes as the most frequently presented genes among the phenotypically confirmed ESBL-producing E. coli. Further whole-genome sequencing and bioinformatic analysis of 27 ESBL-producing E. coli isolates showed that the gene family blaCTX group 1 was the most prevalent, notably CTX-M-55 (55.55 % [15/27]), followed by CTX-M-15 (22.22 % [6/27]). The most common sequence types (STs) were ST359 and ST1011, with three evident clusters identified based on phylogenomic analysis, aligned with isolates from specific production companies. Analysis of plasmid incompatibility types revealed IncFIB, IncFII, Incl2, and IncX1 as the most commonly featured plasmids. The findings of this study indicate a noticeable prevalence and high counts of ESBL-producing E. coli in chicken sampled from supermarkets in the UAE. The high rates of antimicrobial resistance to clinically important antibiotics highlight the potential public health risk associated with consuming chicken contaminated with ESBL-producing E. coli. Overall, this study emphasizes the importance of continued antimicrobial resistance monitoring in the UAE food chain and calls for further exposure risk assessment of the consumption of ESBL-producing E. coli via chicken meat.

Assessing the Prevalence and Potential Risks of Salmonella Infection Associated with Fresh Salad Vegetable Consumption in the United Arab Emirates.

This study aimed to investigate the occurrence and characteristics of Salmonella isolates in salad vegetables in the United Arab Emirates (UAE). Out of 400 samples tested from retail, only 1.25% (95% confidence interval, 0.41-2.89) were found to be positive for Salmonella, all of which were from conventional local produce, presented at ambient temperature, and featured as loose items. The five Salmonella-positive samples were arugula (n = 3), dill (n = 1), and spinach (n = 1). The Salmonella isolates from the five samples were found to be pan-susceptible to a panel of 12 antimicrobials tested using a disc diffusion assay. Based on whole-genome sequencing (WGS) analysis, only two antimicrobial resistance genes were detected-one conferring resistance to aminoglycosides (aac(6')-Iaa) and the other to fosfomycin (fosA7). WGS enabled the analysis of virulence determinants of the recovered Salmonella isolates from salad vegetables, revealing a range from 152 to 165 genes, collectively grouped under five categories, including secretion system, fimbrial adherence determinants, macrophage-inducible genes, magnesium uptake, and non-fimbrial adherence determinants. All isolates were found to possess genes associated with the type III secretion system (TTSS), encoded by Salmonella pathogenicity island-1 (SPI-1), but various genes associated with the second type III secretion system (TTSS-2), encoded by SPI-2, were absent in all isolates. Combining the mean prevalence of Salmonella with information regarding consumption in the UAE, an exposure of 0.0131 salmonellae consumed per person per day through transmission via salad vegetables was calculated. This exposure was used as an input in a beta-Poisson dose-response model, which estimated that there would be 10,584 cases of the Salmonella infection annually for the entire UAE population. In conclusion, salad vegetables sold in the UAE are generally safe for consumption regarding Salmonella occurrence, but occasional contamination is possible. The results of this study may be used for the future development of risk-based food safety surveillance systems in the UAE and to elaborate on the importance for producers, retailers, and consumers to follow good hygiene practices, particularly for raw food items such as leafy salad greens.

Campylobacter contamination in broiler carcasses and correlation with slaughterhouses operational hygiene inspection.

This study investigates factors associated with Campylobacter contamination of broiler carcasses, using survey data collected from nine Belgian slaughterhouses in 2008 in accordance with a European Union baseline study. Campylobacter were detected in 51.9% (202/389) (95% confidence interval, 46.8%-56.9%) of broiler carcasses. Campylobacter concentration was <10 CFU/g in 49.6% of carcasses, while 20.6% were contaminated with ≥ 1000 CFU/g. The mean Campylobacter concentration, as calculated by maximum likelihood estimation for left-censored data, was 1.8 log(10) CFU/g, with a standard deviation of 1.9 log(10) CFU/g. There was statistically significant variation among slaughterhouses in prevalence and concentrations of Campylobacter in their sampled carcasses. Campylobacter prevalence (but not concentrations) was positively associated with increase in broilers age. Both Campylobacter prevalence and concentration were significantly higher in carcasses sampled during June and September (but not in July and August) than carcasses sampled in January. We also investigated the correlation (Spearman's rank correlation test) between the scores of official control inspections and Campylobacter prevalence for eight out of the nine slaughterhouses. The control inspections were routinely performed by the Belgian Federal Agency for the Safety of the Food Chain, and the concluded inspection scores were used as a general numerical indicator for the status of operational hygiene and quality of management in the slaughterhouses. Ranking of slaughterhouses based on their inspection scores was statistically correlated (Spearman's correlation coefficient = 0.857) with their ranking based on prevalence of Campylobacter. In the present study we demonstrate how the outcomes from a routine baseline survey could be coupled with other readily available data from national control authorities in order to enable a better insight over Campylobacter contamination status in broiler slaughterhouses. Findings from this work call for subsequent in-depth investigations on technical and hygiene management factors that could impact Campylobacter contamination across broiler slaughterhouses.