Quantitative assessment and genomic profiling of Campylobacter dynamics in poultry processing: a case study in the United Arab Emirates integrated abattoir system.

In the United Arab Emirates, no previous research has investigated the dynamics of the foodborne pathogen Campylobacter in broiler abattoir processing. This study conducted in one of the largest poultry producers in the UAE, following each key slaughter stage-defeathering, evisceration, and final chilling-five broiler carcasses were collected from 10 slaughter batches over a year. Additionally, one caecum was obtained from 15 chickens in each slaughter batch to evaluate the flock colonization. In total, 300 samples (150 carcasses and 150 caeca) were collected and enumerated for Campylobacter using standard methods. Campylobacter was pervasive in caecal samples from all slaughter batches, with 86% of carcasses post-defeathering and evisceration stages and 94% post-chilling tested positive for Campylobacter. Campylobacter coli predominates in 55.2% of positive samples, followed by Campylobacter jejuni in 21%, with both species co-existing in 23.8% of the samples. Campylobacter counts in caecal contents ranged from 6.7 to 8.5 log10 CFU/g, decreasing post-defeathering and evisceration to 3.5 log10 CFU/g of neck skin and further to 3.2 log10 CFU/g of neck skin post-evisceration. After chilling, 70% of carcasses exceeded 3 log10 CFU/g of neck skin. Whole-genome sequencing (WGS) of 48 isolates unveiled diverse sequence types and clusters, with isolates sharing the same clusters (less than 20 single nucleotide polymorphisms) between different farms, different flocks within the same farm, as well as in consecutive slaughter batches, indicating cross-contamination. Multiple antimicrobial resistance genes and mutations in gyrA T86I (conferring fluoroquinolone resistance) and an RNA mutation (23S r.2075; conferring macrolide resistance) were widespread, with variations between C. coli and C. jejuni. WGS results revealed that selected virulence genes (pglG, pseD, pseI, flaA, flaB, cdtA, and cdtC) were significantly present in C. jejuni compared to C. coli isolates. This study offers the first insights into Campylobacter dynamics in poultry processing in the UAE. This work provides a base for future research to explore additional contributors to Campylobacter contamination in primary production. In conclusion, effective Campylobacter management demands a comprehensive approach addressing potential contamination sources at every production and processing stage, guided by continued microbiological surveillance and genomic analysis to safeguard public health and food safety.

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.

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.

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.

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 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.

High efficacy and enhanced synergistic activity of the novel siderophore-cephalosporin cefiderocol against multidrug-resistant and extensively drug-resistant Klebsiella pneumoniae from inpatients attending a single hospital in the United Arab Emirates.

BACKGROUND: Cefiderocol (CFDC) is a novel siderophore-cephalosporin, which usually penetrates the bacteria through the iron-uptake pathways. Data is limited on the factors affecting CFDC activity and methods for overcoming resistance development. Synergistic approaches are needed to tackle antimicrobial resistance. This study aimed to determine CFDC activity on Klebsiella pneumoniae isolates from patients attending a single hospital in the United Arab Emirates (UAE), to explore the effect of ß-lactamases on CFDC activity and to enhance CFDC susceptibility in both iron-depleted and iron-enriched conditions. METHODS: We investigated 238 K. pneumoniae strains from diverse clinical sources. ß-lactamase genes were detected by PCR. Susceptibility to CFDC and 12 comparator antibiotics were tested. Combinations of CFDC with ß-lactamase inhibitors (BLIs) and/or an outer membrane (OM) permeabilizer (polymyxin B nonapeptide) were tested in iron-depleted and iron-enriched conditions. RESULTS: CFDC exhibited efficacy of 97.9%, against multidrug-resistant (MDR), and extensively drug-resistant (XDR) strains, in addition to strains resistant to the last resort drugs such as colistin and tigecycline, including dual carbapenemase-producers (blaNDM and blaOXA-48-like) with MIC ≤ 0.06-8 µg/ml. It was effective in killing strains with single and multiple ß-lactamases; however, it lost activity in iron-enriched conditions. Synergy was achieved with dual combination of CFDC and BLIs, especially avibactam, which caused a significant reduction in MICs even in iron-enriched conditions. A significant reduction was seen with the triple combination including an OM permeabilizer plus avibactam. Killing-kinetic studies proved that the combination therapy caused dose reduction and faster killing by CFDC than the monotherapy. CONCLUSIONS: CFDC was deemed effective against MDR and XDR K. pneumoniae. Synergistic combination of CFDC with BLIs and OM permeabilizers could be effective to treat infections in iron-rich sites, but this should be investigated in vivo.