Search Results (588)

Background/Objectives: Multidrug-resistant (MDR) Escherichia coli resistant to third-generation cephalosporins are a growing One Health concern, but data on extraintestinal pathogenic E. coli (ExPEC) from wildlife in North Africa remain scarce. We aimed to characterize ESBL/AmpC-producing ExPEC from captive wild mammals in Tunisia and to situate these isolates in a global genomic context. Methods: In 2018, 30 fecal samples from 14 captive wild mammals in a private farm were screened on cefotaxime agar. Four cefotaxime-resistant E. coli isolates were recovered from a llama, lion, hyena, and tiger. Antimicrobial susceptibility testing and Illumina whole-genome sequencing were combined with in silico typing, resistome and virulome profiling, plasmid and mobile element analysis, human pathogenicity prediction and core-genome MLST-based minimum-spanning trees. Results: All isolates were MDR but remained susceptible to carbapenems, colistin and tigecycline. Two ST162/B1 isolates from the llama and tiger carried bla_CMY-2, whereas two ST69/D isolates from the lion and hyena harbored bla_CTX-M-15 and qnrS1. Genomes encoded 61–68 antimicrobial resistance genes and 114–131 virulence-associated genes, together with IncF-, IncI1- and IncY-type plasmids and IS26-rich insertion sequence profiles. Mating-out assays yielded cefotaxime-resistant transconjugants, supporting plasmid transferability of bla_CMY-2 or bla_CTX-M-15. PathogenFinder predicted a ≥0.93 probability of human pathogenicity for all isolates. cgMLST-based trees showed that Tunisian ST69 and ST162 clustered within internationally disseminated lineages containing human, animal and food isolates, rather than forming wildlife-restricted branches. Conclusions: Captive wild mammals in Tunisia can harbor high-risk ExPEC lineages combining ESBL/AmpC production, multidrug resistance and extensive virulence and mobility gene repertoires. These findings highlight captive wildlife as potential reservoirs and sentinels of clinically relevant E. coli and underscore the need for integrated WGS-based One Health surveillance at the human–animal–environment interface in North Africa. Full article

This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (bla_CTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four bla_CTX-M subtypes were identified. bla_CTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the bla_CTX-M gene, and 96.29% of strains successfully transferred the bla_CTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of bla_CTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework. Full article

Patients undergoing cervical conization for cervical intraepithelial neoplasia grade II (CIN II) may develop postoperative bloodstream infections (BSIs), and multidrug-resistant (MDR) Escherichia coli isolates with distinct resistance profiles can complicate antimicrobial management. In this case-based study, two E. coli strains, HBFY-1 and HBFY-2, were recovered from blood cultures obtained from a 38-year-old CIN II patient with postoperative fever. The isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing, conjugation assays, and comparative genomics against publicly available genomes matched by sequence type and serotype. Fever occurred on postoperative day 2. HBFY-1 was fluoroquinolone-resistant; belonged to ST744/O101:H9; carried the extended-spectrum β-lactamase (ESBL) gene bla_CTX-M-27; was phenotypically confirmed as an ESBL producer; and grouped within a multi-source near-neighbor clade consistent with a conserved fluoroquinolone-associated resistance backbone in ST744/O101:H9. HBFY-2 was carbapenem-resistant; belonged to ST48/O113:H32; carried bla_NDM-5 on an IncY-associated plasmid bin; was phenotypically confirmed as a metallo-carbapenemase producer; and did not harbor any ESBL gene. Within the matched ST48/O113:H32 dataset, bla_NDM-5 was detected only in HBFY-2, which clustered within an Asia-enriched lineage, including China-derived human and swine genomes. The bla_CTX-M-27-associated and bla_NDM-5-associated elements were transferred to E. coli C600 at frequencies of 5.3 × 10⁻² and 4.6 × 10⁻⁶, respectively, and transfer of the bla_NDM-5-associated element imposed no detectable growth penalty under the tested conditions. As this study is based on a single clinical case, the findings should be interpreted cautiously, yet they still highlight the potential value of integrating susceptibility testing with rapid genomic characterization for identifying mobilizable carbapenem-resistance platforms. Full article

Hospital wastewater represents a critical hotspot for the dissemination of antibiotic resistance genes (ARGs), serving both as an environmental reservoir and a transmission pathway for multidrug-resistant bacteria into receiving ecosystems. The intense antibiotic selective pressure within healthcare facilities promotes the emergence, persistence and amplification of resistant strains, posing substantial risks to public health and environmental integrity. This study aimed to characterize Escherichia coli (E. coli) isolates recovered from hospital wastewater effluents in multiple cities across Gabon, with emphasis on bacterial loads, antimicrobial resistance patterns and associated genetic determinants. Wastewater samples were aseptically collected from sewer outlets of eleven healthcare facilities distributed across five provinces over a 12-week period, structured into two six-week sampling campaigns to capture temporal variability. A total of 158 bacterial isolates were obtained, among which 49 were confirmed as E. coli. Mean concentrations of presumptive E. coli ranged from 7.1 × 10³ to 1.49 × 10⁹ CFU/mL, indicating substantial microbial contamination of hospital effluents. Antimicrobial susceptibility testing using the Kirby–Bauer disk diffusion method against 19 antibiotics revealed that all isolates exhibited multidrug-resistant phenotypes. Resistance rates were particularly high to β-lactams and third-generation cephalosporins, reaching 90–100% in most facilities, reflecting strong selective pressure and widespread circulation of resistance mechanisms in urban aquatic environments. In contrast, carbapenems and amikacin remained comparatively effective, with resistance levels below 40%, suggesting partial preservation of last-resort therapeutic options. The values of the Multiple Antibiotic Resistance Index (MARI) ranged from 0.21 to 0.84, indicating selection pressure on different classes of antibiotics. Phylogenetic analysis showed a predominance of phylogroup A, traditionally considered commensal but increasingly associated with the spread of resistance. Groups B2, D/E and F proved to be the most resistant. These groups showed marked resistance to first-line antibiotics. The blaCTX-M-1 was the most prevalent resistance determinant (66.6%), occurring twice as frequently as blaSHV (33.3%), a finding that confirms the significant circulation of extended-spectrum β-lactamase-producing E. coli. Overall, these findings highlight hospital wastewater as a major reservoir and dissemination source of multidrug-resistant E. coli, underscoring the urgent need for improved wastewater treatment, strengthened antimicrobial stewardship and integrated One Health-based surveillance strategies. Full article

Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analyzed 295 non-duplicate Escherichia coli isolates derived from 104 clinical, 173 animal [diseased (123) and healthy (50)], 14 sewage and four water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of 50 ESBL and non-ESBL Escherichia coli from the three interfaces underwent whole genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was lowest in the animal interface. Sewage isolates harbored the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognized ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, and E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate, pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs; although AMR profile was quite distinct across the three interfaces, human isolates demonstrated greater resistance than animal isolates, suggesting healthcare-driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies. Full article

Background: Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is increasingly recognized as a multidrug-resistant (MDR) nosocomial pathogen. However, subspecies-level genomic data from Ecuador remain limited. Methods: Four clinical E. hormaechei isolates from a hospital in northern Ecuador were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Genomic characterization included multilocus sequence typing (MLST), resistome profiling, plasmid replicon detection, integron screening, genomic island analysis, and phylogenetic comparison with publicly available Ecuadorian genomes. Results: WGS identified three isolates as subsp. xiangfangensis (ST136 and ST337) and one as subsp. hoffmannii (ST145). Two ST136 isolates exhibited extensive MDR phenotypes associated with bla_CTX-M-15, bla_OXA-1, bla_ACT-16, and additional aminoglycoside and fluoroquinolone resistance genes. ST145 showed moderate resistance, whereas ST337 remained largely susceptible despite harboring bla_ACT-16. Multiple genomic islands and plasmid replicons (IncF/IncR or IncHI2) were detected. Phylogenetic analysis demonstrated clustering with previously reported Ecuadorian lineages. Conclusions: This study provides subspecies-level genomic characterization of clinical E. hormaechei in Ecuador and describes heterogeneous resistance profiles and associated mobile genetic elements, contributing baseline data for regional surveillance. Full article

Background/Objectives: Multidrug-resistant Salmonella enterica serovar Enteritidis, especially those isolated from humans, remains a public concern. In the present study, S. Enteritidis strain 31404 was obtained clinically from a fecal sample of a fifteen-year-old girl, who was positive for bla_NDM-13. Methods: Antibiotic susceptibility testing and whole genome sequencing were performed. Core genome MLST and hierarchical clustering (HierCC) were performed using EnteroBase. Population structure analysis of 57 S. Enteritidis isolates collected between 2023 and 2025 in Jiaxing city was conducted. A comparative structure analysis of bla_NDM-13-positive plasmids was also performed. Results: S. Enteritidis strain 31404 was resistant to 13 antimicrobial agents. We found that strain 31404 belonged to ST11 and carried resistance genes, such as bla_NDM-13, bla_CTX-M-14, ble_MBL, fosA3, qnrS, and tet (A). bla_NDM-13 was located on an IncI1-I (α) plasmid designated as p31404-NDM13. S. Enteritidis isolate 31404 was closely related to PNUSAS514422, which was isolated from the United States in 2025. Comparative genetic environment related to bla_NDM-13-positive plasmids available in the NCBI database indicates that ΔTn125-mediated contexts were commonly associated with bla_NDM-13. IS1294 (IS91 family), which replaces ISAba125, is likely to mobilize bla_NDM-13. Conclusions: The findings in this study provide insights into the molecular characterization and diversification of bla_NDM-13. The identification of bla_NDM-13-containing transferable plasmids in different serotypes of Salmonella isolates (such as S. Rissen, S. Typhimurium, and S. Enteritidis) in different cities in China highlights the risk of the spread of carbapenem-resistant genes among Salmonella isolates. Full article

Wildlife can serve as a potential reservoir and spreader of resistant and pathogenic bacteria. Raptors, occupying the ecological position of apex or mesopredators, integrate exposure across different habitats and therefore serve as bioindicators of environmental dissemination of pathogens. In this study, we isolated 54 Escherichia coli (E. coli) strains from feces sampled from 64 raptors admitted to a wildlife rescue center in Central Italy. Phenotypic antimicrobial susceptibility testing was conducted, followed by molecular screening for resistance genes. Additionally, the presence of intestinal E. coli pathotypes, including STEC, EHEC, EPEC, ETEC, EAEC, EIEC, and NTEC, was evaluated through virulence gene analysis. Results indicated notable resistance to commonly used antimicrobials, with the highest percentages observed for ampicillin (40.74%), fluoroquinolones (31.48%), and tetracycline (25.93%). Molecular analysis of phenotypically resistant isolates identified the presence of several resistance genes, including bla_TEM (13 isolates), bla_CTX-M (4 isolates), bla_CMY-2 (3 isolates), bla_SHV (1 isolate), tet(A) (9 isolates), tet(B) (4 isolates), cat1 (1 isolate), and cmlA (2 isolates). Furthermore, 29.63% of isolates were classified as multidrug-resistant (MDR) and 7.41% as extensively drug-resistant (XDR). Regarding virulence profiles, one isolate harboring eaeA, escV, and astA genes was classified as atypical EPEC, while 27.78% isolates had only the astA gene, preventing precise pathotype assignment. These findings highlight the circulation of antimicrobial-resistant and potentially pathogenic E. coli strains within raptor populations in Central Italy, emphasizing the zoonotic potential and reaffirming the role of raptors as bioindicators within a One Health approach. Full article

Background/Objectives: Antimicrobial agents have revolutionized disease management in humans and animals; however, their misuse and overuse have accelerated the emergence and spread of antimicrobial resistance (AMR) and antimicrobial resistance genes (ARGs). Dairy farms are recognized as potential hotspots for ARG dissemination, particularly through Escherichia coli, which acts as a reservoir and vector of ARGs, enabling their horizontal transfer via plasmids and other mobile genetic elements. This study aimed to characterize the genomic diversity, ARG profiles, plasmid content, and phylogenetic relationships of E. coli isolated from dairy farm environments and milk using whole-genome sequencing. Methods: A total of 31 E. coli isolates recovered from soil, effluent, cow dung, and milk samples underwent deoxyribonucleic acid extraction, library preparation, and sequencing on the Illumina MiSeq platform, followed by comprehensive bioinformatic analysis. Results: The E. coli isolates exhibited 20 distinct sequence types, including one novel sequence type. Plasmids were detected in 71% of the isolates, with the IncF plasmid family being the most predominant. Furthermore, 12 ARG groups were identified, with β-lactam resistance genes detected in 67.7% of isolates. Notably, blaCTX-M genes were identified in all phenotypically confirmed extended-spectrum β-lactamase-producing isolates. Additional ARGs, including those conferring resistance to tetracyclines (tet(A), tetX4), quinolones (qnrS1), aminoglycosides (aph, aad, ant), and folate pathway inhibitors (dfr and sul), were widely distributed throughout the samples. Phylogenetic analysis revealed clustering of isolates from different sample types, particularly among ST58 isolates, suggesting cross-environmental transmission. Conclusions: This study demonstrates that E. coli from dairy farm environments harbor diverse ARGs and plasmids, confirming their role as reservoirs of AMR. These findings underscore the importance of prudent antimicrobial use, routine genomic surveillance, and enhanced biosecurity measures to limit cross-environmental transmission. Full article

Background: Antimicrobial-resistant Escherichia coli and Klebsiella pneumoniae represent an increasing challenge in community-acquired pediatric diarrheal infections. Understanding the genomic basis and dissemination of resistance in outpatient settings is essential for guiding antimicrobial use. Methods: Eighteen Gram-negative isolates obtained from pediatric outpatients with acute diarrhea were analyzed using selective culture methods, antimicrobial susceptibility testing, and whole-genome sequencing. Multilocus sequence typing, serotyping, virulence profiling, antimicrobial resistance gene detection, plasmid replicon typing, mobile genetic element analysis, and core genome-based phylogenetic analysis were performed. Phenotypic resistance profiles were correlated with genomic resistance determinants. Results: Klebsiella pneumoniae (55.56%) and Escherichia coli (44.44%) were identified, with all isolates exhibiting putative multidrug resistance-associated genomic profiles. Extended-spectrum β-lactamase genes, particularly blaCTX-M variants, were strongly associated with resistance to third-generation cephalosporins. In contrast, fluoroquinolone resistance correlated with gyrA and parC mutations and plasmid-mediated qnr genes. Phylogenetic analysis revealed diverse lineages harboring resistance determinants. In silico plasmid analysis revealed that key resistance genes co-occurred with IncF-type plasmids and mobile genetic elements, including ISEcp1, IS26, and class 1 integrons, suggesting putative plasmid association rather than confirmed localization. Conclusions: These findings highlight the small scale of plasmid-mediated antimicrobial resistance among E. coli and K. pneumoniae causing pediatric community-acquired diarrhea. The integration of phenotypic and genomic analyses underscores the need for continuous resistance surveillance to support rational antibiotic use in outpatient settings. Full article

Background/Objectives: Escherichia coli is a ubiquitous commensal organism in humans, animals, and the environment, but certain strains harbour virulence and antimicrobial resistance (AMR) determinants that can cause significant disease. Food-producing animals, including dairy cattle, may act as reservoirs for AMR E. coli, and raw milk and raw milk products can serve as potential exposure pathways to humans. However, data on the prevalence and genomic characteristics of AMR E. coli in raw milk in Ireland are limited. This study aimed to describe the occurrence of commensal and clinically relevant AMR E. coli in raw milk and raw milk dairy products in Ireland and to characterise their antimicrobial susceptibility and genetic characteristics. Methods: A total of 139 raw milk and raw milk dairy product samples were collected and analysed for commensal E. coli and fluoroquinolone-resistant, extended-spectrum β-lactamase (ESBL)/AmpC β-lactamase and carbapenemase-producing E. coli. AMR patterns were determined in line with EU surveillance guidelines based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines which use minimum inhibitory concentration (MIC) breakpoints. Whole genome sequencing (WGS) was conducted on selected isolates to identify AMR genes (ARG), virulence factors, plasmid replicons, efflux pump, disinfectant resistance genes, multi-locus sequence types (MLSTs) and phylogenetic diversity. Results: A total of forty-seven E. coli isolates were recovered (33.8% isolation rate). Thirteen isolates exhibited resistance to between two and nine antimicrobials, with twelve classified as multidrug resistant (MDR). The highest resistance frequencies were to ampicillin, sulfamethoxazole, trimethoprim and tetracycline. Four fluoroquinolone-resistant isolates, one ESBL producer (bla_CTX-M-3), and one carrying a AmpC promoter mutation were identified; no carbapenemase producers were detected. WGS revealed diverse sequence types, multiple virulence determinants, plasmid replicons, intrinsic efflux pump genes, and limited presence of the disinfectant resistance gene qacEΔ1. Conclusions: Raw milk and raw milk dairy products in Ireland can harbour AMR E. coli, including MDR and potentially pathogenic strains, highlighting the need for ongoing surveillance within the dairy supply chain. Full article

Background/Objectives: Data on antimicrobial resistance (AMR) in goat-derived E. coli within the Gulf Cooperation Council (GCC) region remain limited, and are largely restricted to studies conducted in Saudi Arabia and the UAE, with no published reports from Qatar. This study provides the first baseline characterization of AMR and extended-spectrum β-lactamase (ESBL) profiles of E. coli isolated from goats in Qatar. Methods: A total of 280 fecal samples were collected from goats across nine locations in Qatar (140 healthy and 140 diseased goats; 12 samples did not yield E. coli cultures). A selective agar medium was used to isolate E. coli, and the isolates were subsequently confirmed using the VITEK^® 2 Compact system. Antimicrobial susceptibility testing was performed to determine resistance profiles, and PCR assays were used to detect ESBL-associated genes. Results: 268 E. coli isolates were recovered from 280 samples. AMR analysis revealed a high prevalence of tetracycline resistance among E. coli isolates (53%), consistently observed across all nine sampling locations. Ampicillin resistance was also widespread. AMR was detected in isolates from both healthy and diseased goats; however, gentamicin resistance was found exclusively in the isolates from diseased animals. Overall, 44 isolates (16%) were classified as multidrug resistant (MDR), while nine isolates (3%) demonstrated ESBL production based on cefotaxime resistance. MDR and ESBL-producing E. coli were detected across all nine locations and in both healthy and diseased animals, with MDR strains occurring more frequently than ESBL producers. PCR analysis identified ESBL-associated genes, namely, bla_CTX-M in nine isolates and bla_TEM in three isolates. Conclusions: Goats in Qatar harbor multidrug-resistant and ESBL-producing E. coli, highlighting their role as AMR reservoirs within a One Health framework. The high resistance rates to commonly used antibiotics, particularly tetracycline and ampicillin, across health statuses and geographic locations suggest potential influences of local management practices and environmental factors. The detection of ESBL genes, notably bla_CTX-M and bla_TEM, underscores the need for prudent antimicrobial use and the implementation of integrated One Health surveillance programs to mitigate potential public health risks and to support national AMR surveillance and antimicrobial stewardship efforts across the region. Full article

Background/Objectives: Plasmids are key vehicles for the dissemination of antimicrobial resistance (AMR), yet their contribution to the global resistome architecture of Escherichia coli remains poorly resolved. This study aimed to quantify how plasmid backbones shape the distribution, mobility, and stabilization of resistance genes across diverse phylogenetic backgrounds. Methods: We analyze 9700 high-quality genomes spanning major phylogroups and sequence types. Plasmidome reconstruction was integrated with lineage-resolved antimicrobial resistance gene (ARG) mapping to characterize plasmid–ARG associations and evolutionary patterns. Results: Although most antimicrobial resistance genes (ARGs) are chromosomal, plasmids disproportionately encode clinically important determinants including bla_NDM-5, mcr-1.1, and multiple bla_CTX-M alleles that show strong, recurrent associations with a restricted set of backbone families, most notably IncX3, IncX4, IncI, and IncF. These conserved plasmid–gene modules recur across phylogenetic backgrounds and continental scales. We identify a marked divergence in evolutionary strategies: generalist phylogroups (A, B1, D) maintain plasmid-rich and highly diverse resistomes, whereas globally dominant Extraintestinal Pathogenic E. coli (ExPEC) clones such as ST131 and ST410 exhibit reduced plasmid dependency and frequent chromosomal integration of extended-spectrum β-lactamase (ESBL) genes, particularly bla_CTX-M-15, consistent with a shift toward vertically stabilized resistomes. By integrating plasmidome reconstruction with lineage-resolved ARG mapping, this study delivers the most extensive plasmid-focused resistome analysis to date, revealing highly modular plasmid–ARG networks structured around a small number of high-risk backbone types. These backbones account for the majority of globally relevant ARGs, including 64.6% of bla_NDM-5 and 76.4% of mcr-1.1 detections. Conclusions: Together, our findings establish plasmid lineages rather than individual genes or clones as central units of AMR dissemination and critical targets for future genomic surveillance and intervention strategies. Full article

Antimicrobial-resistant bacteria associated with poultry production pose an ongoing challenge for food safety and veterinary public health. The present study evaluated the prevalence, antimicrobial resistance phenotypes, and selected resistance genes of E. coli recovered from broiler chicken carcasses and cecal content in Romania. Over a 12-month period in 2024, a total of 444 samples were collected, including 300 carcasses obtained from slaughterhouses and retail outlets and 144 cecal samples collected at slaughterhouses. Isolates were recovered using standard microbiological procedures and confirmed through biochemical and automated identification systems. Antimicrobial susceptibility was assessed using a minimum inhibitory concentration–based automated platform, and extended-spectrum β-lactamase (ESBL) production was evaluated phenotypically. Target resistance genes were investigated by PCR. E. coli was identified in 36.0% of carcass samples and 64.6% of cecal samples. High resistance rates were observed for tetracycline (82.6%), ampicillin (68.3%), and trimethoprim–sulfamethoxazole (61.2%), while multidrug resistance occurred in 34.3% of isolates. ESBL production was detected in 11.1% of carcass isolates and 11.8% of cecal isolates and was associated with the presence of blaCTX-M. Additional resistance determinants, including blaTEM, tetA, tetB, sul1, dfrA1, and aadA1, were widely distributed among isolates from both sources. The results suggest that poultry carcasses may contribute to the dissemination of resistant and ESBL-producing E. coli, reflecting intestinal carriage and contamination during processing. Strengthened antimicrobial stewardship, systematic resistance monitoring, and improved hygiene practices throughout the poultry production chain are essential to reduce the public health impact of resistant bacteria. Full article

Background: The emergence of carbapenem-resistant enterobacteriaceae (CRE) co-harboring the mcr-1.1 gene and carbapenemase-encoding genes poses a severe threat to public health. Urban wastewater treatment plants (WWTPs) act as natural reservoirs and hotspots for the dissemination of antimicrobial resistance genes (ARGs). This study aimed to elucidate the molecular characteristics of CRE carrying mcr-1.1 in urban WWTPs. Methods: Samples were collected from the influent of urban WWTPs in Fengxian, Shanghai, from April 2024 to March 2025. mcr-1.1-positive Escherichia coli (E. coli) isolates were screened using real-time PCR, and their antimicrobial susceptibility was determined via the broth microdilution method. Plasmid conjugation assays were performed with E. coli C600 as the recipient strain. Whole-genome sequencing (WGS) was carried out to analyze the molecular characteristics of mcr-1.1-positive E. coli isolates. Results: A total of 312 samples were collected, and 5 (1.6%) mcr-1.1-positive E. coli isolates were identified. All isolates were multidrug-resistant (MDR) but susceptible to tigecycline (TIG). WGS of strain EC0176 (sequence type 156 [ST156], enteroaggregative E. coli [EAEC]) detected the presence of bla_NDM-5, bla_TEM-1, bla_CTX-M-55, and mcr-1.1 as well as related virulence genes. Further analysis revealed that pEC0176 was an IncHI2-type plasmid co-harboring mcr-1.1, bla_NDM-5, arr-3, aph(4)-Ia, aph(3′)-Ia, aac(3)-IVa, and mph(A). The plasmid pEC0176 harbored similar backbones as p20014-MCR, p2017.03.02CC_1, pSC2017167-mcr-256k, pEC17CM13_MCR and pGDE043-mcr1, including the type IV secretion system (T4SS) and IncHI-type conjugal transfer genes. Conjugation experiments confirmed that pEC0176 could be horizontally transferred into E. coli C600, with an average transfer efficiency of 3.3 × 10⁻². Phylogenetic analysis showed that the MCR-1 protein of EC0176 is closely related to that of two human-derived E. coli strains from China (GenBank accession: AVR64822.1 and WP_076611062.1). Conclusions: To our knowledge, this is the first report of E. coli ST156 carrying an IncHI2-type plasmid co-harboring mcr-1.1 and bla_NDM-5 from urban WWTPs in Fengxian, Shanghai. Our findings underscore the severe status of bacterial antimicrobial resistance and emphasize the necessity of enhancing antimicrobial resistance surveillance in urban WWTPs. Full article