Search Results (692)

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The bla_NDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes bla_NDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (bla_TEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding bla_NDM-19 includes ISAba125-IS5-bla_NDM-19-ble_MBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of bla_NDM and its related variants. To our knowledge, this is the first genomic report of a bla_NDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article

Background: The spread of ESBL-producing Enterobacteriaceae (ESBL-PE) strains in food poses a potential risk to human health. The aim of the study was to determine the occurrence of ESBL-PE and to investigate their distribution on foods. Methods: A total of 1000 food samples, including both raw and ready-to-eat products, was analyzed for the presence of ESBL-producing Enterobacteriaceae using chromogenic selective agar. Antibiotic resistance in the isolated strains was assessed using conventional methods, while whole-genome sequencing was employed to predict antimicrobial resistance and virulence genes. Results: The overall occurrence of ESBL-PE strains was 2.8%, with the highest contamination in raw meat samples (10%). A total of 31 multidrug-resistant (MDR) strains was isolated, mainly Escherichia coli, followed by Klebsiella pneumoniae, Salmonella enterica, and Enterobacter hormaechei. All strains exhibited high levels of resistance to at least four different β-lactam antibiotics, as well as to other antimicrobial classes including sulfonamides, tetracyclines, aminoglycosides, and quinolones. Whole-genome sequencing identified 63 antimicrobial resistance genes, with bla_CTX-M being the most prevalent ESBL gene. Twenty-eight (90%) isolates carried Inc plasmids, known vectors of multiple antimicrobial resistance genes, including those associated with ESBLs. Furthermore, several virulence genes were identified. Conclusions: The contamination of food with ESBL-PE represents a potential public health risk, underscoring the importance of the implementation of genomic surveillance to monitor and control the spread of antimicrobial resistance. Full article

Wastewater is a hotspot for the spread of antimicrobial resistance (AR); therefore, bacteriophages offer a promising biocontrol alternative to overcome the limitations of conventional disinfection. This study evaluated the efficacy of bacteriophages and cocktails for the biocontrol of carbapenem-resistant Klebsiella pneumoniae (CR-Kp) (CG258 and ST307) and Escherichia coli producers of extended-spectrum β-lactamases (ESBL-Ec) (ST131) in simulated wastewater. A synthetic wastewater matrix was prepared in which bacterial viability and bacteriophage stability were assessed for 72 h. CR-Kp or ESBL-Ec strain were treated with individual bacteriophages or phage-cocktails (dosed in different ways) and bacterial loads were monitored for 54 h. The Klebsiella phages FKP3 and FKP14 eliminated 99% (−2.9 Log) of CR-Kp-CG258 at 54 h, and FKP10 reduced 99% (−2.15 Log) of the CR-Kp-ST307 strains. The Klebsiella phage-cocktail in a single dose reduced to 99.99% (−4.12 Log) of the CR-Kp-CG258 at 36 h. Coliphage FEC1 reduced to 2.12 Log (99%) of ESBL-Ec-bla_CTX-M-G9, and FEC2 and FEC4 reduced approximately 1 Log (90%) of ESBL-Ec-bla_CTX-M-G9 and bla_CTX-M-G1. The coliphage cocktail increased the reduction up to 2.2 Logarithms. This study provides evidence supporting the use of bacteriophage cocktails for the control of resistant bacteria in wastewater, a sustainable intervention to mitigate the spread of AR and support water reuse safety. Full article

Background/objectives: Proteus mirabilis is a frequent causative agent of urinary and wound infections in both community and hospital settings. It develops resistance to expanded-spectrum cephalosporins (ESCs) due to the production of extended-spectrum β-lactamases (ESBLs) or plasmid-mediated AmpC β-lactamases (p-AmpCs). Recently, carbapenem-resistant isolates of P. mirabilis emerged due to the production of carbapenemases, mostly belonging to Ambler classes B and D. Here, we report an outbreak of infections due to carbapenem-resistant P. mirabilis that were observed in a psychiatric hospital in Zagreb, Croatia. The characteristics of ESBL and carbapenemase-producing P. mirabilis isolates, associated with an outbreak, were analyzed. Materials and methods: The antibiotic susceptibility testing was performed by the disk-diffusion and broth dilution methods. The double-disk synergy test (DDST) and inhibitor-based test with clavulanic and phenylboronic acid were applied to screen for ESBLs and p-AmpCs, respectively. Carbapenemases were screened by the modified Hodge test (MHT), while carbapenem hydrolysis was investigated by the carbapenem inactivation method (CIM) and EDTA-carbapenem-inactivation method (eCIM). The nature of the ESBLs, carbapenemases, and fluoroquinolone-resistance determinants was investigated by PCR. Plasmids were characterized by PCR-based replicon typing (PBRT). Selected isolates were subjected to molecular characterization of the resistome by an Inter-Array Genotyping Kit CarbaResisit and whole-genome sequencing (WGS). Results: In total, 20 isolates were collected and analyzed. All isolates exhibited resistance to amoxicillin alone and when combined with clavulanic acid, cefuroxime, cefotaxime, ceftriaxone, cefepime, imipenem, ceftazidime–avibactam, ceftolozane–tazobactam, gentamicin, amikacin, and ciprofloxacin. There was uniform susceptibility to ertapenem, meropenem, and cefiderocol. The DDST and combined disk test with clavulanic acid were positive, indicating the production of an ESBL. The MHT was negative in all except one isolate, while the CIM showed moderate sensitivity, but only with imipenem as the indicator disk. Furthermore, eCIM tested positive in all of the CIM-positive isolates, consistent with a metallo-β-lactamase (MBL). PCR and sequencing of the selected amplicons identified VIM-1 and VIM-4. The Inter-Array Genotyping Kit CarbaResist and WGS identified β-lactam resistance genes bla_VIM, bla_CTX-M-15, and bla_TEM genes; aminoglycoside resistance genes aac(3)-IId, aph(6)-Id, aph(3″)-Ib, aadA1, armA, and aac(6′)-IIc; as well as resistance genes for sulphonamides sul1 and sul2, trimethoprim dfr1, chloramphenicol cat, and tetracycline tet(J). Conclusions: This study revealed an epidemic spread of carbapenemase-producing P. mirabilis in two wards in a psychiatric hospital. Due to the extensively resistant phenotype (XDR), therapeutic options were limited. This is the first report of carbapenemase-producing P. mirabilis in Croatia. Full article

Background: This study aimed to (a) assess the prevalence of multidrug-resistant (MDR) Enterobacteriaceae in the waters of two rivers and wastewater treatment plants (WWTPs) in a region of Catalonia, Spain; (b) genetically characterize the MDR strains; and (c) compare extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from environmental and human sources. Methods: A total of 62 samples were collected from the influent and effluent of 31 WWTPs and 29 river water samples from 11 sites. Simultaneously, 382 hospitalized patients were screened for MDR Enterobacteriaceae using rectal swabs. All isolates underwent antibiotic susceptibility testing and whole-genome sequencing. Results: MDR Enterobacteriaceae were detected in 48.4% of WWTP samples, with 18.5% ESBL-producing E. coli and 1.5% (one sample) OXA-48-producing K. pneumoniae in influents, and 12.8% ESBL-producing E. coli in effluents. In river waters, 5.6% of samples contained ESBL-producing E. coli and 1.4% (1 sample) contained VIM-producing Enterobacter cloacae complex strains. Among patients, 10.2% (39/382) carried MDR Gram-negative bacilli, of which 66.7% were ESBL-producing E. coli. In aquatic ecosystems E. coli ST131 (13.3%) and ST162 (13.3%) were the most common strains, while in humans the common were E. coli ST131 (33.3%), ST69 (11.1%) and ST410 (7.4%) in humans. The most frequent environmental antibiotic resistance genes (ARG) were bla_CTX-M-15 (24%) and bla_TEM-1B (20%), while the most common ARGs were bla_TEM-1B (20.4%), bla_CTX-M15 (18.4%) and bla_CTX-M-27 (14.3%). IncF plasmids were predominant in environmental and human strains. Conclusions: ESBL-producing E. coli and carbapenemase-producing Enterobacteriaceae are present in aquatic environments in the region. Phylogenetic similarities between environmental and clinical strains suggest a possible similar origin. Further studies are necessary to clarify transmission routes and environmental impact. Full article

Background/Objectives: Among Enterobacterales, OXA-48-like-producing Proteus mirabilis strains have been scarcely detected. Herein, we characterized a bla_OXA-48-harbouring P. mirabilis strain recovered from Greece (Pm GR-1), while phylogenomics and comparative genomics analyses with previously published bla_OXA-48 carriers were also assessed. Methods: Characterization of Pm GR-1 was performed by the Vitek^® Compact and Mass Spectrometry systems, antimicrobial susceptibility testing, detection of beta-lactamases, multilocus-sequence typing (MLST), and whole-genome sequencing (WGS). In silico prediction of mobile genetic elements (MGEs), genomic islands (GIs), antimicrobial resistance genes (ARGs) and virulence factors (VFs), and phylogenetic, core-genome SNP and comparative genomics analyses were executed using bioinformatic tools. Results: Pm GR-1 was isolated from a urine sample of an outpatient in a Greek hospital. It exhibited a multidrug-resistant phenotype, being susceptible only to amikacin and ceftazidime/avibactam. It co-carried several beta-lactamase genes on the chromosome (bla_OXA-48, bla_CTX-M-14, bla_TEM-1) and a plasmid (bla_TEM-2) and several other ARGs, but also mutations associated with quinolone resistance in the DNA gyrase and topoisomerase IV subunits. It belonged to the international clone ST135 that has also been detected among OXA-48-producing P. mirabilis strains from Germany and the USA. Pm GR-1 was genetically related to those from Germany, sharing highly similar MGEs, GIs, ARGs and VFs, including the chromosomal bla_OXA-48 genetic structure, the O-antigen locus, the flagella locus, the MR/P fimbriae operon, and the urease gene cluster. Conclusions: To our knowledge, this is the first report from Greece of a bla_OXA-48-possessing P. mirabilis strain. The emergence of bla_OXA-48 among P. mirabilis strains of the international clone ST135 in different geographical regions is worrying. Close monitoring of these strains is required in One Health settings. Full article

Background: Salmonella enterica and Escherichia coli are common foodborne pathogens of global concern, particularly due to their antimicrobial resistance, notably to cephalosporins. Objective: This study aimed to evaluate a polymerase chain reaction-based lateral flow strip (PCR-LFS) assay for the detection of Salmonella spp. and E. coli harboring the bla_CTX-M gene, which confers resistance to third-generation cephalosporins. Methods: Two duplex PCRs (dPCR) were established to detect E. coli-harboring bla_CTX-M (set 1) and Salmonella-harboring bla_CTX-M (set 2). 600 bacterial isolates and raw pork mince spiked with bla_CTX-M-harboring E. coli and Salmonella were used to evaluated. Results: Both dPCR assays successfully detected bla_CTX-M-positive E. coli or Salmonella strains, while strains lacking the gene showed no amplification. Non-E. coli and non-Salmonella strains were PCR-negative unless they carried bla_CTX-M. The dPCR-LFS showed 100% validity including accuracy, sensitivity, specificity, positive predictive value, and negative predictive value for both E. coli or Salmonella spp. harboring or lacking bla_CTX-M. The assay accurately detected target strains without cross-reactivity with other bacteria or antimicrobial resistance genes. Cohen’s Kappa coefficient indicated perfect agreement (κ = 1), reflecting the high reliability of the dPCR-LFS. The assay could detect as low as 25 CFU/mL for bla_CTX-M-positive E. coli and 40 CFU/mL for bla_CTX-M-positive Salmonella in spiked raw pork mince. Conclusions: This assay is rapid, easy to interpret, and suitable for large-scale screening in surveillance programs. Full article

Background: Klebsiella variicola is a Gram-negative, capsulated, nonmotile, facultative anaerobic rod. It is one of the species belonging to the K. pneumoniae complex. The objective of this study was to gain insights into the antimicrobial resistance and virulence of K. variicola strains isolated from clinical samples from oncologic patients. Methods: Strain identification was performed using a mass spectrometry method. Whole genome sequencing was conducted for all analyzed strains. Antimicrobial susceptibility was determined using an automated method. The presence of antimicrobial resistance mechanisms and genes encoding extended-spectrum beta-lactamases (ESBL) was assessed using the double-disc synergy test and genotypic methods. Results: All isolates were identified as K. variicola using mass spectrometry and whole genome sequencing (WGS). All isolates were ESBL-positive, and two of them harbored the bla_CTX-M-15 gene. In our study, the bla_LEN-17 gene was detected in all strains. Genome sequence analysis of the K. variicola isolates revealed the presence of virulence factor genes, including entAB, fepC, ompA, ykgK, and yagWXYZ. Two different plasmids, IncFIB(K) and IncFII, were identified in all of the analyzed K. variicola strains. The detected virulence factors suggest the ability of the bacteria to survive in the environment and infect host cells. All isolates demonstrated in vitro susceptibility to carbapenems. Conclusions: Further studies are needed to confirm whether multidrug-resistant K. variicola strains represent an important pathogen in infections among oncologic patients. Full article

Microplastic particles (MPs) are an emerging global pollutant of increasing concern due to their widespread occurrence, persistence, and multifaceted impact on aquatic ecosystems. This study provides a comprehensive review of peer-reviewed literature from 2011 to 2025, analysing the presence, distribution, and microbiological associations of MPs in surface waters across five continents. The findings confirm that MPs are present in both marine and freshwater systems, with concentrations varying by region, hydrology, and proximity to anthropogenic sources. Polyethylene and polypropylene were identified as the most common polymers, often enriched in river mouths, estuaries, and aquaculture zones. A key focus of this review is the plastisphere—microbial biofilms colonizing MPs—which includes both environmental and pathogenic bacteria such as Vibrio, Pseudomonas, and Acinetobacter. Notably, MPs serve as vectors for the spread of antibiotic resistance genes (ARGs), including sul1, tetA and ermF, and β-lactamase genes like blaCTX-M. This highlights their role in enhancing horizontal gene transfer and microbial dissemination. The results emphasize the need for standardized monitoring protocols and further interdisciplinary research. In light of the One Health approach, understanding the microbial dimension of MP pollution is essential for managing risks to environmental and public health. Full article

Background/Objectives: European hedgehogs (Erinaceus europaeus) are present in areas where there is human activity; therefore, they can be a source of pathogens for other animals and humans. Methods: Eighteen hedgehog carcasses were collected and analyzed for Staphylococcus spp. Isolated strains were typed and analyzed for exfoliative toxins genes and the phenotypic and genotypic characteristics of antimicrobial resistance. Results: A total of 54 strains were isolated and typed as S. aureus, S. xylosus, S. sciuri, S. pseudintermedius, S. simulans, S. chromogenes, S. epidermidis, S. hyicus, and S. lentus. No strains had the eta and etb genes coding for exfoliative toxins. Overall, 39/54 (72.20%) isolates showed phenotypic resistance to at least one antimicrobial and 21/54 (38.80%) showed more than one resistance. The lowest efficacy was observed for erythromycin, with 40/54 (74.08%) strains classified as intermediate and 6/54 (11.11%) classified as resistant. Among the 29 isolates shown to be penicillin-resistant, 11 (37.93%) were oxacillin-resistant, with a minimum inhibitory concentration (MIC). Among the 54 staphylococcal strains, 2 (3.70%) were resistant to vancomycin, both with an MIC value equal to the maximum concentration of the antibiotic tested (256 μg/mL) and 2 (3.70%) had an intermediate resistance profile with an 8 μg/mL MIC value. No strains had the genes vanA and vanB. Two of the 29 (6.90%) penicillin-resistant strains had the blaZ gene; 8 (27.13%) strains had the mecA gene. Overall, 2/54 (3.70%) isolates were classified as extensively drug-resistant (XDR) and 9/54 (16.66%) were classified as multidrug-resistant (MDR). Conclusions: Hedgehogs can harbor antimicrobial-resistant staphylococci and can be sources of these bacteria for other animals and humans. They can also serve as bioindicators of the pathogens and antimicrobial-resistant bacteria circulating in a given habitat. Full article

Infections caused by oxacillin-resistant Staphylococcus pseudintermedius are increasingly common in veterinary medicine. The indiscriminate use of antibiotics by pet owners worsens this problem, reducing treatment efficacy and creating the need for alternative therapies. This study aimed to evaluate the inhibitory effect of clove essential oil (Syzygium aromaticum) on both oxacillin-resistant and susceptible S. pseudintermedius. Thirty-five isolates from dogs with otitis externa were analyzed. The bacteria were identified by phenotypic tests and tested for susceptibility to 22 antibiotics using disk diffusion. Resistance genes (mecA and blaZ) were detected using conventional PCR. Among the isolates, 34.28% (12/35) were positive for mecA, and 97.14% (34/35) for blaZ. The essential oil’s efficacy was assessed using broth microdilution to determine its minimum inhibitory concentration (MIC). Clove oil showed an average MIC and minimum bactericidal concentration (MBC) of 6.4 mg/mL, inhibiting both resistant and susceptible isolates. In conclusion, clove essential oil demonstrated in vitro antimicrobial activity against S. pseudintermedius. Full article

Staphylococcus saprophyticus (S. saprophyticus) is an opportunistic coagulase-negative staphylococcus (CoNS) known to cause urinary tract infections in humans and is increasingly recognized in veterinary medicine. The aim of this study was to provide an epidemiological characterization of S. saprophyticus strains and to identify potential virulence factors that may contribute to interspecies transmission. This research is particularly important, as companion animals represent an understudied reservoir of this microorganism, and their role in the spread of resistant pathogens remains insufficiently understood. A total of 61 S. saprophyticus strains isolated from humans, dogs, and cats were analyzed. Identification was performed using MALDI-TOF MS and confirmed by PCR targeting the hrcA gene. Antimicrobial susceptibility was assessed using the disk diffusion and broth microdilution methods, while resistance genes were detected by PCR. The blaZ and mecA genes were present in all strains; additionally, the majority harbored the resistance genes ermA, ermB, tetM, and tetK. Multidrug resistance (MDR) was identified in 21/61 strains (34.4%). Biofilm-forming capacity was temperature-dependent, with the strongest biofilm production observed at 37 °C (70.5%). At 38 °C and 39 °C, the proportion of strong biofilm producers decreased to 50.8% and 52.5%, respectively. All tested strains demonstrated pathogenic potential in the Galleria mellonella larvae infection model, with the highest mortality recorded for selected feline and canine strains. These findings indicate that S. saprophyticus strains from both humans and companion animals possess notable virulence and multidrug resistance. The detection of genotypically and phenotypically resistant strains in animals highlights their potential role as reservoir for zoonotic transmission. Full article

Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (bla_KPC and bla_VIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying bla_CTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments. Full article

Avian pathogenic Escherichia coli (APEC) poses a global threat to poultry health and public safety due to its high lethality, limited treatment options, and potential for zoonotic transmission via the food chain. However, long-term genomic surveillance remains limited, especially in countries like China where poultry farming is highly intensive. This study aimed to characterize the population structure, virulence traits, and antimicrobial resistance of 81 APEC isolates from diseased chickens collected over 16 years from Shandong and neighboring provinces in eastern China. The isolates were grouped into seven Clermont phylogroups, with A and B1 being dominant. MLST revealed 27 STs, and serotyping identified 29 O and 16 H antigens, showing high genetic diversity. The minor phylogroups (B2, C, D, E, G) encoded more virulence genes and had higher virulence-plasmid ColV carriage, with enrichment for iron-uptake, protectins, and extraintestinal toxins. In contrast, the dominant phylogroups A and B1 primarily carried adhesin and enterotoxin genes. Antimicrobial resistance was widespread: 76.5% of isolates were multidrug-resistant. The minor phylogroups exhibited higher tetracycline resistance (mediated by tet(A)), whereas the major phylogroups showed increased resistance to third- and fourth-generation cephalosporins (due to bla_CTX-M-type ESBL genes). These findings offer crucial data for APEC prevention and control, safeguarding the poultry industry and public health. Full article

Clinically significant antimicrobial-resistant bacteria and resistance genes are increasingly being reported in wildlife. In this study, 127 splenic samples from red foxes (Vulpes vulpes) from northern and central Italy were analysed for the presence of resistance genes against antimicrobials such as tetracycline, sulphonamide, β-lactam, and colistin, which were previously extensively used in human and veterinary management of bacterial diseases. One or more antimicrobial resistance genes were detected in 78 (61%) of 127 splenic samples. Polymerase chain reaction positivity was revealed for 13 genes—tet(A), tet(B), tet(K), tet(L), tet(M), tet(O), tetA(P), tet(Q), tet(S), tet(X), sul1, sul2, and bla_TEM-1—out of the 21 tested genes. Our results, corroborated by reports in the literature, confirm the potential role of the red fox as a sentinel for antimicrobial-resistant bacteria in contaminated environments and suggest that detecting resistance genes in biological samples by a culture-independent method might be an effective tool for the epidemiological study of antimicrobial resistance in wildlife. Full article