Search Results (382)

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/Objectives: Campylobacteriosis in human populations is an ongoing issue in both developed and developing countries. Poultry production is recognized as a reservoir for antimicrobial resistance and main source of human Campylobacter infection. Methods: In this study, sixty-five Campylobacter isolates were cultured from fecal samples collected from 17 flocks of broiler chickens in Alberta, Canada over two years (2015–2016). Susceptibility assays and PCR assays were performed to characterize resistance phenotypes and resistance genes. Conjugation assays were used to examine the mobility of AMR phenotypes. Results: Campylobacter jejuni was the predominant species recovered during both years of sampling. There were no Campylobacter coli isolates found in 2015; however, approximately 33% (8/24) of isolates collected in 2016 were Campylobacter coli. The two most frequent antimicrobial resistance patterns in C. jejuni collected in 2015 were tetracycline (39%) and azithromycin/clindamycin/erythromycin/telithromycin resistance (29%). One isolate collected in 2015 has resistance pattern ciprofloxacin/nalidixic acid/tetracycline. The tetO gene was detected in all tetracycline resistant isolates from 2015. The cmeB gene was detected in all species isolates with resistance to azithromycin/clindamycin/erythromycin/telithromycin, and from two isolates with tetracycline resistance. Alignment of the nucleotide sequences of the cmeB gene from C. jejuni isolates with different resistance patterns revealed several single nucleotide polymorphisms. A variety of multi-drug resistance patterns were observed through conjugation experiments. Conclusions: These data suggest that poultry production may serve as a potential reservoir for and source of transmission of multi-drug resistant Campylobacter jejuni and supports the need for continued surveillance. 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

Pasteurella multocida (Pm) is a zoonotic pathogen that poses a significant threat to animal health and causes substantial economic losses, further aggravated by rising tetracycline resistance. To restore the efficacy of tetracyclines to Pm, we evaluated the synergistic antibacterial activity of doxycycline combined with metformin, an FDA-approved antidiabetic agent. Among several non-antibiotic adjuvant candidates, metformin exhibited the most potent in vitro synergy with doxycycline, especially against capsular serogroup A strain (PmA). The combination demonstrated minimal cytotoxicity and hemolysis in both mammalian and avian cells and effectively inhibited resistance development under doxycycline pressure. At 50 mg/kg each, the combination of metformin and doxycycline significantly reduced mortality in mice and ducks acutely infected with PmA (from 100% to 60%), decreased pulmonary bacterial burdens, and alleviated tissue inflammation and damage. Mechanistic validation confirmed that metformin enhances membrane permeability in Pm without compromising membrane integrity, dissipates membrane potential, increases intracellular doxycycline accumulation, and downregulates the transcription of the tetracycline efflux gene tet(B). Morphological analyses further revealed pronounced membrane deformation and possible leakage of intracellular contents. These findings highlight metformin as a potent, low-toxicity tetracycline adjuvant with cross-species efficacy, offering a promising therapeutic approach for managing tetracycline-resistant Pm infections. 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

Escherichia coli (E. coli) is an opportunistic pathogen widely distributed in nature, and multi-drug resistance (MDR) E. coli has been widely recognized as a critical reservoir of resistance genes, posing severe health threats to humans and animals. A total of 288 E. coli strains were isolated and purified from fresh fecal samples of forest musk deer collected from farms in Sichuan, Shaanxi, and Yunnan Provinces of China between 2013 and 2023. This study aimed to conduct antibiotic susceptibility testing and resistance gene detection on the isolated forest musk deer-derived E. coli, analyze the correlations between them, investigate the presence of CRISPR systems within the strains, and perform bioinformatics analysis on the CRISPR systems carried by the strains. Results showed that 138 out of 288 E. coli strains were MDR, with the highest resistance to tetracycline (48.3%), cefalexin (45.1%), and doxycycline (41.7%). Prevalent genes were tetA (41.0%), sul2 (30.2%), blaTEM (27.1%), with 29 gene–phenotype pairs correlated. CRISPR system-negative strains had higher resistance rates to 16 antibiotics and lower detection rates only for aac (6′)-Ib-cr, qnrA, and qnrB compared to CRISPR system-positive strains. Regional analysis showed that the problem of drug resistance in Sichuan and Shaanxi was more serious, and that the detection rate of antibiotic resistance genes was relatively high. This study guides E. coli infection control in forest musk deer and enriches resistance research data. 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

Epigenetic modifications act as crucial regulators of gene activity and are influenced by both internal and external environmental factors, with diet being the most impactful external factor. On the other hand, cellular metabolism encompasses a complex network of biochemical reactions essential for maintaining cellular function, and it impacts every cellular process. Many metabolic cofactors are critical for the activity of chromatin-modifying enzymes, influencing methylation and the global acetylation status of the epigenome. For instance, dietary nutrients, particularly those involved in one-carbon metabolism (e.g., folate, vitamins B12 and B6, riboflavin, methionine, choline, and betaine), take part in the generation of S-adenosylmethionine (SAM), which represents the main methyl donor for DNA and histone methylation; α-ketoglutarate and ascorbic acid (vitamin C) act, respectively, as a co-substrate and cofactor for Ten-eleven Translocation (TET), which is responsible for DNA demethylation; and metabolites such as Acetyl-CoA directly impact histone acetylation, linking metabolism of the TCA cycle to epigenetic regulation. Further, bioactive compounds, such as polyphenols, modulate epigenetic patterns by affecting methylation processes or targeting epigenetic enzymes. Since diet and nutrition play a critical role in shaping epigenome functions and supporting human health, this review offers a comprehensive update on recent advancements in metabolism, epigenetics, and nutrition, providing insights into how nutrients contribute to metabolic balance, epigenome integrity maintenance and, consequently, disease prevention. 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

Background/Objectives: Clostridioides difficile is a “One Health” pathogen and a cause of antibiotics-associated diarrhea and pseudomembranous colitis. Mobile genetic elements (MGEs) have been documented in the genomes of clinical C. difficile strains; however, the presence of MGEs in environmental strains remains poorly characterized. Thus, the present study was conducted with the objective of identifying the prevalence of MGEs, including mobilizable transposons (MTns), conjugative transposons (CTns), plasmids, and insertion sequences, in whole genome sequences (WGSs) of environmental C. difficile isolates. Methods: The analysis of MGEs was conducted using 166 WGSs obtained from C. difficile strains isolated from various environmental sources contaminated with feces. The MGEs were identified using bioinformatic tools. Results: A total of 48.2% (80/166) of the studied genomes were identified to harbor nine transposons, including Tn916, Tn6194-like, Tn5397, Tn6215, Tn4001, Tn6073, Tn6110, Tn6107, or Tn5801-like. The majority of MTns and CTns could be found within C. difficile sequence types ST11, ST3, and ST35. The results demonstrated close genetic relatedness among the studied genomes, the array of antimicrobial resistance (AMR) genes, such as tetM, ermB, and aac(6′)-aph(2″), and the presence of CTns. Furthermore, the analysis revealed that 24.7% (41/166) of the genome sequences of isolates were associated with various predominant plasmid groups, including pCD6, pCD-ECE4-6, pCD-WTSI1-4, pCDBI1, and pCd1_3, which belonged to 16 different sequence types. Furthermore, several plasmids were identified as harboring the prophage phiCDHM19. Conclusions: The results of the current study suggest that the identified plasmids are abundant and may encode functions that are relevant to C. difficile physiology. The genomes of C. difficile strains examined contain closely related CTns, suggesting that horizontal transfer of AMR is important in this species or other bacterial species. Further research is required to ascertain the effect of these genetic elements and their transferability on the biology of C. difficile. Full article

Antibiotics are frequently used in the poultry industry, which has led to the emergence of bacterial strains that are resistant to antimicrobial treatments. The main objectives of this research were to conduct a multimodal risk assessment, to determine the extent of contamination of chicken meat with Escherichia coli, assess the prevalence of strains resistant to extended-spectrum cephalosporins (ESC), and characterise the genes associated with resistance and virulence. A standardised procedure involving enrichment in buffered peptone water and isolation of E. coli on MacConkey agar was carried out on 100 chicken carcasses. Subsequently, the sensitivity of the strains was tested against 21 antibiotic discs. Additionally, ESBL production was detected using a double synergy test. Specific PCRs were employed to identify resistance to critical antibiotics in human medicine (such as cephalosporins, carbapenems, fluoroquinolones, and colistin), as well as the presence of virulence genes. The contamination rate of chicken meat with E. coli was 82%. The prevalence of ESC-resistant isolates was 91.2%. Furthermore, 76.5% of the isolates exhibited ESBL production, with the different beta-lactamase genes (bla_CTXM, bla_TEM, and bla_SHV). The mcr-1 gene, associated with colistin resistance, was detected in four strains (5.9%). Some isolates also carried resistance genes such as sul1, sul2, sul3, tetA, tetB, qnrB, and qnrS. In addition, several virulence genes were detected. In our study, we were able to link the expression of AMR to the iron metabolic regulatory elements using a multimodal machine learning approach; this mechanism could be targeted to mitigate the bacteria virulence and resistance. The high prevalence of ESBL-producing and multi-resistant E. coli strains in poultry presents significant human health risks, with the focus on antibiotic-resistant uropathogenic strains since poultry meat could be an important source of uropathogenic strains, underscoring the danger of hard-to-treat urinary tract infections, stressing the need for controlled antibiotic use and thorough monitoring. Full article

Avian pathogenic Escherichia coli (APEC) causes avian colibacillosis, leading to significant economic losses and concerns for food safety in the poultry industry. This study focused on examining the virulence gene profile, antibiotic resistance prevalence, and resistance patterns of APEC isolates. A total of 250 bacterial strains were collected from birds affected by colibacillosis. Serogrouping revealed diverse serotypes, with O2 being the most common (16%), followed by O1, O8, and O76. All isolates tested positive for at minimum one virulence gene, with 7.2% carrying all five targeted genes, particularly in serogroups O1, O8, O45, and O88. The most detected gene was iss, present in 79.6% of isolates, followed by tsh, iucC, sitA, and papC. The antibiotic resistance analysis showed that all isolates exhibited multidrug resistance, although they remained susceptible to gentamicin, amikacin, ciprofloxacin, and chloramphenicol. Moreover, specific antibiotic resistance genes were known in the isolates, with tetA detected in 54.8%, tetB in 51.7%, sul1 in 50%, and aadA1 in 29.2%. These findings highlight the widespread antibiotic resistance in chicken carcasses, which poses a hazard to human health in terms of transfer of resistance to humans, reduced effectiveness of antibiotics and impaired ability to contain infectious diseases. Therefore, it is crucial to implement strict monitoring programs to regulate antibiotic usage in poultry production. Full article

Background/Objectives: Antimicrobial resistance (AMR) has become a serious public health threat worldwide. Among the various surveillance domains, hospital wastewater (HWW) has been overlooked, and it is the major reason for the threats posed by AMR. Therefore, the HWW domain is of paramount importance for tackling the AMR. In this regard, the present study investigated the occurrence of Gram-negative bacteria from HWW and evaluated the isolates’ multi-drug-resistant (MDR) pattern in the study environment. Methods: This descriptive study involves HWW samples (n = 24) consecutively collected across 6 months. The samples were cultured for bacteria, identified, and subjected to antimicrobial susceptibility testing via Kirby–Bauer. PCR confirmed the presence of drug-resistance genes in Gram-negative bacterial isolates. Results: High rates of Enterobacterales resistant to carbapenems and cephalosporins observed in isolates from final treated effluent. The molecular screening showed tetD, tetE, tetG, catA1, catA2, bla_NDM-1, quinolones, qnrA, qnrB, qnrS, and qepa. Conclusions: Overall, our results suggest that microbiological surveillance and identification of resistance genes of clinically important pathogens in HWW can be a general screening method for early determination of under-detected antimicrobial resistance profiles in hospitals and early warning of outbreaks and difficult-to-treat infections. Full article

Gram-negative enteric rods (GNERs) are transient members of the oral microbiota and are considered a superinfection in patients with periodontitis that poses local and systemic risks due to associations with infections and multidrug resistance, including extended-spectrum beta-lactamases. These pathogens often resist antibiotics such as amoxicillin, doxycycline, and ciprofloxacin, complicating dental treatments. Though their resistance patterns vary, links between specific resistance genes and phenotypic resistance remain unclear. Objectives: To determine the correlation between resistance genes (blaTEM, blaSHV, tetQ, tetM, qnrB, qnrS, and mph(A)) and phenotypic resistance in GNERs isolated from oral cavity samples. Methods: A total of 90 oral isolates of GNERs were isolated from patients in a dental clinic, and bacteria were identified by the BD BBL Crystal biochemical panel. The antibiotic susceptibility testing was conducted through broth microdilution following CLSI standards for drives such as amoxicillin, amoxicillin/clavulanic acid, doxycycline, ciprofloxacin, and azithromycin. Resistance genes, including blaTEM, blaSHV, tetQ, tetM, qnrS, qnrB, and mph(A), were detected using polymerase chain reaction and gel electrophoresis. The proportions of species, resistance genes, and minimum inhibitory concentration values were statistically analyzed. Conclusions: As expected, most enteric bacteria showed natural resistance to beta-lactams. Significant resistance to azithromycin was observed in some species. Genotypic and phenotypic profiles suggest the existence of alternative resistance mechanisms; therefore, other mechanisms associated with antibiotic resistance should be investigated. Full article

Colibacillosis in nursery pigs, caused by Escherichia coli (ETEC, EPEC, and STEC pathotypes), remains a major economic concern in the swine industry. This study evaluated the effects of in-feed or in-water chlortetracycline (CTC) administration on the fecal prevalence of virulence genes and pathotypes associated with colibacillosis. A total of 1296 weaned piglets (21 days old) were allocated to 48 pens (16 pens/treatment; 27 piglets/pen) and assigned randomly to no CTC, in-feed CTC, or in-water CTC groups. CTC was administered from days 0 to 14. Fecal samples from five piglets per pen on days 0, 14, and 28 were enriched, screened by 11-plex PCR, cultured for pathotypes, and tested for CTC susceptibility and tetracycline resistance genes. None of the 360 fecal samples or 3267 E. coli isolates were positive for bfpA or aggA. Prevalence of estB (96.9%) and astA (92.8%) was highest. ETEC was the dominant pathotype (41.2%), with astA (29%) and estB (21.9%) as predominant enterotoxin genes. CTC administration had no significant effect on fecal prevalence of virulence genes or pathotypes (p > 0.05). stx2 and STEC were detected only at day 28, all harboring stx2e. All pathotypes were CTC-resistant, with tetA as the predominant resistance gene. Full article