Antimicrobial resistance (AMR) is a global public health concern that has developed at an alarming rate due to rapid genetic mutation, horizontal gene transfer, and the misuse of antibiotics. The current traditional methods used for the detection of ARGs and the development of new antibiotics are not only inefficient but also lack accuracy. AI and ML promise to address AMR through advanced computation techniques such as supervised learning, deep learning, reinforcement learning, and natural language processing. AI-based models use data from genomic sequences, microbiome profiles, and clinical records to predict the emergence of outbreaks of AMR, identify resistance determinants, and aid in drug discovery.

The transformer-based AI models show superior performance in analyzing genomic data, predicting bacterial resistance profiles, and unveiling the key ARG relationships. Furthermore, AI facilitates novel antibiotics through the modeling of the structure–activity relationship, Raman spectroscopy, and mass spectrometry. AI-based clinical decision support systems further optimize antibiotic prescription by reducing the misuse and development of resistance. However, in AMR research, AI faces the challenge of ethical issues and data privacy; the bias found in algorithms poses another significant concern. Future work on AI methods, especially combining pre-trained models of genomics, will enable the improved accuracy of predictions and implementation of precision medicine approaches for infection management. Indeed, with growing advancements in AI technology, this integration will provide the foundation on which the strategy of bacterial resistance control will thrive, preserving the efficacy of available antibiotics.

Background

Antimicrobial-resistant (AMR) bacteria in chronic wound infections contribute to delayed healing, prolonged treatment, increased mortality, and rising healthcare costs. In resource-limited settings like Abakaliki, Southeastern Nigeria, improper antibiotic use worsens wound infection management. This study evaluates the antimicrobial resistance profiles of biofilm-forming E. coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae and identifies antimicrobial resistance genes in chronic wound infections.

Materials and Methods: From February to September 2024, pus samples from chronic wounds (≥12 weeks) were collected at Alex Ekwueme Federal University Teaching Hospital, Abakaliki. Bacteria were isolated using standard microbiological techniques, biofilm formation was assessed via Congo Red Agar (CRA), and antimicrobial resistance genes were detected through Polymerase Chain Reaction (PCR).

Results: Of 600 samples analyzed, 476 (79.3%) had bacterial growth: E. coli (31.8%), P. aeruginosa (26.2%), and K. pneumoniae (21.3%). Biofilm formation was observed in 41.8% of the isolates, predominantly P. aeruginosa (19.8%), followed by E. coli (12.2%) and K. pneumoniae (9.8%). All isolates were resistant to amoxicillin–clavulanic acid (100%). E. coli showed high resistance to ceftriaxone (86.3%) and ampicillin (87.6%), while P. aeruginosa resisted colistin (100%) and cefotaxime (84.0%). K. pneumoniae exhibited resistance to cefoxitin (67.8%). No resistance was found against imipenem, ofloxacin, and gentamicin. E. coli carried blaCTX-M-9 (63%), blaTEM (54.7%), and blaSHV (41.1%), all P. aeruginosa harbored blaCTX-M-9, blaSHV and blaTEM (100 %) while K. pneumoniae harbored blaCTX-M-9 (100%) and blaTEM (49.1%). The mcr-1 gene was present in all isolates.

Conclusion: The AMR burden in Abakaliki presents a significant challenge in treating chronic wound infections. Addressing this issue requires antimicrobial stewardship, infection control, routine surveillance, education, and research to improve regional wound infection management.

Listeria monocytogenes is a well-known foodborne pathogenic bacterium responsible for severe diseases in humans and animals. Additionally, the increase in antibiotic resistance rates of L. monocytogenes strains after exposure to preservatives, antibiotics, and stress conditions has become another major public health issue. This study focuses on the serological identification of 11 L. monocytogenes isolates from milk (n=1), whey (n=2), and ice creams (n=8) and the investigation of the pathogen's antibiotic resistance. The serological typing of the strains involved using multiplex PCR for each of the strains, with 63.6% of them belonging to serogroup IVb, 27.3% to serogroup IIb, and 9.1% to serogroup IIa. It was noteworthy that all the strains of serogroup IVb, which includes serotype 4b, most commonly responsible for listeriosis outbreaks in humans, were isolated from one of the three companies from which the samples were taken, and concerned the ice cream production line. Regarding the antibiotic resistance of the strains, antibiograms of the pathogen isolations were assessed against a group of seven selected antibiotics (erythromycin, tetracycline, penicillin, trimethoprim–sulfamethoxazole, ampicillin, ciprofloxacin, and meropenem) which showed that six strains exhibited resistance to at least one of the examined antibiotics, while no strain exhibited resistance to ampicillin and meropenem, with the former being the drug of choice for the treatment of listeriosis. Two strains of serogroups IIb and IVb exhibited resistance to four and three antibiotics, respectively. The findings of this study are useful and could be utilized for epidemiological research on L. monocytogenes in the food-processing environment, revealing potential contamination scenarios, resistance to sanitization, and the persistence of the pathogen in the food-processing environment, as well as acquired microbial resistance along the food production chain.

In addition to its presence in foods for human consumption, the foodborne pathogenic bacteria Salmonella spp. and Listeria monocytogenes can also be detected in animal feeding stuff.

The aim of this work was to phenotypically confirm the presence of the above microorganisms in feed samples, through biochemical and/or serological testing of the microbial isolates following the microbiological analysis for the detection of these pathogens. Thus, 15 strains of Salmonella spp. and 9 strains of L. monocytogenes were confirmed. Multiplex PCR was utilized to assign the isolated strains to the four most prevalent and most important public health-related Salmonella serotypes as well as to the four most frequently identified PCR-serogroups of L. monocytogenes.

Serotyping revealed the presence of Salmonella serotypes Thompson (60%), Typhimurium (6.7%) and Enteritidis (6.7%), whereas four strains were identified as Salmonella spp. (26.6%) but were not assigned to any of the detected serotypes. L. monocytogenes isolates were classified into the PCR-serogroups IIa (44.5%), IIb (11.1%), IIc (11.1%) and Ivb (33.3%).

Furthermore, the bacterial isolates were screened for AMR. Strains of Salmonella spp. were susceptible to five of the antibiotics tested (tetracycline, norfloxacin, ciprofloxacin, gentamicin, meropenem), while they showed resistance to ampicillin (2/15), cefotaxime (7/15) and ceftazidime (5/15), without any multi-drug resistance being recorded whatsoever. L. monocytogenes strains were only susceptible to erythromycin and ampicillin, while one strain of the pathogen was multi-drug resistant to the remaining five antibiotics (tetracycline, penicillin, sulfamethoxazole, ciprofloxacin, meropenem). Moreover, the recorded AMR of L. monocytogenes isolates was as follows: tetracycline (11.1%), penicillin (11.1%), sulfamethoxazole (55.5%), ciprofloxacin (22.2%) and meropenem (11.1%).

The results of the present study demonstrate the presence of important foodborne pathogenic bacteria with increased AMR to antibiotics caused at the primary production and at the farm level by the inappropriate use of pharmacological substances used to treat animal diseases, resulting in the potential detection of resistant bacterial strains of the pathogens to animal-originated food products.

The emergence of MDR Acinetobacter baumannii (Ab) represents a critical global health threat. We aimed to investigate the antibacterial properties of ENOblock, a compound identified through HTS of the EU-OPENSCREEN library, as potential treatment for MDR Ab.

In vitro assays were conducted to evaluate ENOblock’s antibacterial activity using microdilution, time-kill curves, and SYTOX Green membrane permeability tests. Bacterial cytological profiling (BCP) was employed to assess morphological changes after ENOblock treatment, shedding light on its mechanism of action (MoA). To identify the ENOblock molecular target, computational docking was performed to analyze its binding affinity to Ab enolase. Target validation was achieved using an enolase-deficient mutant (Δeno) by measuring changes in the MIC and bacterial growth. Synergistic effects of ENOblock combined with antibiotics were assessed in reference and colistin-resistant strains. Finally, ENOblock's efficacy was further evaluated in human epithelial and macrophage cells and in a Galleria mellonella model.

ENOblock demonstrated potent antibacterial activity with an MIC50 of 16 mg/L against clinical carbapenem- and colistin-resistant Ab strains, surpassing the MIC50 values of colistin and imipenem/meropenem. SYTOX Green assay revealed that ENOblock caused rapid and extensive membrane damage. BCP analysis revealed unique morphological changes not observed with clinically used antibiotics, suggesting a distinct ENOblock MoA. Computational docking indicated strong binding of ENOblock to enolase. The Δeno strain exhibited a four-fold increase in MIC and greater growth resistance to ENOblock, supporting enolase as its probable target. Importantly, ENOblock exhibited synergistic effects with colistin, enhancing its efficacy against both reference and colistin-resistant strains. Furthermore, ENOblock significantly reduced Ab adherence/invasion in epithelial and macrophage cells in vitro and improved survival rates in G. mellonella infected with Ab, demonstrating its therapeutic potential.

These findings highlight ENOblock as a promising candidate for antimicrobial development, with the potential to combat the critical threat posed by MDR Ab infections.

Bacteria of the genus Enterococcus are an integral part of the gastrointestinal (GI) tract of the animal microbiome and can be found in fermented meat and dairy products, mostly due to poor food handling and their ability to grow under extreme conditions. Bacterial infections are treated with antibiotics, and the rise of enterococci, which are resistant to a variety of antibiotics and have the ability to transfer genetic material, is a notable problem in modern medicine. The uptake of heavy metals in animal feed and resistance to them has been associated with resistance to glycopeptides and macrolides for many years. We wanted to determine the presence of genes encoding for acquired resistance to antibiotics and heavy metals like copper. To this end, enterococcal isolates from different ecosystems were used in this study. The enterococcal isolates were obtained from the faeces of wild boar (Sus scofa) (n = 30), spontaneously fermented sausages produced from the meat of wild boar and domestic pigs (Sus domesticus) (n = 10), and traditionally produced Istrian cheese (n = 5). Antibiotic-resistant genes for erythromycin and tetracycline and those for heavy metal copper were confirmed using multiplex PCR methods. The gene coding for erythromycin was found in 33.33% of faecal isolates, in 20% of cheese isolates, and in 10% of sausage isolates, and the gene coding for tetracycline was found in 80% of faecal isolates, in 20% of sausage isolates, and in none of the cheese isolates. A gene coding for copper was detected in 56.66% of the faecal isolates, then in 40% of the cheese isolates, and 30% of the sausage isolates. Our results suggest that genes encoding for acquired resistance to antibiotics and the heavy metal copper are present in the collected enterococcal isolates, and that even though isolates were collected from different ecosystems, they show similar trends for the presence of resistance genes.

Introduction. Haemorrhoidal disease is probably the most common pathological condition; it leads to high morbidity and seriously impacts the patients' lifestyle. Surgery for haemorrhoids is a naturally contaminated procedure that may require antibiotic prophylaxis to lower the risk of infection. However, little data are available emphasizing antibiotic use for this condition.

Methods. Eighty-two patients participated in the study following a selection and exclusion procedure. Among them, 51.2% were female, and 48.8% were male, with a mean age of 49.4 ± 12.8 years. The prevalence of preoperative risk factors for surgical site infection included 18.3% with a smoking history, 6.1% with diabetes mellitus type II, 2.43% receiving systemic steroids, and 3.7% with other local factors including IBD. All patients underwent multimodal treatment (conservative and surgery). All surgeries performed were hemorrhoidectomies, predominately for classic 3-column (left lateral, right anterior, and right posterior positions), prolapsed internal, and mixed internal and external hemorrhoid disease. Single administration or a short duration (one-day) of antibiotic prophylaxis was employed. Oral doxycycline 100 mg or Levofloxacin 500 mg were used.

Results. Antibiotic prophylaxis was used in an approximately same number of surgeries (46.3% vs 53.7%, closed and open procedures, respectively). Overall, there were only 2.43% of documented postoperative infections identified. All those patients who developed postoperative surgical site infections did not receive antibiotic prophylaxis. However, no perioperative risk factor was reliably associated with an increased risk of developing a surgical site infection after hemorrhoidectomies. In addition, there were no adverse antibiotic-related complications such antibiotic-associated diarrhoea or C. deficile colitis in patients receiving antibiotic prophylaxis.

Conclusions. The study results are confusing, probably because of low rate of the surgical site infection following hemorrhoidectomies. Conversely, no patients with antibiotic prophylaxis demonstrated postoperative surgical site infection, and from this point of view its use appears plausible. Further studies with significantly larger involvement of patients may clarify the issue.

Introduction: P. aeruginosa is an opportunistic pathogen that is a major cause of morbidity and mortality in patients with cystic fibrosis and immunocompromised individuals. The eradication of P. aeruginosa is becoming increasingly difficult due to its ability to resist antibiotics.

Aim The aim of this study was to study the susceptibility to antimicrobial drugs and the presence of carbapenemases in P. aeruginosa isolates from patients with cystic fibrosis.

Methods: Antibiotic susceptibility was determined by the broth microdilution method, whereas carbapenemases were determined by real-time PCR.

Results: A total of 95 P. aeruginosa strains isolated in 2022-2023 were studied. Resistance to meropenem and imipenem was 14% and 56%, respectively. Sensitivity with increased exposure was 19% and 44%, respectively. Between 22% and 27% of isolates were resistant to aminoglycosides. A total of 21% and 14% were resistant to ceftolozane/tazobactam and ceftazidime/avibactam, respectively. Resistance to aztreonam, ciprofloxacin, ceftazidime and piperacillin/tazobactam was 16%, 37%, 29% and 28%, respectively. It is worth noting that we identified 2% of strains resistant to colistin. When performing PCR for strains resistant to meropenem and/or imipenem, it was determined that six isolates had VIM carbapenemase (NDM, IMP carbapenemases were not detected). All VIM+ isolates retained susceptibility to colistin, four isolates were also susceptible to amikacin and five isolates showed susceptibility with increased exposure to aztreonam.

Conclusions: The resistance of P. aeruginosa to antibiotics of different classes ranged from 2 to 56%. Only six isolates were found to have metallo-β-lactamase VIM. Resistance to meropenem was demonstrated by 13 isolates and to imipenem by 52 isolates. Resistance to carbapenems in P. aeruginosa isolated from cystic fibrosis patients is probably associated with other properties of the bacterium.

The role of fish farming in the dissemination spread of antibiotic resistance genes (ARGs) has become an urgent environmental and public health concern. Fish farms, particularly those using intensive or semi-intensive aquaculture practices, serve as hotspots for the selection and proliferation of antibiotic-resistant bacteria (ARB). Labella et al. demonstrated a significantly higher incidence of multi-resistant bacterial strains in aquaculture centers (10%) compared to coastal areas (4%) in the Adriatic Sea​ [1]. Tetracycline resistance was particularly prominent, with up to 50% of bacterial isolates from specific zones, showing resistance., In contrast, resistance to flumequine remained low (0.3%), highlighting selective pressures imposed by antibiotic use patterns. Horizontal gene transfer, facilitated by mobile genetic elements, allows for the spread of ARGs among bacterial populations in fish farm effluents, sediments, and biofilms. Effluent water from aquaculture systems has been identified as a critical matrix contributing to ARG dissemination.

The frequent use of oxytetracycline, flumequine, and trimethoprim–sulfadiazine in fish farms exacerbates ARG selection. Studies have also shown cross-resistance, where exposure to older antibiotics like flumequine induces resistance to clinically relevant fluoroquinolones (e.g., ciprofloxacin), posing a direct threat to human health [2]. Furthermore, elevated water temperatures during summer were correlated with increased resistance incidence, suggesting environmental factors may amplify the selective pressures within aquaculture systems [2] .

This review highlights the role of aquaculture practices in driving antibiotic resistance, with fish farms acting as reservoirs for ARBs and ARGs.

[1] Labella, A., et al (2013). High incidence of antibiotic multi-resistant bacteria in coastal areas dedicated to fish farming.. Marine pollution bulletin, 70 1-2, 197-203 . https://doi.org/10.1016/j.marpolbul.2013.02.037.

[2] Jo, H., et al (2021). Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea.. Environmental pollution, 276, 116764 . https://doi.org/10.1016/j.envpol.2021.116764.

Among the current antibiotics in clinical practice, fluoroquinolone ciprofloxacin (CPX) stands out for its broad-spectrum antimicrobial activity. However, the emergence of multidrug-resistance phenomena significantly undermines its therapeutic efficacy, with several bacterial strains, including Pseudomonas aeruginosa, acquiring a resistant phenotype, making them no longer susceptible to CPX. Being a leading opportunistic bacterium, this pathogen is reported to cause severe, often life-threatening infections, especially in hospitalized immunocompromised patients. Pieces of evidence have highlighted the huge potential of targeting P. aeruginosa (Ps) carbonic anhydrase (CA, EC: 4.2.1.1) metalloenzymes, which play a critical role in the bacterium virulence and have recently emerged as attractive innovative pharmacological targets for the development of novel antibacterial agents.
This work provides a response to this challenge, based on the design and development of an extensive library of CPX hybrid derivatives incorporating recognized CA-inhibiting chemotypes, i.e., benzenesulfonamides and coumarins. Enzymatic and biological assays revealed the potent nanomolar inhibition of PsCA activity, along with remarkable antibacterial effects, including bactericidal and anti-biofilm properties for some compounds. Suboptimal PK properties for two representative compounds emerged from a preliminary study in vitro. Moreover, no toxicity was observed in the 3R-compliant Galleria mellonella larvae model, indicating a safety profile. In silico docking simulations and crystallization studies were helpful to gain valuable insights into the binding modes of such compounds to CA enzymes, guiding further optimization efforts.
Altogether, our findings underscore the potential of CPX CA-inhibiting hybrids as a valuable strategy to fight P. aeruginosa infections, particularly in the context of rising antibiotic resistance.

Reference
Marinacci B, D'Agostino I, Angeli A, Carradori S, Melfi F, Grande R, Corsiani M, Ferraroni M, Agamennone M, Tondo AR, Zara S, Puca V, Pellegrini B, Vagaggini C, Dreassi E, Patrauchan MA, Capasso C, Nicolotti O, Carta F, Supuran CT. J Med Chem. 2024 Nov 14;67(21):19077-19102. doi: 10.1021/acs.jmedchem.4c01555.