Resistance Profiles Research Articles

Plastic Litter: A Hidden Reservoir for Antibiotic-Resistant Pathogens in Coastal Ecosystems

Plastic litter carrying pathogenic bacteria pose serious threats to the health of human and aquatic life. We enumerated the abundance of Escherichia coli and Vibrio species in different types of plastic litter (biomedical, food packages, sanitary, fishing material and miscellaneous) collected from the beaches of Agatti and Kavaratti in the Lakshadweep islands of India using quantitative real-time PCR. Further the antimicrobial resistance profile of E. coli and Vibrio species isolated from these samples were also tested. A very high number (more than three thousand gene copies per gram of plastic litter) of Escherichia coli, and Vibrio spp. were detected in the plastic litter. Vibrio spp. in the plastic litter were identified as V. harveyi, V. neocaledonicus, V. japonicus, V. parahaemolyticus and V. campbelli. More than sixty percentage of E. coli and Vibrio spp. isolated from all samples except the E. coli isolated from fishing gear of Kavaratti had multiple antibiotic resistance index of more than 0.25. Most of the bacteria were resistant towards ampicillin, erythromycin, and moxifloxacin, while least resistance was observed against gatifloxacin, gentamicin, imipenem, meropenem, norfloxacin and trimethoprim. These results indicate that plastic litter may act as a conduit for the attachment and transport of multiple antibiotic resistant pathogens, causing severe setbacks to the global efforts on attaining sustainable development goals 3 (health), 6 (clean water) and 14 (life under water). Therefore, strict implementation of plastic waste management rules, awareness campaigns for cleaning beaches and citizen science initiatives to monitor and remove plastics are proposed for protecting the beaches from the deleterious effects of mismanaged plastics.

Impact of inappropriate empirical antibiotic therapy on in-hospital mortality: a retrospective multicentre cohort study of patients with bloodstream infections in Chile, 2018–2022

IntroductionEmpirical antibiotic therapy is essential for treating bloodstream infections (BSI), yet there is limited evidence from resource-limited settings. We quantified the association of inappropriate empirical antibiotic therapy (IEAT) with in-hospital...

Detection of antimicrobial-induced survival/dead bacteria via mEos4b photoconversion: a preliminary study

The escalating prevalence of hospital-acquired infections poses a critical challenge for healthcare systems worldwide. Effective management requires rapid identification of pathogens and their antibiotic resistance profiles. In this study, we utilized the photoconvertible mEos4b protein, which transitions from green to red fluorescence upon blue light exposure, to distinguish live from dead bacteria. The mEos4b gene was cloned into a prokaryotic vector and expressed inEscherichia coliBL21. The Minimum Inhibitory Concentration (MIC) of the transgenic bacteria was determined for five antibiotics, followed by a post-antibiotic effect assessment over a two-hour exposure period. The optimal photoconversion time for mEos4b was established as 90 s, and confocal microscopy was used to visualize live (green) and dead (red) cells post-exposure. The mEos4b-TR system proved highly specific, accurately distinguishing live and dead bacteria without producing false positives, even in control groups, which is a common issue in commercial live-dead kits. By relying on cellular metabolic activity rather than dyes, this system minimizes nonspecific interactions and contamination, making it more reliable than traditional methods prone to false readings. These results highlight the potential of the mEos4b-TR system as a superior alternative for rapid, precise bacterial viability assessments, particularly in determining antibiotic susceptibility. This preliminary study demonstrates the system's differentiation of viable and non-viable cells, suggesting its potential application in future studies involving novel antibacterial agents to refine antibiotic sensitivity testing.

Unveiling the Dynamics of Antimicrobial Resistance: A Year-Long Surveillance (2023) at the Largest Infectious Disease Profile Hospital in Western Romania

Background/Objectives: Antimicrobial resistance (AMR) is a critical global health threat, leading to increased morbidity, mortality, and healthcare costs. This study aimed to identify the most common bacterial pathogens and their resistance profiles from 2179 positive clinical cultures from inpatients at “Victor Babes” Hospital of Infectious Disease and Pneumoftiziology Timisoara in 2023. Methods: Samples were collected from sputum, bronchial aspiration, hemoculture, urine, wound secretions, catheter samples, and other clinical specimens. Results: Key pathogens identified included Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii, with notable resistance patterns, observed K. pneumoniae exhibited high resistance rates, notably 41.41% in Quarter 1, while E. coli showed 35.93% resistance in the same period. S. aureus, particularly MRSA, remained a persistent challenge, with 169 cases recorded over the year. A. baumannii and P. aeruginosa displayed alarming levels of multi-drug resistance, especially in Quarter 3 (88.24% and 22.02%, respectively). Although there was a general decline in resistance rates by Quarter 4, critical pathogens such as S. aureus and K. pneumoniae continued to exhibit significant resistance (81.25% and 21.74%, respectively). Conclusions: The study’s findings align with the broader antimicrobial resistance trends observed in Romania, where high resistance rates in K. pneumoniae, E. coli, S. aureus (MRSA), Acinetobacter, and Pseudomonas species have been widely reported, reflecting the country’s ongoing struggle with multi-drug-resistant infections. Despite some reductions in resistance rates across quarters, the persistent presence of these resistant strains underscores the critical need for strengthened antimicrobial stewardship, infection control measures, and continuous surveillance to combat the growing threat of AMR in Romania and similar healthcare settings.

Diversity and Resistance Profiles of ESBL-Producing Gram-Negative Bacteria from Dairy Farms in Southern Türkiye

Background/Objectives: The increasing occurrence of extended-spectrum β-lactamase (ESBL)–producing Enterobacterales, most commonly Escherichia coli, has become a serious problem. The aim of this study was to determine the presence of ESBL-producing Gram-negative bacteria in dairy cattle, goat and sheep farms located in southern Türkiye. Methods: Samples (409 quarter milk samples and 110 fresh faecal samples from cattle, 75 bulk tank milk samples and 225 rectal swab samples from goats and sheep) were subjected to selective isolation on MacConkey agar with ceftazidime (2 µg/mL). Isolates were identified by MALDI-ToF MS. The antimicrobial susceptibility profile of the isolates was determined by the broth microdilution method. To obtain a deeper insight into the genetic diversity of isolates substantially contributing to an efficient spread of their ESBL-determinants (23-MO00001: an E. coli from mastitis and 23-MO00002 Citrobacter freundii), the transmission potential and the genetic background of the plasmid carrying the blaCTX-M determinant was studied with whole genome analysis using Illumina sequencing. Results: Of the samples tested, 47 from the bovine faecal samples, 1 from the subclinical mastitis milk sample, 9 from the goat/sheep rectal swab samples and 5 from the goat/sheep bulk tank milk samples had ceftazidime-resistant Gram-negative strains with the ESBL phenotype. Of the 33 ESBL-producing E. coli isolates, 66.6% were resistant to tetracycline, 57.6% to sulfamethoxazole, 48.9% to nalidixic acid, 42.4% to ciprofloxacin and 33.3% to trimethoprim. Pulsed field gel electrophoresis (PFGE) results showed that the majority of E. coli isolates (16/33) and all Enterobacter spp. isolates (n = 5) were not clonally related (80% similarity cut value). The sequenced strains were observed to efficiently transfer their ceftazidime resistance to the recipient strain E. coli J53 at 37 °C (transfer rates: 101–102 transconjugants per donor cell). S1-PFGE showed that the transconjugants J53(p23MO01-T1) and J53(p23MO02-T1) had acquired plasmids of about 82 kb and 55 kb plasmids, respectively. According to WGS results, the E. coli isolate was assigned to ST162, while the C. freundii isolate was assigned to ST95. Conclusions: This study demonstrates that dairy animals are reservoirs of ESBL-producing bacteria.

PREVALÊNCIA E PERFIL DE RESISTÊNCIA BACTERIANA EM RECÉM-NASCIDOS NA UTI NEONATAL: UMA REVISÃO DE LITERATURA

Healthcare-associated infections (HAIs) are a significant challenge in neonatal intensive care units (NICUs), primarily affecting newborns due to their immature immunity. The aim of this study was to analyze the prevalence and bacterial resistance profile in newborns admitted to the NICU, based on a literature review. The research followed an exploratory-descriptive design with a qualitative approach, and data were obtained from articles published between 2019 and 2024 in the Google Scholar, SciELO, and PubMed databases. The search was structured with keywords such as "prevalence of bacterial resistance," "neonatal ICU," "hospital infection," and "bacterial resistance profile," covering articles available in both Portuguese and English. The results showed that the most prevalent bacteria in the NICU include Pantoea agglomerans, Acinetobacter baumannii, Pseudomonas aeruginosa, Candida parapsilosis, MR (methicillin-resistant) bacteria, Escherichia coli, Staphylococcus sp., Klebsiella sp., and coagulase-negative Staphylococcus. The studies highlighted the complexity of bacterial infections, the diversity of pathogens, and the need for early diagnosis to ensure effective treatment. Antimicrobial resistance, especially among Gram-negative bacteria and coagulase-negative staphylococci, remains an ongoing challenge, requiring stringent prevention and monitoring strategies. Therefore, monitoring the microbiological profile in neonatal ICUs is essential to improve prevention and treatment strategies, reducing infection rates and antimicrobial resistance. The evidence underscores the importance of early interventions and targeted therapies to control these infections in vulnerable neonates.

Whole genome sequencing-based characterization and determination of quinolone resistance among methicillin-resistant and methicillin-susceptible S. Aureus isolates from patients attending regional referral hospitals in Tanzania

BackgroundThe emergence of multidrug-resistant termed Methicillin-resistant Staphylococcus aureus (MRSA) strain, driven by the acquisition of resistance gene mecA imposes a substantial challenge in the treatment and control of their related infections. Although quinolones have historically been effective against both MRSA and methicillin-susceptible S. aureus (MSSA) strains, the rising resistance to quinolones among S. aureus isolates, particularly in MRSA, has severely curtailed their potency and further narrowed down the therapeutic options. This study aimed to determine the burden of MRSA among isolates, as well as their resistance profile, genotypic characterization, and molecular relatedness through the construction of a phylogenetic tree.Materials and methodsArchived clinical S. aureus isolates from a descriptive, cross-sectional study involving six regional referral hospitals in Dodoma, Songea, Kigoma, Kitete, and Morogoro in the mainland Tanzania and Mnazi Mmoja in Zanzibar were analyzed. Bacterial identification was performed using both classical microbiology and whole genome sequencing on Illumina Nextseq 550 Sequencer. Species identification was done using KmerFinder 3.2, Multilocus Sequence Typing using MLST 2.0, SCCmec typing using SCCmecFinder 1.2, resistance genes using ResFinder 4.1, and phylogenetic relatedness using CSI Phylogeny 1.4.ResultsOut of the 140 isolates analyzed, 69 (49.3%) were identified as MRSA, with 57 (82.6%) exhibiting quinolone resistance. Conversely, 71 isolates were identified as MSSA, and none of them exhibited resistance to quinolones. Spa-typing revealed six spa types, with t355, t1476, and t498 being the most common. Moreover, all (69) MRSA were found to carry SCCmec type IV. The isolates exhibited 14 different sequence types (STs). Notably, ST152 was prevalent among MSSA (50 isolates, 70%), while ST8 was the predominant sequence type among MRSA (58 isolates, 84%). The antimicrobial resistance profile revealed at least three horizontally acquired resistance genes, with blaZ, dfrG, tet(K), and aac (6’)-aph (2’’) genes being highly prevalent.ConclusionThere is a high genetic diversity among the S. aureus isolates existing in Tanzania regional hospitals, with a concerning burden of quinolone resistance among MRSA isolates. The diversity in resistance genes among MRSA lineages emphasizes the necessity for the development of sustainable antimicrobial stewardship and surveillance to support evidence-based guidelines for managing and controlling MRSA infections in both community and hospital settings.

Year-Long Prevalence and Antibiotic Resistance Profiles of Salmonella enterica Serogroups Isolated from a Wisconsin Dairy Farm

Year-Long Prevalence and Antibiotic Resistance Profiles of Salmonella enterica Serogroups Isolated from a Wisconsin Dairy Farm

Prevalence, virulence potential, antibiotic resistance profile, heavy metal resistance genes of Listeria innocua: A first study in consumed foods for assessment of human health risk in Northern Turkey.

Listeria (L.) innocua is typically considered a non-pathogenic bacterium that can sometimes act as an opportunistic pathogen in severely immunocompromised patients. However, it plays an important role in food safety because it acts as an indicator organism for potential contamination and the effectiveness of sanitation methods. The aim of this study was to determine the prevalence, virulence genes, antibiotic resistance profiles, heavy metal and disinfectant resistance genes of L. innocua isolates from animal-derived foods. In this study, we isolated and characterized 39 L. innocua strains recovered from commonly 400 consumed beef meat, fresh fish meat, raw cow milk, and traditional cheese samples collected in Giresun, Turkey. The occurrence of virulence-associated genes was detected, such as plcA (97.4%), iap (35.8%), and hlyA (15.3%). A high incidence of resistance was recorded for fusidic acid (100%), followed by oxacillin (97.4%), clindamycin (82%), trimethoprim/sulfamethoxazole (69.2%), benzylpenicillin (41%), nitrofurantoin (35.8%), and fosfomycin (35.8%). Overall, 100% (39/39) of the isolates were resistant to at least one antibiotic, while 92.3% (36/39) of the isolate strains were multidrug resistant in the antimicrobial susceptibility tested. Among the L. innocua isolates (n = 39), 51.2%, 38.4%, 20.5%, 7.6%, 5.1%, 2.5%, and 2.5% were positive for qacH, cadA1, qacE, qacEΔ1-sul, qacJ, qacF, and qacG heavy metal and disinfectant resistance genes, respectively. The results highlight the need for more comprehensive studies to understand the monitoring and surveillance of L. innocua and their potential hazards to both humans and animals.

Prevalence, Antimicrobial Susceptibility, and Resistance Genes of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Broilers Sold in Open Markets of Dakar, Senegal.

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) poses a significant public health concern due to its widespread prevalence and resistance to multiple antibiotics. This study aimed to assess the prevalence, resistance profile, and carriage of ESBL-encoding genes in ESBL-Ec isolates from broilers in two markets of Dakar, Senegal. Sampling over a one-year period revealed that 61.7% of broilers carried ESBL-Ec in their cecum. Antibiotic susceptibility testing of 186 ESBL-Ec isolates showed high resistance to β-lactam antibiotics, including ampicillin, ticarcillin, and third-generation cephalosporins. Notably, all isolates were susceptible to imipenem. Multidrug resistance was frequent, with 91.4% of the isolates displaying this phenotype. Comparison between the two markets revealed variations in resistance to quinolones. PCR analysis detected blaCTX-M genes in all isolates, with blaCTX-M-1 being the most prevalent subgroup. Additionally, blaTEM and blaOXA genes were found in 26.3% and 2.7% of isolates, respectively, while no blaSHV genes were detected. Combinations of ESBL genes were common, with blaCTX-M15-blaTEM being the most frequent. These findings highlight the widespread prevalence of ESBL-Ec in broilers from Dakar markets, indicating a potential risk of transmission to humans through the food chain. Effective surveillance and intervention strategies are crucial to mitigate the spread of antimicrobial resistance in humans and animals.

Outbreak of Esophagitis and Ingluvitis Caused by Salmonella Typhimurium in Passeriform Birds of the Genus Sporophila Seized from Wildlife Trafficking.

The occurrence of esophagitis and ingluvitis caused by Salmonella Typhimurium in passerines seized from illegal wildlife trafficking is described. This illegal activity causes stress and leads to lowered immunity in the birds. Additionally, inadequate hygiene conditions predispose the birds to diseases such as salmonellosis. Few studies report the occurrence of Salmonella-induced lesions in the esophagus and crop of passerines; therefore, this study aimed to describe the disease in birds of the genus Sporophila, as well as to investigate the presence of the bacterium in the environment and determine the antimicrobial resistance profile of the isolated bacteria. Three birds of the genus Sporophila were necropsied. In the esophagus and crop, yellowish plaques corresponding to necrosis with bacterial aggregates were observed. Salmonella spp. was isolated from these lesions, with genus confirmation via MALDI-TOF mass spectrometry. Environmental samples were collected from the enclosures and cages where the animals were quarantined, and the same bacterium was isolated. In two birds, the serotype S. Typhimurium was identified. Antibiograms performed on the strains from the birds and the environment revealed resistance to antibiotics in the classes of penicillins, sulfonamides, aminoglycosides, monobactams, tetracyclines, and first and third-generation cephalosporins. To the authors' knowledge, this is the first report of this agent causing death in Sporophila due to esophagitis and ingluvitis. It is also the first report of salmonellosis in three species of passerines in Brazil. The study underscores the importance of understanding the pathogens circulating in wild animals, especially within the context of One Health.

Pooled prevalence of Escherichia coli phenotypic and genotypic antimicrobial resistance profiles in poultry: systematic review and meta-analysis

Pooled prevalence of Escherichia coli phenotypic and genotypic antimicrobial resistance profiles in poultry: systematic review and meta-analysis

Microalgae-Assisted Treatment of Wastewater Originating from Varied Sources, Particularly in the Context of Heavy Metals and Antibiotic-Resistant Bacteria

The increasing prevalence of heavy metals and antibiotic-resistant bacteria in wastewater (WW) raises serious environmental and public health concerns. This study investigates the efficiency of the microalgal strain Chlorella vulgaris EV-465 in treating wastewater and evaluates the antibiotic resistance profile of bacterial strains obtained from WW samples. Chlorella vulgaris EV-465 was used to treat four types of wastewater—domestic, municipal, hospital, and industrial wastewater—through 21 days of incubation. The findings demonstrated pH stabilization and significant decreases in nutrients (total nitrogen—TN, total phosphorus—TP), biological oxygen demand (BOD), chemical oxygen demand (COD), heavy metal (HM) concentrations, and bacterial count. Copper (Cu) showed the highest reduction, decreasing by 80% in industrial wastewater within 14 days, while lead (Pb) proved more resistant to removal, with only a 50% decrease by day 21. Additionally, the algae decreased bacterial counts, lowering colony-forming units (Log CFU/mL) from 9.04 to 4.65 in municipal wastewater over the 21-day period. Antibiotic susceptibility tests for isolated bacterial strains revealed high levels of resistance, with seven out of nine bacterial strains exhibiting multidrug resistance. Notably, Enterococcus faecium (PBI08), Acinetobacter baumannii (YBH19), and Pseudomonas aeruginosa (NBH16) displayed resistance to all nine antibiotics tested. Among the tested antibiotics, Ciprofloxacin showed the highest efficacy, with 66% susceptibility of tested bacterial strains. Cluster and phylogenetic analyses showed that the majority of the isolated bacterial strains belonged to the genera Pseudomonas and Escherichia, highlighting their genetic diversity and varied resistance mechanisms.

Antibacterial Mechanisms and Clinical Impact of Sitafloxacin.

Sitafloxacin is a 4th generation fluoroquinolone antibiotic with broad activity against a wide range of Gram-negative and Gram-positive bacteria. It is approved in Japan and used to treat pneumonia and urinary tract infections (UTIs) as well as other upper and lower respiratory infections, genitourinary infections, oral infections and otitis media. Compared to other fluoroquinolones, sitafloxacin displays a low minimal inhibitory concentration (MIC) for many bacterial species but also activity against anaerobes, intracellular bacteria, and persisters. Furthermore, it has also shown strong activity against biofilms of P. aeruginosa and S. aureus in vitro, which was recently validated in vivo with murine models of S. aureus implant-associated bone infection. Although limited in scale at present, the published literature supports the further evaluation of sitafloxacin in implant-related infections and other biofilm-related infections. The aim of this review is to summarize the chemical-positioning-based mechanisms, activity, resistance profile, and future clinical potential of sitafloxacin.

Elucidating the augmented resistance profile of Scedosporium/Lomentospora species to azoles in a cystic fibrosis mimic environment.

Scedosporium/Lomentospora species are ranked as the second most frequently isolated filamentous fungi from cystic fibrosis (CF) patients. Previously, we demonstrated that the minimum inhibitory concentration (MIC) for voriconazole and posaconazole increased when performed on a mucin-containing synthetic CF sputum medium (SCFM) compared to the standard medium, RPMI-1640. In this study, we have expanded the MIC comparison to four additional azoles and investigated characteristics linked to azole resistance in Scedosporium apiospermum, Scedosporium minutisporum, Scedosporium aurantiacum and Lomentospora prolificans. MIC was assayed by CLSI protocol, efflux pump activity was assessed by rhodamine 6G and sterols were analysed by gas chromatography-mass spectrometry (GC-MS). Overall, MICs for fluconazole, itraconazole, voriconazole, posaconazole, miconazole and ketoconazole increased by least 2-fold when susceptibility tests were performed using SCFM compared to RPMI. The activity of efflux pumps was similar in both media; however, in RPMI, but not in SCFM, the activity was induced by voriconazole and fluconazole. Additionally, MICs for those antifungals decreased more noticeably in SCFM than in RPMI in the presence of the efflux pump inhibitor PaβN. The SCFM-grown cells presented fewer sterols in their composition, and consequently higher membrane fluidity, than RPMI-grown cells. GC-MS analysis demonstrated a remodulation in the sterol profile in SCFM- compared to RPMI-grown cells. Accordingly, when the MIC assay was performed in the presence of the membrane stressor NaCl (3%), the susceptibility to voriconazole and fluconazole increased more in SCFM- than RPMI-grown cells. Scedosporium/Lomentospora species undergo cellular adaptations in SCFM that favours their growth in face of the challenges imposed by azole antifungals.

Antimicrobial Resistance Profile of Zoonotic Clinically Relevant WHO Priority Pathogens.

The World Health Organization announced critically important bacterial and fungal pathogens displaying alarming levels of antimicrobial resistance, which currently represent difficult-to-treat cases of morbidity. Within this grouping, the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are causative of significant morbidity and mortality. Studies described herein demonstrate the presence of critically important fungal and ESKAPE bacterial species in companion animals which are zoonotic in nature. The relationship between the environment, animals, and human infectious disease has long been recognized as part of One Health. This research investigates the resistance patterns of isolated zoonotic pathogens using recognized in vitro methodologies, namely disk diffusion, minimum inhibitory concentration testing, and genetic screening. Antibiotic susceptibility testing and gene analysis demonstrated an association between multi-drug resistance and extended beta spectrum lactamase production in critical-priority bacteria. Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa exhibit great levels of multi-drug resistance. Fungal isolates demonstrated high levels of resistance, with Amphotericin B proving the most effective antifungal agent investigated. The level of antimicrobial resistance present in clinically relevant bacterial and fungal pathogens isolated from animal cases of morbidity in this study is alarming. In conclusion, this study shows that animals can act as a reservoir facilitating the transmission of antibiotic-resistant pathogens and genes zoonotically.

Antimicrobial Resistance in Lactococcus spp. Isolated from Native Brazilian Fish Species: A Growing Challenge for Aquaculture.

Lactococcus spp. has emerged as a pathogen that is affecting global aquaculture, with L. garvieae, L. petauri, and L. formosensis causing piscine lactococcosis. While antimicrobials are commonly used to treat diseases in aquaculture, reports of antimicrobial resistance in fish isolates are increasing. However, little is known about the susceptibility patterns of Lactococcus spp. strains isolated from native fish species in Brazil. This study aimed to assess the antimicrobial susceptibility of these strains and establish a provisional epidemiological cutoff value for L. garvieae using the normalized resistance interpretation approach. A total of 47 isolates were tested: 17 L. garvieae, 24 L. petauri, and 6 L. formosensis. The isolates were classified as wild-type (WT) or non-wild-type (NWT) based on inhibition zone diameters. Isolates classified as NWT for three or more antimicrobial classes were considered multidrug-resistant, and the multiple antibiotic resistance (MAR) index was calculated. The results revealed heterogeneity in antimicrobial resistance profiles, with higher resistance to trimethoprim/sulfamethoxazole and norfloxacin. Resistance to other antimicrobials, including florfenicol and oxytetracycline (approved for use in Brazil), varied according to the bacterial species. Lactococcus petauri (87.5%) and L. formosensis (66.7%) showed the highest multidrug resistance, compared to L. garvieae (11.7%), along with higher MAR index values. These findings suggest that multidrug-resistant strains could pose future challenges in the production of native species, underscoring the need for ongoing monitoring of antimicrobial resistance and responsible use of antimicrobials in aquaculture.

Decoding Acute Myeloid Leukemia: A Clinician's Guide to Functional Profiling.

Acute myeloid leukemia (AML) is a complex clonal disorder characterized by clinical, genetic, metabolomic, and epigenetic heterogeneity resulting in the uncontrolled proliferation of aberrant blood-forming precursor cells. Despite advancements in the understanding of the genetic, metabolic, and epigenetic landscape of AML, it remains a significant therapeutic challenge. Functional profiling techniques, such as BH3 profiling (BP), gene expression profiling (GEP), proteomics, metabolomics, drug sensitivity/resistance testing (DSRT), CRISPR/Cas9, and RNAi screens offer valuable insights into the functional behavior of leukemia cells. BP evaluates the mitochondrial response to pro-apoptotic BH3 peptides, determining a cell's apoptotic threshold and its reliance on specific anti-apoptotic proteins. This knowledge can pinpoint vulnerabilities in the mitochondria-mediated apoptotic pathway in leukemia cells, potentially informing treatment strategies and predicting therapeutic responses. GEP, particularly RNA sequencing, evaluates the transcriptomic landscape and identifies gene expression alterations specific to AML subtypes. Proteomics and metabolomics, utilizing mass spectrometry and nuclear magnetic resonance (NMR), provide a detailed view of the active proteins and metabolic pathways in leukemia cells. DSRT involves exposing leukemia cells to a panel of chemotherapeutic and targeted agents to assess their sensitivity or resistance profiles and potentially guide personalized treatment strategies. CRISPR/Cas9 and RNAi screens enable systematic disruption of genes to ascertain their roles in leukemia cell survival and proliferation. These techniques facilitate precise disease subtyping, uncover novel biomarkers and therapeutic targets, and provide a deeper understanding of drug-resistance mechanisms. Recent studies utilizing functional profiling have identified specific mutations and gene signatures associated with aggressive AML subtypes, aberrant signaling pathways, and potential opportunities for drug repurposing. The integration of multi-omics approaches, advances in single-cell sequencing, and artificial intelligence is expected to refine the precision of functional profiling and ultimately improve patient outcomes in AML. This review highlights the diverse landscape of functional profiling methods and emphasizes their respective advantages and limitations. It highlights select successes in how these methods have further advanced our understanding of AML biology, identifies druggable targets that have improved outcomes, delineates challenges associated with these techniques, and provides a prospective view of the future where these techniques are likely to be increasingly incorporated into the routine care of patients with AML.

Gene profile of virulence, antimicrobial resistance and action of enterocins in Campylobacter species isolated from broiler carcasses.

Campylobacteriosis is among the most reported zoonoses in the world, caused by species of Campylobacter, this disease is characterized by gastroenteritis in humans. The main species involved is Campylobacter jejuni, followed by Campylobacter coli. Contaminated chicken meat is often identified as an important source of infection related to human cases and Brazil is the largest exporter of chicken meat in the world, which makes the characterization of brazilian isolates crucial for the establishment of control measures. The objective was to evaluate the contamination of chilled and frozen carcasses sold in the Northeast of Brazil, by Campylobacter species, identify virulence genes, evaluate bacterial resistance to antibiotics and verify the antimicrobial action of the Crude Extract Containing Enterocins (CECE) produced by a probiotic strain of Enterococcus faecium. In this study, 12 chilled carcasses and 12 frozen carcasses were collected, sold retail in supermarkets. The following regions of the carcass were sampled: breast skin, wing skin, belly skin, neck skin, gizzard and liver. Samples of chicken carcasses were analyzed following ISO 10272-2 guidelines for the isolation of Campylobacter spp. The isolates were tested by PCR to identify genus, species C. jejuni, C. coli and C. lari and genes cdtA, cdtB, cdtC, sodB, dnaJ, cmeA, cmeB, cmeC. The assessment of susceptibility to antibiotics was carried out using the standard disk diffusion method and the antimicrobial activity of CECE was determined using the Minimum Inhibitory Concentration (MIC), the methodologies followed the recommendations and cutoff points according to EUCAST and CLSI. A total of 376 isolates of Campylobacter spp. were obtained, among these, 26 (7.0%) were positive for C. jejuni and no isolates were detected for C. coli and C. lari. The highest frequency of C. jejuni was obtained in chilled carcasses with 23 isolates (88.5%, p < 0.0001), in frozen carcasses three isolates were obtained (11.5%). The most frequency site of C. jejuni was the chest skin (7/27.0%), followed by skin of the wing (6/23.0%), skin of the cloaca (5/19.0%), gizzard (4/15.0%), skin of the neck (2/8.0%) and liver (2/8.0%), no significant differences were found between the sites sampled. The gene frequency was determined in: cdtA (3/11.5%), cdtB (3/11.5%), cdtC (5/19.0%), sodB (9/34.5%), dnaJ (3/11.5%), cmeA (4/15.0%), cmeB (4/15.0%) and cmeC (4/15.0%). The three efflux pump genes were amplified in four isolates (15.3%) and all tested genes were amplified in three isolates (11.5%). All C. jejuni isolates (26/100.0%) were found to be multiresistant to three or more classes of antimicrobials. The index of multiple resistance to antimicrobial drugs (IRMA) ranged from 0.4 to 1.0 among isolates of C. jejuni. The antimicrobial activity of CECE was able to inhibit at least 98.5% of the growth of all C. jejuni isolates. Therefore, chilled chicken carcasses present a greater risk of contamination than frozen carcasses, for this reason it is necessary to adopt practices that avoid cross-contamination during the preparation of chicken meat, in order to prevent campylobacteriosis. Furthermore, the presence of multiresistant and potentially virulent isolates highlights the need for further investigations to better understand the use of enterocins as alternative methods in the control of Campylobacter.

An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networks.

Timely and effective use of antimicrobial drugs can improve patient outcomes, as well as help safeguard against resistance development. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used in clinical diagnostics for rapid species identification. Mining additional data from said spectra in the form of antimicrobial resistance (AMR) profiles is, therefore, highly promising. Such AMR profiles could serve as a drop-in solution for drastically improving treatment efficiency, effectiveness, and costs. This study endeavors to develop the first machine learning models capable of predicting AMR profiles for the whole repertoire of species and drugs encountered in clinical microbiology. The resulting models can be interpreted as drug recommender systems for infectious diseases. We find that our dual-branch method delivers considerably higher performance compared to previous approaches. In addition, experiments show that the models can be efficiently fine-tuned to data from other clinical laboratories. MALDI-TOF-based AMR recommender systems can, hence, greatly extend the value of MALDI-TOF MS for clinical diagnostics. All code supporting this study is distributed on PyPI and is packaged at https://github.com/gdewael/maldi-nn.