Resistance Genes Research Articles

Clinicopathological findings and etiological characterization in caprine gangrenous mastitis

Gangrenous mastitis ranks among the most economically significant diseases affecting small ruminants. In the present study, along with clinicopathological studies, the etiological characterisation and the contribution of various virulence factors of caprine gangrenous mastitis was studied. Staphylococcus aureus with colony count ranging from 106 to 108 CFU/mL has been identified as the etiological agent in 15 gangrenous mastitis affected goats based on cultural isolation, biochemical characteristics and molecular confirmation. Haematological and serum biochemical analysis was carried out in the affected goats which revealed leucocytosis with thrombocytopenia and hypoproteinemia. Phenotypic identification of antibiotic resistance revealed significantly high resistance to enrofloxacin, sulpha-trimethoprim, tetracycline, and gentamicin whereas the antibiotics cefoperazone, ceftriaxone- tazobactam and amoxicillin clavulanate showed least resistance. Toxin genes lukMF, and hla were detected in 66.7 per cent and 60 per cent of the isolates respectively. Antibiotic resistant genes blaZ (13.3%), tetM (20%), sul1 (13.3%), mecA (80%) and biofilm forming genes like icaA (26.6%) icaD (40%) were also detected in the S. aureus isolates. Majority of the isolates revealed significantly higher antibiotic resistance along with toxin genes and all the isolates showed biofilm formation. Biofilm forming ability of S. aureus plays a crucial role in its virulence whereas, antimicrobial resistance has a significant role in potentiating the virulence of pathogen.

Gut microbiota and antibiotic resistance genes in endangered migratory Scaly-sided merganser (Mergus squamatus) in northeast China

Studying the diversity of gut microbiota and antibiotic resistance genes (ARGs) in endangered migratory birds, as well as their responses to different environments, can reflect the health status of migratory birds and the ecological risk of ARG transmission. The globally endangered Scaly-sided merganser (Mergus squamatus) is a typical migratory bird, yet the diversity of its intestinal microbiota and ARGs has not been reported. In this study, fecal samples were collected from two major riparian foraging areas utilized by M. squamatus in the Changbai Mountains of China: the Lushui River and the Manjiang River. The gut microbiota and ARG composition were characterized using 16S rRNA amplicon and metagenomic sequencing. The results indicated that the relative abundance of gut microbiota in the two habitats differed significantly, but the core flora was similar. Moreover, the relative abundance of pathogenic bacteria was high, suggesting that M. squamatus faces a high risk of disease. A total of 382 ARGs were identified, which were primarily resistant to multidrug, tetracycline, macrolides-lincosamides-streptogramins, and mupirocin. MsbA, abcA, rpoB2, and tetT were the most abundant shared ARGs between the two sites. The findings demonstrate that habitat influences the diversity of gut microbiota and ARGs in the endangered migratory M. squamatus. This species could serve as a reservoir for pathogenic bacteria and ARGs. Therefore, monitoring the diversity of gut microbiota and ARGs in M. squamatus across different habitats is essential for a comprehensive assessment of its health status and the ecological risk of ARG transmission in the future.

A single phosphorylatable amino acid residue is essential forthe recognition of multiple potyviral HCPro effectors by potato Nytbr.

Potato virus Y (PVY, Potyviridae) is among the most important viral pathogens of potato. The potato resistance gene Nytbr confers hypersensitive resistance to the ordinary strain of PVY (PVYO), but not the necrotic strain (PVYN). Here, we unveil that residue 247 of PVY helper component proteinase (HCPro) acts as a central player controlling Nytbr strain-specific activation. We found that substituting the serine at 247 in the HCPro of PVYO (HCProO) with an alanine as in PVYN HCPro (HCProN) disrupts Nytbr recognition. Conversely, an HCProN mutant carrying a serine at position 247 triggers defence. Moreover, we demonstrate that plant defences are induced against HCProO mutants with a phosphomimetic or another phosphorylatable residue at 247, but not with a phosphoablative residue, suggesting that phosphorylation could modulate Nytbr resistance. Extending beyond PVY, we establish that the same response elicited by the PVYO HCPro is also induced by HCPro proteins from other members of the Potyviridae family that have a serine at position 247, but not by those with an alanine. Together, our results provide further insights in the strain-specific PVY resistance in potato and infer a broad-spectrum detection mechanism of plant potyvirus effectors contingent on a single amino acid residue.

EIF2Bβ confers resistance to Turnip mosaic virus by recruiting ALKBH9B to modify viral RNA methylation.

Eukaryotic translation initiation factors (eIFs) are the primary targets for overcoming RNA virus resistance in plants. In a previous study, we mapped a BjeIF2Bβ from Brassica juncea representing a new class of plant virus resistance genes associated with resistance to Turnip mosaic virus (TuMV). However, the mechanism underlying eIF2Bβ-mediated virus resistance remains unclear. In this study, we discovered that the natural variation of BjeIF2Bβ in the allopolyploid B. juncea was inherited from one of its ancestors, B. rapa. By editing of eIF2Bβ, we were able to confer resistance to TuMV in B. juncea and in its sister species of B. napus. Additionally, we identified an N6-methyladenosine (m6A) demethylation factor, BjALKBH9B, for interaction with BjeIF2Bβ, where BjALKBH9B co-localized with both BjeIF2Bβ and TuMV. Furthermore, BjeIF2Bβ recruits BjALKBH9B to modify the m6A status of TuMV viral coat protein RNA, which lacks the ALKB homologue in its genomic RNA, thereby affecting viral infection. Our findings have applications for improving virus resistance in the Brassicaceae family through natural variation or genome editing of the eIF2Bβ. Moreover, we uncovered a non-canonical translational control of viral mRNA in the host plant.

The combination of FLCWK with 5-FU inhibits colon cancer and multidrug resistance by activating PXR to suppress the IL-6/STAT3 pathway.

5-fluorouracil (5-FU) is a preferred chemotherapeutic agent for the treatment of colon cancer. Nonetheless, its clinical effectiveness is frequently hampered by suboptimal therapeutic outcomes and the emergence of drug resistance. Therefore, there exists a pressing demand for novel therapeutic agents to circumvent chemoresistance. The pregnane X receptor (PXR) exerts a pivotal regulatory influence on the proliferation, invasion, and chemoresistance mechanisms in colon cancer. Activation of PXR drives up the transcription of the multidrug resistance gene (MDR1), thus prompting the expression of P-glycoprotein (P-gp) responsible for conferring tumour resistance. This study scrutinized the potential of Fengliao Changweikang (FLCWK) in augmenting the efficacy of 5-FU in the management of colon cancer. To this end, we engineered colon cancer cells with varied levels of PXR expression via lentiviral transfection, subsequently validating the findings in nude mice. By means of MTT assays, flow cytometry apoptosis analysis, Western blotting and immunofluorescence, we probed into the prospective impacts of FLCWK and 5-FU on cellular viability and resistance. Our results revealed that while upregulation of PXR amplified the therapeutic benefits in colon cancer treatment, it concurrently heightened resistance levels. FLCWK demonstrated a capacity to reduce P-gp expression, with the combined administration of FLCWK and 5-FU effectively reversing resistance mechanisms. Furthermore, activation of PXR was found to impede the IL-6/STAT3 signalling pathway. In an effort to mimic the development of colon cancer, we established an azomethane oxide (AOM)/ dextran sodium sulfate (DSS) mouse model, showing that FLCWK bolstered the inhibitory effects of 5-FU, impeding the progression of colon cancer. In summation, our findings point towards the potential of FLCWK in the treatment of colon cancer, particularly in strengthening the therapeutic efficacy of 5-FU in the prevention and control of the disease.

Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken

Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.

Microplastic and antibiotics in waters: Interactions and environmental risks.

Antibiotics (ATs) are ubiquitously detected in natural waters worldwide, and their tendency to co-migrate with microplastics (MPs) post-adsorption leads to heightened environmental risk. Research on the adsorption of ATs on MPs and their subsequent effects on the environmental risks is gaining significant attention globally. This adsorption process predominantly occurs through hydrophobic forces, hydrogen bonds, and electrostatic interactions and is influenced by various environmental factors. The interaction between MPs and ATs exhibited varying degrees of efficiency across different pH levels and ionic strengths. Furthermore, this paper outlines the environmental risks associated with the co-presence of MPs and ATs in aquatic environments, emphasizing the potential effect of MPs on the distribution of antibiotic resistance genes (ARGs) and related environmental risks. The potential hazards posed by MPs and ATs in aquatic systems warrant serious consideration. Future research should concentrate on the adsorption of ATs/ARGs on MPs under real environmental conditions, horizontal gene transfer on MPs, as well as biofilm formation and agglomeration behavior on MPs that needs to be emphasized.

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach

Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.

Degradation of oxytetracycline in soil by a Pseudomonas strain

Oxytetracycline (OTC) is used extensively in animal husbandry and enters the soil in different forms, causing severe environmental pollution. Previous studies have shown that the genus Pseudomonas can potentially degrade antibiotics in the soil environment. Environmental conditions, such as the initial concentration of antibiotics, incubation temperature and others, have significant impacts on the activity of antibiotic-degrading bacteria. However, few reports have clarified the environmental impacts on the effectiveness of Pseudomonas spp. In the present study, we investigated the effects of different initial concentrations of OTC and incubation temperatures, as well as soil sterilization, on OTC degradation by Pseudomonas <pg=>strain T4. We also focused on the microbial degradation pathways of OTC, and variations in both antibiotic resistance genes (ARGs) and microbial communities with T4 functioning under optimal conditions. The results showed that the most effective degradation occurred under an initial OTC concentration of 2.5 mg kg-1 at 30°C in unsterilized soil spiked with T4. These conditions yielded an OTC degradation rate of 69.53% within 63 days. The putative degradation pathways of OTC in the presence of T4 included dehydration, demethylation, deamination, hydroxylation, oxidation and ring opening. Bacteroidetes, Proteobacteria and Acidobacteria played key roles in the biodegradation of OTC with T4 in the soil. The results also showed that tet(G) was the most frequently detected among the 13 common tetracycline ARGs that were investigated. The bacterial community shift observed in this study may provide new insights into the microbial degradation of OTC in soil.

First report and genomic characterization of Escherichia coli O111:H12 serotype from raw mussels in Türkiye

BackgroundThis study aimed to assess the prevalence and genomic characteristics of Shiga-toxigenic (STEC) and Enteroaggregative E. coli (EAEC) strains in raw mussels and ready-to-eat (RTE)-stuffed mussels, focusing on potential public health implications for identifying virulence and antimicrobial resistance genes.ResultsThe genome sequence analysis identified the E. coli strain named 23EM as serotype O111:H12, with adhesion (fimH-54) and fumarate hydratase (fumC-11) genes. The draft genome (4.9 Mb, 50.6% GC content, 111 contigs, 4,688 genes) is available in NCBI GenBank (accession JAWXVJ000000000). The strain, classified as ST292 and CC ST10, showed high similarity to nonpathogenic E. coli MG1655 but was distinct from pathogenic strains such as EAEC and ExPEC. In silico serotyping revealed the presence of O111-antigen flippase (wzx) and H12-antigen flagellin (fliC) genes. The strain harbors an IncFII (pCoo) plasmid with 96.95% identity. PathogenFinder predicted a 92% probability of being a human pathogen, supported by 720 pathogenic protein families. CRISPR analysis identified one high-evidence sequence with nine spacers and six low-evidence sequences. Phylogenetic analysis using RAxML positioned 23EM close to nonpathogenic E. coli but distant from other pathogenic strains. Antimicrobial resistance genes across multiple classes, including macrolides, fluoroquinolones, and aminoglycosides, were identified. The strain also contains several virulence factors, such as adhesins (e.g., ECP, ELF, TIF, type IV pili), and autotransporter genes (espP, pic), highlighting its significant pathogenic potential and public health risk.ConclusionsThis study highlights the ability of the detection of E. coli strains harboring virulence and antimicrobial resistance genes in mussels, thus emphasizing the importance of ongoing surveillance and careful consideration of the potential risks associated with the consumption of these shellfish.

Heavy metal pollution in farmland soils surrounding mining areas in China and the response of soil microbial communities

Mining activities lead to significant heavy metal pollution in nearby farmland soils, affecting the soil's microbial community and functions. To comprehensively investigate the heavy metal contamination in farmland soils caused by mining activities and the impacts on soil microbial communities and functions, we collected 87 soil samples from farmlands near 29 mining sites nationwide, measured levels of cadmium, lead, copper, and zinc. Our findings revealed that 75.8% of the sampled farmlands exhibited varying degrees of heavy metal pollution. Cadmium contamination stood out, being 2.84 to 5.35 times higher compared to other metals. This pollution notably decreased microbial diversity in agricultural soils (P ≤ 0.04), causing a shift from intricate interconnected microbial co-occurrence modules to a higher number of simpler ones, indicating a fragmentation of the microbial interaction network. Additionally, heavy metal contamination led to a 10.9% increase in the importance of the heterogeneous selection process in community assembly. Despite reduced microbial alpha diversity, we observed an increase in the diversity and abundance of metal resistance genes (MRGs) and intensified microbe-MRG interaction. This suggests that microbial communities, even when altered, maintain functionality through enhanced redundancy, which probably facilitates the preservation of microbial activities. We also identified key taxa with intense connectivity in the microbial interaction networks, 58% of which have been recognized in previous studies for their predictive effects on soil health. These findings offer important insights for developing strategies to enhance soil health, such as promoting the presence of "super-connectors" in microbial networks for the maintenance of microbial community.

The landscape of sequence variations between resistant and susceptible hot peppers to predict functional candidate genes against bacterial wilt disease

BackgroundBacterial wilt (BW), caused by Ralstonia solanacearum (Ral), results in substantial yield losses in pepper crops. Developing resistant pepper varieties through breeding is the most effective strategy for managing BW. To achieve this, a thorough understanding of the genetic information connected with resistance traits is essential. Despite identifying three major QTLs for bacterial wilt resistance in pepper, Bw1 on chromosome 8, qRRs-10.1 on chromosome 10, and pBWR-1 on chromosome 1, the genetic information of related BW pepper varieties has not been sufficiently studied. Here, we resequenced two pepper inbred lines, C. annuum ‘MC4’ (resistant) and C. annuum ‘Subicho’ (susceptible), and analyzed genomic variations through SNPs and Indels to identify candidate genes for BW resistance.ResultsAn average of 139.5 Gb was generated among the two cultivars, with coverage ranging from 44.94X to 46.13X. A total of 8,815,889 SNPs was obtained between ‘MC4’ and ‘Subicho’. Among them, 31,190 (0.35%) were non-synonymous SNPs (nsSNPs) corresponding to 10,926 genes, and these genes were assigned to 142 Gene Ontology (GO) terms across the two cultivars. We focused on three known BW QTL regions by identifying genes with sequence variants through gene set enrichment analysis and securing those belonging to high significant GO terms. Additionally, we found 310 NLR genes with nsSNP variants between ‘MC4’ (R) and ‘Subicho’ (S) within these regions. Also, we performed an Indel analysis on these genes. By integrating all this data, we identified eight candidate BW resistance genes, including two NLR genes with nsSNPs variations in qRRs-10.1 on chromosome 10.ConclusionWe identified genomic variations in the form of SNPs and Indels by re-sequencing two pepper cultivars with contrasting traits for bacterial wilt. Specifically, the four genes associated with pBWR-1 and Bw1 that exhibit both nsSNP and Indel variations simultaneously in ‘Subicho’, along with the two NLR genes linked to qRRs-10.1, which are known for their direct involvement in immune responses, are identified as most likely BW resistance genes. These variants in leading candidate genes associated with BW resistance can be used as important markers for breeding pepper varieties.

BlaGES-producing ST654 comprises a quarter of all carbapenem-resistant Pseudomonas aeruginosa in blood isolates from 15 hospitals.

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) are of major clinical concern. We analyzed 85 P. aeruginosa blood isolates non-susceptible to carbapenems collected during 2021-2023 from 15 medical centers in Israel. We aimed to determine the prevalence of high-risk clones, examine clonality, test antibiotic susceptibility, and assess the presence of acquired resistance genes, including carbapenemases. Whole-genome sequencing was performed using Illumina sequencing technology. Susceptibly was determined using the broth microdilution method. In the entire sample, 43.5% were high-risk clones. A main clade (27.1% of isolates) found in multiple hospitals comprised 19 isolates belonging to the high-risk ST654 clone and four closely related isolates. The isolates in this main clade harbored a broad set of resistance genes, including GES-type genes, and 91% had a mutated outer membrane protein (OprD). Isolates in the main clade were uniformly tobramycin (TOB) resistant and 83% were ceftolozane/tazobactam resistant. In the entire sample, we found high resistance to most antipseudomonal agents, including new beta-lactam/beta-lactamase inhibitor combinations. No uniform susceptibility to an antipseudomonal agent was found. Carbapenemases were carried by 9.4% of isolates (5.9% blaGES-5 and 3.5% blaNDM-1) and oprD was mutated in 67% of isolates. Thus, the epidemiology of CRPA is explained by a combination of clonal expansion of a dominant high-risk clade and sporadic occurrence of mutated strains. Our findings highlight the importance of susceptibility testing using a wide panel of antibiotics when CRPA is detected. Prevention measures tracking and controlling emerging high-risk clades and clones are crucial to limit the spread of CRPA.

Genomic Epidemiology of Antimicrobial Resistance: Tracking the Global Spread of Resistant Pathogens

The rapid development and spread of antimicrobial resistance have been one of the most prominent health crises globally, which significantly challenges treating infectious diseases. This paper will address the contribution that genomic epidemiology makes to track and understand the global spread of antimicrobial-resistant pathogens. Genomic epidemiology, an area combining pathogen genomics with epidemiological data, allows for an extremely powerful approach in the identification of resistance mechanisms and tracing transmission routes for guiding public health interventions. This review Emphasizes major bacterial pathogens, such as Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae, which harbor major resistance genes: blaCTX-M, mecA, and blaKPC. These genes contribute to the worldwide dissemination of resistance, mainly through mechanisms involving horizontal gene transfer and selective antibiotic pressure. Thus, genomic surveillance, phylogenetic analysis, and bioinformatics approaches allow for the pinpointing of transmission hotspots, mapping of resistance gene distribution, and tracking of emerging resistant strains in real time. It also provides information on how genomic data are being used to improve antimicrobial stewardship programs and inform clinical treatment decisions. Public health responses can further be tailored by recognizing regional resistance patterns, hence enhancing interventions. However, several challenges persist—for example, the need for standardized sharing of data, interpretation of genomic data, and integration of these insights into public health systems, especially in low-resource settings. This abstract highlights the transformative impact of genomic epidemiology in the management of the AMR crisis while emphasizing the continued need for global cooperation, enhanced data infrastructures, and policy initiatives to ensure the effective use of genomic data in public health.

Exploring the Role of Cuprotosis-Associated Genes in Cancer Progression and Therapy Resistance: A Comprehensive Analysis across Multiple Cancer Types

This review presents a comprehensive overview of the role of cuprotosis-associated genes in various cancer types, highlighting their significance in tumor progression and therapy resistance. In breast cancer and colorectal cancer (CRC), dysregulation of genes involved in mitochondrial function and copper metabolism, such as FDX1, LIAS, LIPT1, DLD, DLAT, and PDHA1/PDHB, promotes metabolic reprogramming and enhances cancer cell survival. Ovarian cancer exhibits unique dysregulations in genes like ATP7B, CCS, and COMMD1, influencing copper metabolism and redox signaling pathways, thereby contributing to chemoresistance and tumor growth. Head and neck cancer involves upregulation of MT1X, ATP7A, and CCS, potentially aiding cancer cell survival under oxidative stress conditions. Lung cancer is characterized by distinct dysregulation of genes like SLC31A1, ATOX1, and COMMD1, modulating copper homeostasis and redox signaling to support tumor proliferation. Liver cancer and kidney cancer each present unique sets of dysregulated cuprotosis-associated genes, such as SLC39A4, SCO2, and ATP7A, suggesting novel therapeutic targets specific to these cancer types. Pathway analysis reveals enrichment in mineral absorption pathways, emphasizing the importance of these genes in maintaining cellular mineral homeostasis. Understanding the intricate interplay between cuprotosis-associated genes and cancer biology offers insights into potential therapeutic strategies targeting copper metabolism for improved treatment outcomes across various cancer types.

Carbapenem resistance in gram-negative pathogens in an Iranian hospital: high prevalence of OXA-type carbapenemase genes.

The widespread dissemination of carbapenem-resistant Gram-negative bacteria poses a significant threat to global public health. This study aimed to investigate the prevalence of carbapenem resistance in Gram-negative bacteria isolated from patients at the Children's Medical Center Hospital, Tehran, Iran, to understand the molecular mechanisms underlying this resistance. During the period spanning from June 2019 to June 2020, 777 Gram-negative bacterial strains were isolated. Antibiotic susceptibility testing was performed according to Clinical and Laboratory Standards Institute. Polymerase chain reaction was used to detect carbapenem resistance genes including bla OXA23, bla OXA24, bla OXA48, bla OXA51, bla OXA58, bla OXA143, bla KPC, bla IMP, bla VIM, and bla NDM. Among the total bacterial isolates, 141 (18.1%) exhibited carbapenem resistance. Escherichia coli was the most prevalent (57.4%), followed by Klebsiella pneumoniae (11.3%) and Acinetobacter baumannii (10.6%). Other notable contributors included Enterobacter spp. (5.7%), Salmonella spp. (3.5%), and Stenotrophomonas maltophilia (2.8%). Citrobacter spp., Proteus mirabilis, and Pseudomonas aeruginosa contributed to the distributions of two, one, and three isolates, respectively. Notably, bla OXA48 showed the highest prevalence (33%), followed by bla OXA143 and bla OXA58 (27% and 24%, respectively). In addition, bla OXA24 was present in 11% of the total isolates, bla OXA23 in 10%, and bla NDM in 10%, whereas bla KPC, bla VIM, and bla IMP were not detected. Our study highlights the prevalence of carbapenemase-producing Gram-negative isolates among pediatric patients. Notable resistance patterns, especially in K. pneumoniae and E. coli, underline the urgent need for proactive interventions, including appropriate antibiotic prescription practices and strengthening of antibiotic stewardship programs.

Genetic profile of carbapenem-resistant &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; strains

The purpose of the research: the molecular genetic characteristic ofA. baumanniicarbapenem-resistant strains, including clonal affiliation, resistome and virulome pattern analysis, description of genetic environment resistance determinants, comparative genetic analysis, and assessment of phylogenetic relationships are presented in the work. The studiedA. baumanniistrains belonged to sequence types ST2Pas/ST2062.2063Oxf(n = 5) and ST78Pas/ST1757Oxf(n = 2). The nucleotide sequences of the studiedA. baumanniiST2Pas/ST2062.2063Oxfstrains were grouped into a single cluster according to phylogenetic analysis. And the sequences of theA. baumanniiST78Pas/ST1757Oxfstrains were combined with the nucleotide sequence of theA. baumanniiAbCTX5 strain, isolated in France in 2015. The presence of intrinsic (OXA-51-like) and acquired carbapenemases genes was shown inA. baumanniistrains. In particular,blaOXA-23are identified in members of ST2Pas/ST2062.2063Oxf, and inA. baumanniiST78Pas/ST1757Oxfstrains —blaOXA-72as part of the plasmid DNA. TheA. baumanniiST78Passtrains possessed additional extended-spectrum beta-lactamase genes. Тhe CTX-M-115 cephalosporinase gene are present in both strains, and theA. baumanniistrain NNAb_2023.3 has theblaCARB-16gene. MostA. baumanniistrains are characterized by the presence of acquired genes for enzymatic modification of macrolides(mph(E), msr(E)), chloramphenicols(catB8), aminoglycosides(aadA, aph(3'')-Ib, aph(6)-Id, aac(6')-Ib, aph(3')-Ia, armA). A comparative analysis showed that inA. baumanniiST2Pas/ST2062.2063Oxfstrains the resistance determinants to macrolides and aminoglycosides are located in the Tn6279-like transposon, and the aminoglycosidases genesaph(3'')-Ib, aph(6)-Idare associated with theIS91-like mobile element. InA. baumanniiST78Pas/ST1757Oxfstrains, resistance genes to aminoglycosides, macrolides, sulfonamides, and beta-lactamase genes are grouped in a region from 60 to 80 Kb long between theglmSandhutCgenes. The presence of mutations in thegyrAandparCgenes associated with resistance to fluoroquinolones were characterized in allA. baumanniistrains. Thus, new knowledge about the genetic profile of carbapenem-resistantA. baumanniistrains representing epidemically significant international clonal lineage has been obtained.

Impacts of soil type on the temporal dynamics of antibiotic resistance gene profiles following application of composted manure

Farmland application of composted manure is associated with a risk of dissemination of antibiotic resistance genes (ARGs) in agricultural soils. However, the impact of soil type on the temporal dynamics of ARGs in agricultural soil remains largely unclear. The aims of this study were to study the persistence of composted manure-derived ARGs in six soil types representative for Chinese agriculture and to explore the underlying environmental drivers of soil ARG profiles in a controlled greenhouse experiment. Temporal dynamics of manure-derived ARGs was strongly affected by soil type. High persistence of fertilizer-derived ARGs was evident in red soil, yellow soil and sierozem soil, while a rapid decrease to near pre-fertilization levels (low persistence) was observed in yellow-brown soil, black soil and brown earth soil. The distribution of ARGs was linked to soil properties such as soil texture, pH and concentrations of heavy metals. More complex co-occurrence networks of ARGs and bacteria in red soil, yellow soil, and sierozem soil suggested a higher dissemination potential, which was consistent with the significantly increased abundance of MGEs in these three types of soils. Our findings highlight the necessity for developing tailored fertilization strategies for different soil types to mitigate environmental dissemination of ARGs.

An antimicrobial resistance gene situationer in the backyard swine industry of a Philippine City

Antimicrobial resistance (AMR) as a result of antimicrobial overuse and misuse in agriculture is a growing concern, especially in the predominant but poorly regulated backyard or smallholder swine farms of the Philippines. A city-scale surveillance of antimicrobial resistance genes (ARGs) was conducted through selected backyard swine farms to obtain a comprehensive understanding of the AMR situation in the backyard sector of Davao City, Philippines. The ARGs encoding resistance to four antimicrobial classes (β-lactams: blaCTX−M, blaOXA, blaSHV, blaTEM, mecA; quinolones: qnrS and qnr-A2; macrolides: ermA and ermB; tetracycline: tetM) were quantified in swine feces via real-time PCR, and point maps were generated to visualize the ARG geographic distribution. The ARGs bla-TEM, ermB, qnrS, and tetM were detected in all farms at relatively intermediate to high levels, consistently representing the four most used antimicrobial classes in Philippine farms. All the investigated ARGs were present in some local barangay units, indicating potential emergence of AMR hotspots. A 0.5 quantile regression analysis identified specific backyard farm attributes associated with ARG occurrence and diversity, which may influence the ecological spread of the ARGs. These findings provide support for evidence-based guidelines to reinforce a One Health framework for the Philippine National Action Plan to Combat AMR.

Virulence and resistance genes in &lt;i&gt;Campylobacter spp&lt;/i&gt; isolated from asymptomatic children at Kibera slum in Nairobi, Kenya

BACKGROUND Campylobacter spp. are among the global causes of food poisoning and harbour virulence and resistance genes which play a role in invasion and antibiotic resistance. This study aimed to detect selected resistance and virulence genes in archived Campylobacter spp. isolated from children in Kibera, Nairobi, Kenya. MATERIALS AND METHODS This was a retrospective laboratory-based cross-sectional study on archived samples of Campylobacter spp. at the Department of Public Health, Pharmacology and Toxicology, University of Nairobi. Campylobacter isolates were cultured on modified charcoal cefoperazone deoxycholate agar (mCCDA) media. The presence of selected virulence genes and resistance genes was detected by multiplex polymerase chain reaction (mPCR). STATA13 was used in data analysis. Binary logistic regression was used to ascertain the association between the genes and the Campylobacter spp. RESULTS The Campylobacter spp. under this study were Campylobacter jejuni (C. jejuni) (50%), Campylobacter coli (C. coli) (38%) and Campylobacter lari (C. lari) (12%). The virulence genes detected were cgtB 37 (25%), pldA (20%), cdtA (17%), cdtB (16%), cdtC (6%), wlaN (5%), iam (4%), ciaB (4%) and VirB11 (3%). The virulence gene waaC was not detected in any of the isolates. The resistance genes detected were TetA (42%), Tet B (26%), GyrB (18%) and GyrA (14%). CONCLUSION The study revealed the presence of various virulence and resistance genes in Campylobacter spp. isolated from children. This information could help guide the development and enhancement of guidelines for the management of Campylobacter infections.