Transmission Of Resistance Genes Research Articles

Genomic insights into a clinical Salmonella Typhimurium isolate carrying plasmid mediated blaNDM-5

ObjectivesHighly carbapenem resistant Salmonella has emerged worldwide in recent years, largely associated with the multiform transmission of resistance genes, which poses a huge challenge on clinical practices. Our study delves into the resistance mechanism and epidemiology of blaNDM-carrying plasmid. MethodsWhole genome sequencing (WGS) was utilized to analyze the molecular characteristics and antimicrobial resistance mechanism of Salmonella isolate recovered from the feces of a pediatric patient at Children's Hospital of Nanjing Medical University. Moreover, we conducted the epidemiology analysis and focused on studying the mechanism of plasmid mediated blaNDM transmission, incorporating genomes deposited in the NCBI Pathogen Detection database. ResultsThe clinical isolate 23S9 belonged to serovar Typhimurium, antigenic profile is 4:i:-, ST34 and carried pNDM_23S9 harboring several antimicrobial resistance genes, including aac(6’)-Ib-cr6, OXA-1, catB3, arr-3, qacEdeltal and blaNDM. Comparative analysis revealed blaNDM-5 can exist in different plasmids of different isolates, proving its transmission through plasmids. Furthermore, blaNDM-carrying isolates mostly resistant to beta-lactams, aminoglycoside, sulphonamide, macrolide and trimethoprim. ConclusionsThese findings provided thorough and intuitive insights into the intercontinental spread of blaNDM-carrying Salmonella. Ongoing surveillance is essential for effectively monitoring the worldwide dissemination of this high-risk carbapenem resistant Salmonella.

Prevalence of blaOXA-48 and other carbapenemase encoding genes among carbapenem-resistant Pseudomonas aeruginosa clinical isolates in Egypt

BackgroundResistance to carbapenem, the last line of treatment for gram-negative bacterial infections has been increasing globally and becoming a public health threat. Since integrons may aid in the transmission of resistance genes, the purpose of this study was to detect the frequency of class 1, 2, and 3 integrons as well as carbapenem-resistant genes in clinical isolates of P. aeruginosa that are resistant to carbapenem.MethodsThis study was carried out on 97 clinical isolates of P. aeruginosa isolated from wound and urine samples. The antimicrobial susceptibility for all isolates was tested by the disc diffusion method. The presence of integrons and carbapenem-resistant genes among carbapenem-resistant P. aeruginosa isolates was evaluated by conventional PCR.ResultsThe antimicrobial resistance rate among P. aeruginosa clinical isolates was high, with imipenem resistance in 58.8% of the studied isolates. In this study, 86% of the carbapenem-resistant P. aeruginosa isolates carry carbapenemase genes, with blaVIM being the most common gene followed by the blaOXA−48 gene. Class 1 and class 2 integrons were reported in 37 (64.9%) and 10 (17.5%) of the tested carbapenem-resistant P. aeruginosa isolates, respectively.ConclusionOur data reported a high prevalence of class 1 integrons in carbapenem-resistant P. aeruginosa clinical isolates, suggesting the important role of integrons in carbapenem-resistant gene transfer among such isolates.

First Report of Carbapenem-Resistant Klebsiella michiganensis Co-Harboring bla KPC-2 and TmexCD2-ToprJ2 Isolated from Wastewater at a Tertiary Hospital in Beijing.

Klebsiella michiganensis is an emerging human pathogen that causes nosocomial infections. Its prevalence and spread in the environment should not be ignored. This study identified and characterized Klebsiella michiganensis co-harboring bla KPC-2 and TmexCD2-ToprJ2 in hospital wastewater samples. Twelve K. michiganensis strains were isolated from wastewater samples collected at a tertiary hospital in Beijing, China. The genomic characteristics of K. michiganensis strains were analyzed using whole-genome sequences, providing information on the comparison between the genome of K. michiganensis strains and the reference genome, antibiotic resistance genes (ARGs), virulence genes, secretion systems, and mobile genetic elements (plasmids, insertion sequences [ISs], and prophages). Genome analysis showed that the twelve multi-drug resistant (MDR) strains carried a variety of ARGs and virulence genes, as well as four macromolecular secretion systems (T1SS, T2SS, T5aSS, T5bSS, and T4aP). The genetic environments of both the TmexCD2-ToprJ2 gene cluster and bla KPC-2 gene contained ISs. The plasmids carrying TmexCD2-ToprJ2 gene cluster of nine strains in clade 1 and two strains in clade 2 were annotated as IncR plasmid and rep_cluster_1254 type, respectively. The plasmids carrying bla KPC-2 in 10 strains in clade 1 were identified as IncU, and the plasmids carrying bla KPC-2 in the k11 and k12 strains in clade 2 were IncU and IncX6. The phylogenetic tree and heatmap revealed that the secretion system of type VI (T6SSi) existed in 10 strains in clade 1, and Type IV (T4SS) only existed in the k11 strain in clade 2. In addition, K. michiganensis strains carried 13 plasmids, 14 ISs, and 138 prophages. In this study, the whole genome sequencing demonstrated the diversity of K. michiganensis genome despite 12 K. michiganensis strains from a hospital wastewater, which lays the foundation for further genetic research and drug resistance gene transmission.

Understanding the interests of academics from diverse disciplines to identify the prospective focus for a UK-based transdisciplinary network involving farm-to-fork stakeholders on antimicrobial resistance in agrifood systems: An online survey

Antimicrobial resistance (AMR) evolution and onward transmission of resistance genes is impacted by interrelated biological and social drivers, with evidence and impacts observed across human, animal and environmental One Health domains. Systems-based research examining how food production impacts on AMR in complex agrifood systems is lacking, with little written on management approaches in the UK that might prevent and respond to this challenge. One approach is the creation of a transdisciplinary network to enhance capacity, capability and collaboration between agrifood-focused disciplines and stakeholders. This co-creation platform for network-wide systems-based activities would reduce inefficiencies in AMR-related activities around agrifood, providing a cross-cutting, cohesive community to deliver transformational guidance on relevant, practical agrifood solutions that add value by reducing AMR, antimicrobial usage and associated costs, and decreasing resultant environmental contamination by prioritising challenges, sharing knowledge and best practice, and co-creating practical solutions with key stakeholders. An online survey determined prospective network focus, structure and priorities, with responses analysed using mixed methods.Survey results suggested respondents have interests in synthesising data using systems-approaches and using certain disciplines such as ‘social sciences’ within network activities. There were disconnects in how and whom to work with on this, with generalised use of ‘social science/scientists’ but lack of disciplinary understanding (e.g., anthropology, sociology) suggesting disciplinary differences awareness-training is useful. A similar generalisation is seen for mathematics/statistics. There are strong interests in working with food system practitioners (e.g., farmers/vets), providing opportunities for farm/field visits/knowledge exchange, and human health, reflecting the need for farm-to-fork understanding of impacts. There were notable mentions of policy/governance, emphasising translational research desires to create meaningful change. Disciplines/fields did not always align with identified interests e.g., systems and implementation science, suggesting the utility of network activity around introducing these disciplines e.g., methodology-focused rather than subject-focused conferences exploring lateral thinking about subjects. We suggest starting by developing understanding of the most important research questions by working with stakeholders, then working back to how we would achieve desirable project outcomes and who else is needed for this.

Assessment of the presence of multidrug-resistant Escherichiacoli, Salmonella and Staphylococcus in chicken meat, eggs and faeces in Mymensingh division of Bangladesh

The emergence of bacteria that is resistant to several drugs of clinical importance poses a threat to successful treatment, a phenomenon known as multidrug resistance that affects diverse classes of antibiotics. The purpose of this study was to evaluate the prevalence of multidrug-resistant Escherichiacoli, Salmonella spp. and Staphylococcusaureus in chicken egg, meat and faeces from four districts of Bangladesh. A total of 120 chicken samples were collected from different poultry farms. Conventional culture and molecular detection methods were used for identification of bacterial isolates from the collected samples followed by antibiotic susceptibility test through the disc diffusion method, finally antibiotic resistant genes were detected by PCR. E. coli, Salmonella spp. and Staphylococcusaureus were detected in meat, egg and faecal samples. Antimicrobial susceptibility results revealed isolates from faeces were 100 % resistant to amoxicillin, while all S.aureus and Salmonella sp. from faeces were resistant to doxycycline, tetracycline and erythromycin. Salmonella spp. isolates from eggs indicated 100 % resistance to erythromycin, amoxycillin, while E.coli were 100 % resistant to erythromycin. E.coli and S.aureus from meat were 100 % resistant to amoxicillin and erythromycin. However, Salmonella spp. from eggs were 100 % susceptible to doxycycline, gentamicin, levofloxacin and tetracycline. The mecA and aac(3)-IV genes were only found in S.aureus and E.coli, respectively. The Sul1,tetB, and aadA1 were highest in Salmonella spp. and S.aureus, while the sul1,tetA and blaSHV were higher in E.coli. Isolates from all samples were multidrug resistant. These findings indicate a high risk of transmission of resistance genes from microbial contamination to food of animal origin. The study emphasizes the need for effective biosecurity measures, responsible antibiotic use, and strict regulations in poultry production to prevent the spread of antibiotic resistance.

Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer

Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 108 to 1012 particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.

Insight into the responses of performance, bacterial community and three-fraction resistance genes to different quaternary ammonium compounds in nitrifying system under the stress of environmental ciprofloxacin

In recently years, an increasing number of quaternary ammonium compounds (QACs) enter waster wastewater treatment plants (WWTPs), and coexist with the environmental antibiotics in WWTPs. In this study, dodecyl trimethyl ammonium chloride (ATMAC-C12), dodecyl benzyl dimethyl ammonium chloride (BAC-C12) and didodecyl dimethyl ammonium chloride (DADMAC-C12) were added to nitrifying system treating sewage containing environmental concentration of ciprofloxacin (CIP) (0.2 mg/L), respectively, to explore the different responses of resistance genes (RGs) under the co-occurrence of different kinds of QACs and CIP in nitrifying system. Results showed that partial nitrification was achieved by QACs and CIP co-loading, and the co-occurrence of ATMAC-C12 and CIP had more serious inhibitory in the ammonia oxidation activity, functional genes, extracellular polymeric substances (EPS), and bacterial community structures than BAC-C12 and DADMAC-C12 in nitrifying system. Moreover, the co-occurrence of ATMAC-C12 and CIP stimulated the proliferation of more intracellular RGs in sludge (si-RGs), while more extracellular RGs in sludge (se-RGs) and RGs in water (w-RGs) were enriched under the co-occurrence of DADMAC-C12 and CIP. Mobile genetic elements (MGEs) cooperated with bacteria to alter the profiles of RGs. Partial least-squares path model further confirmed that MGEs had positive effects on the proliferation and transmission of si/se/w-RGs (λ = 0.647, 0.918 and 0.627), and EPS had a most important effect (λ = 1.163) on the w-RGs under the co-occurrence of QACs and CIP. Therefore, it should pay attentions to the consumptions of QACs, and avoid the proliferation and transmission of RGs caused by the co-occurrence of QACs and environmental antibiotics.

Multiomics analysis of the effects of manure-borne doxycycline combined with oversized fiber microplastics on pak choi growth and the risk of antibiotic resistance gene transmission

In this study, oversized microplastics (OMPs) were intentionally introduced into soil containing manure-borne doxycycline (DOX). This strategic approach was used to systematically examine the effects of combined OMP and DOX pollution on the growth of pak choi, analyze alterations in soil environmental metabolites, and explore the potential migration of antibiotic resistance genes (ARGs). The results revealed a more pronounced impact of DOX than of OMPs. Slender-fiber OMPs (SF OMPs) had a more substantial influence on the growth of pak choi than did coarse-fiber OMPs (CF OMPs). Conversely, CF OMPs had a more significant effect on the migration of ARGs within the system. When DOX was combined with OMPs, the negative effects of DOX on pak choi growth were mitigated through the synthesis of indole through the adjustment of carbon metabolism and amino acid metabolism in pak choi roots. In this process, Pseudohongiellaceae and Xanthomonadaceae were key bacteria. During the migration of ARGs, the potential host bacterium Limnobacter should be considered. Additionally, the majority of potential host bacteria in the pak choi endophytic environment were associated with tetG. This study provides insights into the intricate interplay among DOX, OMPs, ARGs, plant growth, soil metabolism, and the microbiome.

Harnessing Nature's Arsenal: Investigating the Antibacterial Efficacy of Commercial Essential Oils against Staphylococcus Strains Isolated from Poultry Meat.

Pathogens prevalent in the food supply chain provide a significant worldwide risk to both human health and the economy. Poultry meat, a staple in global diets, serves as a reservoir for bacterial contamination. Staphylococcus, a gram-positive bacterium belonging to family Staphylococcaceae has been identified as a potential causative agent of food borne illnesses. The presence of antibiotic-resistant Staphylococcus strains in poultry products raises concerns about the transmission of resistance genes through the food chain, necessitating thorough investigations into alternative antimicrobial agents for effective bacterial control. Essential oils (EOs) hold profound importance in terms of their known and potential application. This study focuses on the evaluation of commercial essential oils and their effectiveness against Staphylococcus strains isolated from poultry meat. Briefly, 150 raw chicken meat samples were collected, and Staphylococcus spp. was identified based on morphological and cultural characteristics. Antibiogram analysis and essential oils activity was determined by disc diffusion and agar well diffusion assay respectively. Results showed that 27 (18%) samples tested positive for Staphylococcus spp, out of which S. aureus was identified in 25 isolates (16.66%). The antibiogram profile reveals that three antibiotics namely, gentamicin, vancomycin and ciprofloxacin were the most effective antibiotics showing sensitivity against 74.07%, 70.37% and 62.96% of the isolates respectively. Moreover, amongst the tested essential oils cinnamon oil and clove oil exhibited the highest antimicrobial activities ZOI ranges from 19-41mm and 19-33 mm respectively. While focusing on the evaluation of antimicrobial activity of essential oils, the study endeavors to aid in development of sustainable strategies for mitigating bacterial contamination in the food industry.

Monitoring and analysis of pathogenic microorganisms and resistance genes.

The objectives are to improve the rapid identification method of microbial risk and cut off the route of transmission of resistance genes. When new pathogenic microorganisms are found, intervention can be carried out as early as possible to identify the risk of potential pathogen transmission, and timely cut off the transmission route. Hospital air samples were collected to analyse the distribution of environmental pathogenic microorganisms and the characteristics of ARGs resistance genes. The air samples were collected from 12 sampling sites in the Affiliated Hospital of Yangzhou University. In the infusion room, general ward and intensive care unit, no significant difference was found in microorganisms, and no significant difference was found in microbial resistance genes. There were some differences in resistance genes between east and west districts. Combined with the detection of pathogenic microorganisms and resistance genes in our hospital, it is necessary to improve the daily disinfection measures such as air conditioning and fresh air equipment, cut off the infection route, block the transmission of resistance genes, and monitor pathogens and resistance genes in airborne diseases.

The fate of pharmaceuticals and personal care products (PPCPs) in sewer sediments:Adsorption triggering resistance gene proliferation

In recent years, large quantities of pharmaceuticals and personal care products (PPCPs) have been discharged into sewers, while the mechanisms of PPCPs enrichment in sewer sediments have rarely been revealed. In this study, three PPCPs (tetracycline, sulfamethoxazole, and triclocarban) were added consecutively over a 90-day experimental period to reveal the mechanisms of PPCPs enrichment and the transmission of resistance genes in sewer sediments. The results showed that tetracycline (TC) and triclocarban (TCC) have higher adsorption concentration in sediments compared to sulfamethoxazole (SMX). The absolute abundance of Tets and suls genes increased in sediments under PPCPs pressure. The increase in secretion of extracellular polymeric substances (EPS) and the loosening of the structure exposed a large number of hydrophobic functional groups, which promoted the adsorption of PPCPs. The absolute abundance of antibiotic resistance genes (ARGs), EPS and the content of PPCPs in sediments exhibited significant correlations. The enrichment of PPCPs in sediments was attributed to the accumulation of EPS, which led to the proliferation of ARGs. These findings contributed to further understanding of the fate of PPCPs in sewer sediments and opened a new perspective for consideration of controlling the proliferation of resistance genes.

Resistance risk assessment for benzovindiflupyr in Sclerotium rolfsii and transmission of resistance genes among population.

Sclerotium rolfsii is a destructive soil-borne fungal pathogen which is distributed worldwide. In previous study, the succinate dehydrogenase inhibitor (SDHI) fungicide benzovindiflupyr has been identified for its great antifungal activity against Sclerotium rolfsii. This study is aimed to investigate the resistance risk and mechanism of benzovindiflupyr in Sclerotium rolfsii. Eight stable benzovindiflupyr-resistant isolates were generated by fungicide adaptation. Although the obtained eight resistant isolates have a stronger pathogenicity than the parental sensitive isolate, they have a fitness penalty in the mycelial growth and sclerotia formation compared to the parental isolate. A positive cross-resistance existed in the resistant isolates between benzovindiflupyr and thifluzamide, carboxin, boscalid and isopyrazam. Three-point mutations, including SdhBN180D, SdhCQ68E and SdhDH103Y, were identified in the benzovindiflupyr-resistant isolates. However, molecular docking analysis indicated that only SdhDH103Y could influence the sensitivity of Sclerotium rolfsii to benzovindiflupyr. After mycelial co-incubation of resistant isolates and the sensitive isolate, resistance genes may be transmitted to the sensitive isolate. The in vivo efficacy of benzovindiflupyr and thifluzamide against benzovindiflupyr-resistant isolates was a little lower than that against the sensitive isolate but with no significant difference. The results suggested a low to medium resistance risk of Sclerotium rolfsii to benzovindiflupyr. However, once resistance occurs, it is possible to spread in the population of Sclerotium rolfsii. This study is helpful to understanding the risk and mechanism of resistance to benzovindiflupyr in multinucleate pathogens such as Sclerotium rolfsii. © 2024 Society of Chemical Industry.

Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements

Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.

Impact of bacteriocins on multidrug‐resistant bacteria and their application in aquaculture disease prevention and control

AbstractAquaculture plays an important role in meeting human demand for animal protein. Disease is a critical factor that restricts the green and healthy development of aquaculture. Intensive aquaculture practices can increase the susceptibility of aquatic animals to pathogens due to environmental stress. Antibiotics are commonly used for disease prevention and control, but their frequent use in aquaculture can increase the risk of antibiotic‐resistant bacteria and resistance gene transmission, posing a threat to the health of aquatic animals and humans. Recent studies have shown that bacteriocins have inhibitory effects on different species of bacteria, fungi and viruses, and can even affect natural resistance structures such as bacterial biofilms, presenting promising prospects as antimicrobial agents. Bacteriocins have potential applications in various fields such as agriculture, food and medicine, but limited research has been conducted on their impact on aquaculture disease prevention and control, and the underlying mechanisms remain to be explored. Therefore, this review aims to summarise the classification, sources, preparation methods, antibacterial activity against multidrug‐resistant bacteria and application of bacteriocins as antimicrobial agents in aquaculture disease prevention and control. In addition, limitations of bacteriocin application in aquaculture and future research directions are also discussed.

Food chain milieus: Potential reservoirs and sources of metallo-beta-lactamase-producing antibiotic-resistant bacteria in Southeast Nigeria

Concerted efforts are needed to mitigate the development and transmission of bacterial resistance in the general environment. Metallo-beta-lactamase (MBL) is a carbapenemase that allows bacteria to resist the antimicrobial onslaught of carbapenems (e.g., imipenem [IPM]). We investigated the prevalence of MBL-producing Pseudomonas aeruginosa in poultry farms. Samples from poultry birds (n = 65) were studied for the isolation of antibiotic-resistant bacteria according to the Clinical and Laboratory Standards Institute criteria. The modified Hodge test was used to phenotypically detect MBL. Polymerase chain reaction (PCR) was used to confirm MBL production in the test isolates. To confirm the presence of plasmids in the isolates, a plasmid curing experiment was conducted. High levels of reduced susceptibility to cefotaxime (77.8%), IPM (69.4%), gentamicin (63.9%), amikacin (58.3%), fosfomycin (55.5%), ciprofloxacin (66.7%), tetracycline (75%), ertapenem (55.5%), sulfamethoxazole-trimethoprim (66.7%), and cefoxitin (52.8%) were recorded in the P. aeruginosa isolates. A total of 23 isolates of P. aeruginosa produced MBL. The presence of MBL genes in these P. aeruginosa isolates (n = 23) was confirmed by PCR, which detected blaIMP-1 (47.8%) and blaIMP-2 (26.1%). The isolates were multidrug resistant (50%) and carried plasmids, indicating horizontal transmission of resistance genes. Genes for bacterial resistance can be transmitted through mobile genetic elements. Therefore, sustainable interventions are needed to mitigate antibiotic use in poultry practices in Nigeria to curb the development of MBL-producing bacteria arising from selective (antibiotic) pressures in such an environment. These interventions can help to detect and stop infections caused by resistant bacteria before they become clinical cases in our hospitals.

Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China.

This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were vanT_gene, vanY_gene, adeF, qacG, Mtub_rpsL_STR, vanY_gene_, vanW_gene, Mtub_murA_FOF, vanY_gene, vanH_gene, FosG, rsmA, qacJ, RbpA, vanW_gene, aadA6, vanY_gene, sul4, sul1, and InuF. The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are Streptococcus agalactiae and Streptococcus anginosus; Enterococcus faecalis; Enterococcus faecium; Actinomyces viscosus and Bacillus cereus. Enterococcus faecium; Clostridium tetani; Streptococcus agalactiae and Streptococcus anginosus; Streptococcus agalactiae and Streptococcus anginosus; Acinetobacter baumannii, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Corynebacterium jeikeium, Corynebacterium urealyticum, Mycobacterium kansasii, Mycobacterium tuberculosis, Schaalia odontolytica, and Trueperella pyogenes; Mycobacterium avium and Mycobacterium tuberculosis; Aeromonas caviae, Enterobacter hormaechei, Vibrio cholerae, Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus; Pseudomonas aeruginosa and Pseudomonas fluorescens; Staphylococcus aureus and Staphylococcus equorum; M. avium, Achromobacter xylosoxidans, and Acinetobacter baumannii; Sphingobium yanoikuyae, Acinetobacter indicus, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered.

AMR Threat Perception Assessment of Heterotrophic Bacteria From Shrimp Aquaculture Through Epidemiological Cut off Values.

Emergence and dissemination of antibiotic resistance is one of the major risks associated with the rampant usage of antibiotics in food-producing animals including aquaculture. To determine Epidemiological Cut-OFF (ECOFF) values of heterotrophic bacterial populations from shrimp culture environments against five different antibiotics. In this present study, bacterial samples were isolated from Penaeus vannamei culture environment in different locations of Andhra Pradesh, which is the aquaculture hub of India. The bacterial isolates were assessed for antibiotic resistance towards five antibiotics belonging to different classes (oxytetracycline, chloramphenicol, erythromycin, ciprofloxacin, and co-trimoxazole) by the disc diffusion method. Determination of Epidemiological Cut-OFF (ECOFF) values and analysis by employing normalized resistance interpretation (NRI) was carried out. The most dominant bacterial populations from shrimp culture were Vibrio spp. (pathogenic bacteria) followed by Bacillus spp. (probiotic bacteria). The bacterial isolates showed highest resistance towards oxytetracycline (overall 23.38%) and in location L6 (59.4%) followed by co-trimoxazole (31.1%). ECOFF values calculated by employing NRI showed that the disc diffusion data were distributed in a normalized manner. The maximum ECOFF value was obtained for ciprofloxacin (23.32 mm), while the minimum value was observed for oxytetracycline (9.05 mm). The antibiotic resistant phenotypes showed that the majority of the heterotrophic bacterial isolates (>60%) belonged to the non-wild type phenotype and primarily towards oxytetracycline (90%). The presence of non-wild antibiotic-resistant phenotypes of heterotrophic bacterial populations (which include not only pathogenic bacteria but also probiotic bacteria) indicates that shrimp culture ponds may be a reservoir for drug-resistant bacteria and there is a greater risk associated with transmission of resistant genes across bacterial flora. NRI analysis of antibiotic disc diffusion data of heterotrophic bacterial populations in shrimp aquaculture environments revealed that majority of them belonged to non-wild type (90%) paticularly to oxytetracycline in comparison to other studied antibiotics (chloramphenicol, erythromycin, ciprofloxacin and co-trimoxazole).

The emergence of carbapenem-resistance and New Delhi metallo-β-lactamase-1 (blaNDM-1) among Salmonella spp. in Kerman, Iran.

Salmonella species (spp) are the most prevalent zoonotic pathogens that cause outbreaks of gastroenteritis worldwide. Therefore evaluation of the profile of antibiotic resistance, virulence factors, and plasmid replicon types in these bacteria is necessary to control and prevent the spread of potentially pathogenic and drug-resistant strains. This study was performed on 39 Salmonella spp. The antibacterial susceptibility of isolates to various antibiotic agents was determined using disk diffusion test. β-lactamases (bla) including ESBLs, AmpC, MBLs, and virulence genes were detected by PCR methods. Plasmid incompatibility groups among the isolates were identified using PCR-based replicon typing (PBRT). The most prevalent virulent gene was phoP/Q (84.6%). slyA, sopB, and stn were identified in 79.4% (n=31), 69.2% (n=27), and 2.5% (n=1) of the isolates, respectively. The antibiotic susceptibility testing showed that 30.7% of the isolates were ESBL-producing. blaTEM (41%; n=16) was the most frequent β-lactamase gene among the isolates followed by blaNDM-1 (15.4%; n=6), blaDHA (7.7%; n=3), and blaCTX-M (1.5%; n=1). Six different plasmid replicon types, including IncP (n=9; 23%), IncFIC (n=3; 7.70%), IncY (n=3; 7.70%), IncI1-Iγ (n=2; 5.12%), IncFIIAs (n=1; 2.56%), and IncN (n=1; 2.56%) were observed among the isolates. Our study showed the emergence of carbapenem-resistant and blaNDM-1 among Salmonella spp. for the first time in Kerman, Iran. Since Salmonella spp. plays an important role in the transmission of resistance genes in livestock and humans in the food chains, so more stringent control policies are recommended to prevent the circulation of drug-resistant and potentially pathogenic strains from animals to humans.

MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model.

Mobilization typing (MOB) is a classification scheme for plasmid genomes based on their relaxase gene. The host ranges of plasmids of different MOB categories are diverse, and MOB is crucial for investigating plasmid mobilization, especially the transmission of resistance genes and virulence factors. However, MOB typing of plasmid metagenomic data is challenging due to the highly fragmented characteristics of metagenomic contigs. We developed MOBFinder, an 11-class classifier, for categorizing plasmid fragments into 10 MOB types and a nonmobilizable category. We first performed MOB typing to classify complete plasmid genomes according to relaxase information and then constructed an artificial benchmark dataset of plasmid metagenomic fragments (PMFs) from those complete plasmid genomes whose MOB types are well annotated. Next, based on natural language models, we used word vectors to characterize the PMFs. Several random forest classification models were trained and integrated to predict fragments of different lengths. Evaluating the tool using the benchmark dataset, we found that MOBFinder outperforms previous tools such as MOBscan and MOB-suite, with an overall accuracy approximately 59% higher than that of MOB-suite. Moreover, the balanced accuracy, harmonic mean, and F1-score reached up to 99% for some MOB types. When applied to a cohort of patients with type 2 diabetes (T2D), MOBFinder offered insights suggesting that the MOBF type plasmid, which is widely present in Escherichia and Klebsiella, and the MOBQ type plasmid might accelerate antibiotic resistance transmission in patients with T2D. To the best of our knowledge, MOBFinder is the first tool for MOB typing of PMFs. The tool is freely available at https://github.com/FengTaoSMU/MOBFinder.

The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.

While antibiotics are commonly used to treat inflammatory bowel disease (IBD), their widespread application can disturb the gut microbiota and foster the emergence and spread of antibiotic resistance. However, the dynamic changes to the human gut microbiota and direction of resistance gene transmission under antibiotic effects have not been clearly elucidated. Based on the Human Microbiome Project, a total of 90 fecal samples were collected from 30 IBD patients before, during and after antibiotic treatment. Through the analysis workflow of metagenomics, we described the dynamic process of changes in bacterial communities and resistance genes pre-treatment, during and post-treatment. We explored potential consistent relationships between gut microbiota and resistance genes, and established gene transmission networks among species before and after antibiotic use. Exposure to antibiotics can induce alterations in the composition of the gut microbiota in IBD patients, particularly a reduction in probiotics, which gradually recovers to a new steady state after cessation of antibiotics. Network analyses revealed intra-phylum transfers of resistance genes, predominantly between taxonomically close organisms. Specific resistance genes showed increased prevalence and inter-species mobility after antibiotic cessation. This study demonstrates that antibiotics shape the gut resistome through selective enrichment and promotion of horizontal gene transfer. The findings provide insights into ecological processes governing resistance gene dynamics and dissemination upon antibiotic perturbation of the microbiota. Optimizing antibiotic usage may help limit unintended consequences like increased resistance in gut bacteria during IBD management.