Reservoir Of Antibiotic Resistance Genes Research Articles

Doxycycline induces the rebound of three tetracycline resistance genes during maturation of laying hen manure composting by increasing the abundance of potential host bacteria

Livestock manure is considered as an important reservoir of antibiotic resistance genes (ARGs). Antibiotics used in livestock production can stress microorganisms and lead to the spread of ARGs, yet composting is viewed as an effective means of reducing ARGs. However, it remains unclear why ARGs typically decline at high composting temperatures but rebound during compost maturation with varied concentrations of antibiotics. Two concentrations of doxycycline (5 and 20 mg/kg) were added to manure of laying hen mixed with sawdust for composting to evaluate changes in ten tetracycline resistance genes (TRGs) and two mobile genetic elements (MGEs), and to investigate the rebound of TRGs during compost maturation. The results showed that the total absolute abundances of TRGs continuously decreased in all compost treatments. Compared with the start (day 0), the relative abundance of tetA, tetG and tetX in the three compost treatments significantly decreased at thermophilic stage (day 3-day 8), but rebounded in the maturation stage (day 9-day 25) (P < 0.01). 16S rRNA sequencing showed that the relative abundance of Proteobacteria and Bacteroidetes in the three groups decreased significantly at thermophilic stage (day 3-day 8) compared with the mesophilic stage (day 0-day 2) and then increased significantly during the maturation stage (day 9-day 25) (P < 0.05), while Firmicutes showed the opposite trend. Pearson correlation analysis showed the strong correlation between the rebound TRGs and major bacteria, such as Proteobacteria and Bacteroidetes, under doxycycline stress. It suggested that the potential host bacteria caused the rebound of TRGs during compost maturation under doxycycline stress. RDA and VPA analysis showed that Marinimicrobium, Pusillimonas and Sphingobacterium contributed to the rebound of tetA, tetG and tetX. This study provides insights into the rebound of ARGs typically seen during the compost maturation stage and a reference for evaluating the risk of spreading ARGs in the process of manure composting treatment.

Modulation of the Gut Microbiota to Control Antimicrobial Resistance (AMR)-A Narrative Review with a Focus on Faecal Microbiota Transplantation (FMT).

Antimicrobial resistance (AMR) is one of the greatest challenges facing humanity, causing a substantial burden to the global healthcare system. AMR in Gram-negative organisms is particularly concerning due to a dramatic rise in infections caused by extended-spectrum beta-lactamase and carbapenemase-producing Enterobacterales (ESBL and CPE). These pathogens have limited treatment options and are associated with poor clinical outcomes, including high mortality rates. The microbiota of the gastrointestinal tract acts as a major reservoir of antibiotic resistance genes (the resistome), and the environment facilitates intra and inter-species transfer of mobile genetic elements carrying these resistance genes. As colonisation often precedes infection, strategies to manipulate the resistome to limit endogenous infections with AMR organisms, as well as prevent transmission to others, is a worthwhile pursuit. This narrative review presents existing evidence on how manipulation of the gut microbiota can be exploited to therapeutically restore colonisation resistance using a number of methods, including diet, probiotics, bacteriophages and faecal microbiota transplantation (FMT).

Plastic wastes and surface antibiotic resistance genes pollution in mangrove environments.

Mangroves are located at the intersection of land and sea and are also heavily affected by plastic wastes. Biofilms of plastic wastes in mangroves are reservoirs for antibiotic resistance genes (ARGs). In this study, plastic wastes and ARG pollution were investigated from three typical mangrove areas in Zhanjiang, South China. Transparent was the dominant colors of plastic wastes in three mangroves. Fragment and film shape accounted for 57.73-88.23% of plastic waste samples in mangroves. In addition, 39.50% of plastic wastes in protected area mangroves are PS. The metagenomic results shows that the 175 ARGs were found on plastic wastes of the three mangroves, the abundance accounting for 91.11% of the total ARGs. The abundance of Vibrio accounted for 2.31% of the total bacteria genera in aquaculture pond area mangrove. Correlation analysis shows that a microbe can carry multiple ARGs that may improve resistance to antibiotics. Microbes are the potential hosts of most ARGs, suggesting that ARGs can be transmitted by microbes. Because the mangroves are closely related to human activities and the high abundance of ARGs on plastic increases the ecological risks, people should improve plastic waste management and prevent the spread of ARGs by reducing plastic pollution.

Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem

Aquatic ecosystems in anthropogenically impacted areas are important reservoirs of antibiotic resistance genes (ARGs) of allochthonous origin. However, the dynamics of the different ARGs within the bacterial communities of lakes and rivers, as well as the factors that drive their selection, are not completely understood. In this study, we analysed the fate of the bacterial resistome (total content of ARGs and of metal resistance genes, MRGs) for a period of six months (summer-winter) in a continuum lake-river-lake system (Lake Varese, River Bardello, Lake Maggiore) in Northern Italy, by shotgun metagenomics. The metagenomic data were then compared with chemical, physical and microbiological data, to infer the role of anthropogenic pressure in the different sampling stations. ARGs and MRGs were more abundant and diverse in the River Bardello, characterised by the highest anthropogenic pollution. The date of sampling influenced ARGs and MRGs, with higher abundances in summer (August) than in fall or in winter, when the impact of the treated wastewater discharge in the river was limited by a higher water flow from Lake Varese. ARG and MRG abundances were significantly correlated and they co-occurred in the main network analysis modules with potential pathogenic bacteria. Different levels of anthropogenic impact selectively promoted specific ARGs while others, generally abundant in waters, were not affected by anthropogenic pressure. Reducing the level of anthropogenic pressure resulted in a rapid decrease of most ARGs. From our results, the role of anthropogenic pressure in promoting the spread of specific antibiotic resistances and of potential pathogens in aquatic ecosystem becomes clear. Finally we highlight the strict correlation between ARGs and MRGs suggesting their potential co-selection in stressed aquatic bacterial communities.

Distribution and quantification of antibiotic resistance genes in a large subalpine lake (Lugano Lake) and tributary rivers

Antibiotic resistance genes (ARGs) are causing increasing problems, especially in clinical settings. Nowadays, they are considered important environmental contaminants, but little is known about their fate in the environment or how they affect natural microbial populations. In the environment, especially in water affected by anthropic activities such as discharge of hospital, urban, and industrial wastewater treatment plant (WWTP) and agricultural runoff, antibiotic determinants may become part of the environmental gene pool, spread horizontally, and be ingested by humans and animals via contaminated food and drinking water. The aim of this work was to monitor long-term the presence of antibiotic resistance determinants in water samples collected from a subalpine lake and some tributary rivers located in the southern part of Switzerland, and to assess if anthropic activities could influence the distribution of antibiotic resistance genes present in water environments. We analysed water samples by qPCR to quantify five antibiotic resistance genes that confer resistance to the major classes of antibiotics used in clinical and veterinary settings (β-lactams, macrolides, tetracycline, quinolones, and sulphonamides). Water samples were collected from January 2016 to December 2021, from three rivers located in south Switzerland and from five different sites of Lugano Lake. The most abundant genes were sulII, followed by ermB, qnrS, and tetA; they were found especially in the river influenced by wastewater treatment plants and in the lake near the potable water uptake plant. We observed an overall decrease in the number of resistance genes during the three years. Our results indicate that the aquatic ecosystems monitored in this study are a reservoir of ARGs and could potentially be a setting for the transmission of resistance from the environment to humans.

Distribution of Antibiotic Resistance Genes and Their Association with Microbes in Wastewater Treatment Plants: A Metagenomics Analysis

The extensive use of antibiotics has resulted in the generation and accumulation of antibiotic resistance genes (ARGs) in the environment, and domestic wastewater is one of the main reservoirs of ARGs and resistant bacteria. In this study, Illumina high-throughput sequencing and network analysis were used to study the microbial community characteristics, ARGs’ occurrence status, and resistance mechanism in the influent and effluent of a domestic sewage treatment plant in Changchun, China. A total of 29 phyla were found in the influent and effluent, including 23 bacterial phyla, 3 archaeal phyla, and 3 eukaryotic phyla. In total, 112 ARG subtypes were detected in the samples, and the dominant ARG subtypes were Erm(35) and tet(W/N/W). In this study, ARGs related to tetracycline and macrolide accounted for a high proportion, and the resistance mechanisms of ARGs detected in the samples were mainly antibiotic inactivation and antibiotic efflux pumps. Co-occurrence maps of ARGs and microbes demonstrated by network analysis indicated that the resistance genes kdpE, GES-5, and tetX may easily bind to microbes, potentially making them antibiotic-resistant bacteria. Fifty-seven bacteria in the genera Cupriavidus, Escherichia, and Collinsell are potential hosts of multiple ARGs. The findings can increase our understanding of the distribution of ARGs and their association with microbes in wastewater treatment plants, and also provide a research foundation for controlling the diffusion of ARGs in the environment.

Antibiotic resistance gene abundance and bacterial community composition in macroinvertebrates of an urban stream

Abstract Increase in antibiotic resistance genes (ARGs) in freshwater ecosystems as a consequence of anthropogenic activities is a matter of public health concern. Although researchers have looked at ARG abundance and the factors affecting them in biofilms, water and sediment, the role of freshwater macroinvertebrate gut microbiomes in harbouring and disseminating ARGs is unknown. In the current study, we tested whether: (a) macroinvertebrate gut microbiomes serve as hotspots of ARGs in comparison to their immediate environment, (b) functional feeding groups (FFGs) impact ARG abundance in macroinvertebrate guts, (c) bacterial community composition and ARG abundance are correlated, and (d) macroinvertebrates can be potential vectors of ARGs. Macroinvertebrates, sediment and water samples were collected from seven different sites along northeastern Ohio (U.S.A.) streams and abundances of three ARGs (sulI, sulII and tetW) were determined. Bacterial community composition also was examined for respective microbiomes and a microcosm study was designed for testing hypothesis 4. In many cases, the gut microbiome had higher relative ARG abundance (sulI and sulII) at sites along Tinker's Creek compared to the surrounding substrate and water. ARG abundances along with taxonomic differences in bacterial community composition were different among the FFGs (ARG abundance higher in omnivores). Certain bacterial taxa were significantly correlated with one or more ARGs. We did not find that freshwater macroinvertebrates can serve as vectors of ARGs (from the microcosm study). Overall, our site‐based results suggest that freshwater macroinvertebrate guts may serve as reservoirs of ARGs, differences in ARG abundance among FFGs was possibly a result of differences in bacteria ingested and gut morphophysiological conditions. Because this study indicates that macroinvertebrate guts can be potential reservoirs of ARGs, future studies can be designed to understand the role of macroinvertebrates in dissemination of ARGs in freshwater ecosystems.

Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India

Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.

The honeybee gut resistome and its role in antibiotic resistance dissemination.

There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.

Metagenomic analyses reveal that mesophilic anaerobic digestion substantially reduces the abundance of antibiotic resistance genes and mobile genetic elements in dairy manures

Animal manure is considered one of the main reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) that carry them. There is increasing concern regarding the dissemination of antibiotic resistance due to the application of manure as a soil amendment, and there is an urgent need to define alternatives to minimize this problem. Anaerobic digestion (AD) has shown the potential to reduce the levels of ARGs present in manure. However, little is known about the effect of AD on the entire set of MGEs, which play a crucial role in the dissemination of antibiotic resistance. In this study, we used a set of metagenomic and bioinformatics tools to evaluate the long-term effects of mesophilic anaerobic digestion on ARGs and MGEs in bovine dairy manure and the potential mechanisms driving these changes. The results indicated that the average ARG and MGE levels were significantly reduced by 53% and 74%, respectively, after AD. The results also suggested that microbial groups including Lactobacillales, Bacillales, Eubacteriales, Micrococcales, and Actinomycetales were main groups associated with ARGs and MGEs. The changes in ARG and MGE seemed to result from distinct microbial successions, such as the removal of aerobic species and the decline in facultative bacteria, which led to the establishment of typical microbial communities present in anaerobic digesters. The study also suggested that hydrolytic species are another important group that potentially harbors ARGs and MGEs. Overall, the results indicated that digested manure could have a reduced risk of dissemination of antibiotic resistance.

Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems

Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6′)-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40–55 %), tetracyclines (30–45 %), beta-lactam-resistance (20–35 %), macrolides (18–30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Digestate from Agricultural Biogas Plants as a Reservoir of Antimicrobials and Antibiotic Resistance Genes-Implications for the Environment.

Antimicrobials and antibiotic resistance genes (ARGs) in substrates processed during anaerobic digestion in agricultural biogas plants (BPs) can reach the digestate (D), which is used as fertilizer. Antimicrobials and ARGs can be transferred to agricultural land, which increases their concentrations in the environment. The concentrations of 13 antibiotics in digestate samples from biogas plants (BPs) were investigated in this study. The abundance of ARGs encoding resistance to beta-lactams, tetracyclines, sulfonamides, fluoroquinolones, macrolide-lincosamide-streptogramin antibiotics, and the integrase genes were determined in the analyzed samples. The presence of cadmium, lead, nickel, chromium, zinc, and mercury was also examined. Antimicrobials were not eliminated during anaerobic digestion. Their concentrations differed in digestates obtained from different substrates and in liquid and solid fractions (ranging from 62.8 ng/g clarithromycin in the solid fraction of sewage sludge digestate to 1555.9 ng/L doxycycline in the liquid fraction of cattle manure digestate). Digestates obtained from plant-based substrates were characterized by high concentrations of ARGs (ranging from 5.73 × 102 copies/gDcfxA to 2.98 × 109 copies/gDsul1). The samples also contained mercury (0.5 mg/kg dry mass (dm)) and zinc (830 mg/kg dm). The results confirmed that digestate is a reservoir of ARGs (5.73 × 102 to 8.89 × 1010 copies/gD) and heavy metals (HMs). In addition, high concentrations of integrase genes (105 to 107 copies/gD) in the samples indicate that mobile genetic elements may be involved in the spread of antibiotic resistance. The study suggested that the risk of soil contamination with antibiotics, HMs, and ARGs is high in farms where digestate is used as fertilizer.

Potential influence of antimicrobial resistance gene content in probiotic bacteria on the gut resistome ecosystems.

Antimicrobial resistance (AMR) poses a substantial threat to human health. The commensal bacteria of the gut microbiome were shown to serve as a reservoir of antibiotic resistance genes (ARGs), termed the gut resistome, which has the potential to transfer horizontally to pathogens and contribute to the emergence of drug-resistant bacteria. Namely, AMR traits are generally linked with mobile genetic elements (MGEs), which apart from disseminating vertically to the progeny, may cross horizontally to the distantly related microbial species. On the other hand, while probiotics are generally considered beneficiary to human health, and are therefore widely consumed in recent years most commonly in conjunction with antibiotics, the complexities and extent of their impact on the gut microbiome and resistome have not been elucidated. By reviewing the latest studies on ARG containing commercial probiotic products and common probiotic supplement species with their actual effects on the human gut resistome, this study aims to demonstrate that their contribution to the spread of ARGs along the GI tract merits additional attention, but also indicates the changes in sampling and profiling of the gut microbiome which may allow for the more comprehensive studying of the effects of probiotics in this part of the resistome.

Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments.

Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.

Metagenomic analysis of gut microbiota and antibiotic-resistant genes in Anser erythropus wintering at Shengjin and Caizi Lakes in China.

Migratory birds are the primary source and reservoir of antibiotic-resistant genes (ARGs) related to their gut microbes. In this study, we performed metagenomics analysis to study the gut microbial communities and ARGs of Anser erythropus wintering at Shengjin (SJ) and Caizi (CZ) Lakes. The results showed that bacteria, fungi, viruses, and archaea were the dominant gut microbes. Principal component analysis (PCA) indicated that the microbiota compositions significantly differed between the two populations. Diet may be the most crucial driver of the gut microbial communities for A. erythropus. This species fed exclusively on Poaceae spp. at Shengjin Lake and primarily on Carex spp. at Caizi Lake. Tetracycline, macrolide, fluoroquinolone, phenicol, and peptide antibiotics were the dominant resistant types. ARGs had a significantly higher abundance of operational taxonomic units (OTUs) in the Shengjin Lake samples than in Caizi Lake samples. PCA indicated that most Shengjin Lake samples significantly differed in gut microbiota composition from those obtained at Caizi Lake. This difference in gut microbiota composition between the two lakes' samples is attributed to more extensive aquaculture operations and poultry farms surrounding Shengjin Lake than Caizi Lake. ARGs-microbes associations indicated that 24 bacterial species, commonly used as indicators of antibiotic resistance in surveillance efforts, were abundant in wintering A. erythropus. The results revealed the composition and structural characteristics of the gut microbiota and ARGs of A. erythropus, pointing to their high sensitivities to diet habits at both lakes. This study also provides primary data for risk prevention and control of potential harmful pathogens that could endanger public health and therefore are of major significance to epidemiological and public health.

Prevalence and antimicrobial resistance of food safety related Vibrio species in inland saline water shrimp culture farms.

This study evaluated the potential pathogenicity and antimicrobial resistance (AMR) of Vibrio species isolated from inland saline shrimp culture farms. Out of 200 Vibrio isolates obtained from 166 shrimp/water samples, 105 isolates were identified as V. parahaemolyticus and 31 isolates were identified as V. alginolyticus and V. cholerae, respectively. During PCR screening of virulence-associated genes, the presence of the tlh gene was confirmed in 70 and 19 isolates of V. parahaemolyticus and V. alginolyticus, respectively. Besides, 10 isolates of V. parahaemolyticus were also found positive for trh gene. During antibiotic susceptibility testing (AST), very high resistance to cefotaxime (93.0%), amoxiclav (90.3%), ampicillin (88.2%), and ceftazidime (73.7%) was observed in all Vibrio species. Multiple antibiotic resistance (MAR) index values of Vibrio isolates ranged from 0.00 to 0.75, with 90.1% of isolates showing resistance to ≥ 3 antibiotics. The AST and MAR patterns did not significantly vary sample-wise or Vibrio species-wise. During the minimum inhibitory concentration (MIC) testing of various antibiotics against Vibrio isolates, the highest MIC values were recorded for amoxiclav followed by kanamycin. These results indicated that multi-drug resistant Vibrio species could act as the reservoirs of antibiotic resistance genes in the shrimp culture environment. The limited host range of 12 previously isolated V. parahaemolyticus phages against V. parahaemolyticus isolates from this study indicated that multiple strains of V. parahaemolyticus were prevalent in inland saline shrimp culture farms. The findings of the current study emphasize that routine monitoring of emerging aquaculture areas is critical for AMR pathogen risk assessment.

Deterministic Effect of pH on Shaping Soil Resistome Revealed by Metagenomic Analysis.

Soil is recognized as the major reservoir of antibiotic resistance genes (ARGs), harboring the most diverse naturally evolved ARGs on the planet. Multidrug resistance genes are a class of ARGs, and their high prevalence in natural soil ecosystems has recently raised concerns. Since most of these genes express proton motive force (PMF) driven efflux pumps, studying whether soil pH is a determinant for the selection of multidrug efflux pump genes and thus shaping the soil resistome are of great interest. In this study, we collected 108 soils with pH values ranging from 4.37 to 9.69 from multiple ecosystems and profiled the composition of ARGs for metagenomes and metagenome-assembled genomes. We observed the multidrug efflux pump genes enriched in the acidic soil resistome, and their abundances have significant soil pH dependence. This reflects the benefits of high soil proton activity on the multidrug efflux pump genes, especially for the PMF-driven inner membrane transferase. In addition, we preliminary indicate the putative microbial participants in pH shaping the soil resistome by applying ecological analyzing tools such as stepwise regression and random forest model fitting. The decisive influence of proton activity on shaping the resistome is more impactful than any other examined factors, and as the consequence, we revisited the influence of edaphic factors on the soil resistome; i.e., the deterministic selection of resistance mechanisms by edaphic factors could lead to the bottom-up shaping of the ARG composition. Such natural developing mechanisms of the resistome are herein suggested to be considered in assessing human-driven ARG transmissions.

Unveiling the Antibiotic Susceptibility and Antimicrobial Potential of Bacteria from Human Breast Milk of Pakistani Women: An Exploratory Study.

Human life quality and expectancy have increased dramatically over the past 5 decades because of improvements in nutrition and antibiotic's usage fighting against infectious diseases. Yet, it was soon revealed that the microbes adapted to develop resistance to any of the drugs that were used. Recently, there is great concern that commensal bacteria from food and the gastrointestinal tract of humans and animals could act as a reservoir for antibiotic resistance genes. Methodology. This study was intended for evaluating the phenotypic antibiotic resistance/sensitivity profiles of probiotic bacteria from human breast milk and evaluating the inhibitory effect of the probiotic bacteria against both Gram-negative and Gram-positive bacteria. The results point out that some of the isolated bacteria were resistant to diverse antibiotics including gentamycin, imipenem, trimethoprim sulfamethoxazole, and nalidixic acid. Susceptibility profile to certain antibiotics like vancomycin, tetracycline, ofloxacin, chloramphenicol, streptomycin, rifampicin, and bacitracin was also observed. The antimicrobial qualities of cell-free supernatants of some probiotic bacteria inhibited the growth of indicator bacteria. Also, antimicrobial properties of the probiotic bacteria from the present study attributed to the production of organic acid, bacterial adhesion to hydrocarbons (BATH), salt aggregation, coaggregation with pathogens, and bacteriocin production. Some isolated bacteria from human milk displayed higher hydrophobicity in addition to intrinsic probiotic properties like Gram-positive classification, catalase-negative activity, resistance to gastric juice (pH 2), and bile salt (0.3%) concentration. This study has added to the data of the antibiotic and antimicrobial activity of some probiotic bacteria from some samples of Pakistani women breast milk. Probiotic bacteria are usually considered to decrease gastrointestinal tract diseases by adhering to the gut epithelial and reducing population of pathogens and in the case of Streptococcus lactarius MB622 and Streptococcus salivarius MB620 in terms of hydrophobicity and exclusion of indicator pathogenic strains.

Effect of Protists on Horizontal Transfer of Antimicrobial Resistance Genes in Water Environment

There is much evidence that the environment is a reservoir of antibiotic resistance genes (ARGs). For ARG latency and stability, environmental factors should play a role since ARGs are transferred among bacterial species, which results in their evolution and dissemination. Recent findings have expanded the novel mechanisms of horizontal gene transfer (HGT) beyond classically accepted HGT mechanisms such as conjugation, transformation, and transduction. In these HGT processes, environmental factors directly or indirectly affect the transfer rate and mechanism. Here, we focus on the effect of protists that affect HGT, because HGT is regulated among the microbial community, in which protist grazing is one factor that enhances HGT. Protist grazing eliminates planktonic bacteria. However, it is reported that environmental DNA release and HGT in protist vacuoles are increased by the grazing, although the effect is not uniform and depends on the environmental conditions. Biofilms protect bacteria and accelerate HGT. In these processes, quorum sensing and organic matter contribute to HGT. Although HGT occurs between bacterial cells, other microorganisms such as protists should be recognized as factors relating to HGT. We should pay attention to microbial ecosystem when consider ARG risk from water environment in terms of “one health” aspect.