The novel macrolide resistance genes mef(F) and msr(G) are located on a plasmid in Macrococcus canis and a transposon in Macrococcus caseolyticus

Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis

The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.

Efficacy of new generation biosorbents for the sustainable treatment of antibiotic residues and antibiotic resistance genes from polluted waste effluent

Antimicrobials are frequently used in both humans and animals for the treatment of bacterially-generated illnesses. Antibiotic usage has increased for more than 40% from last 15 years globally per day in both human populations and farm animals leading to the large-scale discharge of antibiotic residues into wastewater. Most antibiotics end up in sewer systems, either directly from industry or healthcare systems, or indirectly from humans and animals after being partially metabolized or broken down following consumption. To prevent additional antibiotic compound pollution, which eventually impacts on the spread of antibiotic resistance, it is crucial to remove antibiotic residues from wastewater. Antibiotic accumulation and antibiotic resistance genes cannot be effectively and efficiently eliminated by conventional sewage treatment plants. Because of their high energy requirements and operating costs, many of the available technologies are not feasible. However, the biosorption method, which uses low-cost biomass as the biosorbent, is an alternative technique to potentially address these problems. An extensive literature survey focusing on developments in the field was conducted using English language electronic databases, such as PubMed, Google Scholar, Pubag, Google books, and ResearchGate, to understand the relative value of the available antibiotic removal methods. The predominant techniques for eliminating antibiotic residues from wastewater were categorized and defined by example. The approaches were contrasted, and the benefits and drawbacks were highlighted. Additionally, we included a few antibiotics whose removal from aquatic environments has been the subject of extensive research. Lastly, a few representative publications were identified that provide specific information on the removal rates attained by each technique. This review provides evidence that biosorption of antibiotic residues from biological waste using natural biosorbent materials is an affordable and effective technique for eliminating antibiotic residues from wastewater.

The emergence of novel macrolide resistance island in Macrococcus caseolyticus and Staphylococcus aureus of food origin

Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus caseolyticus (M. caseolyticus) is a member of the Staphylococcaceae family which plays a vital role in fermented products and disease causation in animals. In our previous study, several Staphylococcus aureus antibiotic-resistant island msr (SaRI_msr) were found in multidrug-resistant S. aureus. In this study, novel SaRI_msr, SaRI_msr-III emerged from S. aureus. Another novel SaRI_msr-like further emerged in M. caseolyticus from food. These isolates' prevalence and genetic environment were investigated and characterized to understand the distribution and transmission of these novel SaRI_msr strains. All SaRI_msr-positive S. aureus isolates exhibited a multidrug resistance (MDR) phenotype, within which a series of antimicrobial resistance genes (ARGs) and virulence factor genes (VFs) were identified. In addition, three SaRI_msr types, SaRI_msr-I (15.1 kb), SaRI_msr-II (16-17 kb), and SaRI_msr-III (18 kb) carrying mef(D)-msr(F), were identified in these isolates' chromosomes. SaRI_msr-(I-III) contains a site-specific integrase gene int and operon mef(D)-msr(F). SaRI_msr-III has an additional orf3-orf4-IS30 arrangement downstream of mef(D) and msr(F). Moreover, the SaRI_msr-like and macrolide-resistant transposon Tn6776 forming a novel mosaic structure coexisted in one M. caseolyticus isolate. Within this mosaic structure, the macrolide-resistant genes mef(D)-msr(F) were absent in SaRI_msr-like, whereas an operon, mef(F)-msr(G), was identified in Tn6776. The SaRI_msr-(I-III) and SaRI_msr-like structure were inserted into the rpsI gene encoding the 30S ribosomal protein S9 in the chromosome. Excision and cyclisation of SaRI_msr-III, SaRI_msr-like, operon mef(D)-msr(F), and orf3-orf4-IS30 arrangements were confirmed using two-step PCR. This study is the first to report MDR S. aureus harbouring novel SaRI_msr-III and M. caseolyticus containing novel mosaic structures isolated from retail foods. Similar SaRI_msr-type resistant islands' occurrence and propagation in Staphylococcaceae species require continuous monitoring and investigation.

Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome

Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.