Antimicrobial resistance of Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp. isolated from the feces of giant panda

Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability

BACKGROUND

One of the main issues facing public health with microbial infections is antibiotic resistance. Nanoparticles (NPs) are among the best alternatives to overcome this issue. Silver nanoparticle (AgNPs) preparations are widely applied to treat multidrug-resistant pathogens. Therefore, there is an urgent need for greater knowledge regarding the effects of improper and excessive use of these medications. The current study describes the consequences of long-term exposure to sub-lethal concentrations of AgNPs on the bacterial sensitivity to NPs and the reflection of this change on the bacterial genome.

RESULTS

Chemical methods have been used to prepare AgNPs and gamma irradiation has been utilized to produce more stable AgNPs. Different techniques were used to characterize and identify the prepared AgNPs including UV-visible spectrophotometer, Fourier Transform Infrared (FT-IR), Dynamic light scattering (DLS), and zeta potential. Transmission electron microscope (TEM) and Scanning electron microscope (SEM) showed 50-100 nm spherical-shaped AgNPs. Eleven gram-negative and gram-positive bacterial isolates were collected from different wound infections. The minimum inhibitory concentrations (MICs) of AgNPs against the tested isolates were evaluated using the agar dilution method. This was followed by the induction of bacterial resistance to AgNPs using increasing concentrations of AgNPs. All isolates changed their susceptibility level to become resistant to high concentrations of AgNPs upon recultivation at increasing concentrations of AgNPs. Whole genome sequencing (WGS) was performed on selected susceptible isolates of gram-positive Staphylococcus lentus (St.L.1), gram-negative Klebsiella pneumonia (KP.1), and their resistant isolates St.L_R.Ag and KP_R.Ag to detect the genomic changes and mutations.

CONCLUSIONS

For the detection of single-nucleotide polymorphisms (SNPs) and the identification of all variants (SNPs, insertions, and deletions) in our isolates, the Variation Analysis Service tool available in the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) was used. Compared to the susceptible isolates, the AgNPs-resistant isolates St.L_R.Ag and KP_R.Ag had unique mutations in specific efflux pump systems, stress response, outer membrane proteins, and permeases. These findings might help to explain how single-nucleotide variants contribute to AgNPs resistance. Consequently, strict regulations and rules regarding the use and disposal of nano waste worldwide, strict knowledge of microbe-nanoparticle interaction, and the regulated disposal of NPs are required to prevent pathogens from developing nanoparticle resistance.

Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions

Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.

Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

A comprehensive analysis of antibiotic resistance genes in the giant panda gut

In this study, we have successfully constructed a comprehensive database of metagenome-assembled genomes (MAGs) pertaining to the gut microbiota of the giant panda. Through our analysis, we have identified significant reservoirs of antibiotic resistance genes (ARGs), namely Escherichia coli, Citrobacter portucalensis, and Klebsiella pneumoniae. Furthermore, we have elucidated the primary contributors to ARGs, including Streptococcus alactolyticus and Clostridium SGBP116, in both captive and wild pandas. Additionally, our findings have demonstrated a higher prevalence of ARGs in the metagenome, with notable expression of the RPOB2 gene in S. alactolyticus. Crucially, 1217 ARGs shared homology with human gut ARGs, underscoring the interaction relationship between pandas and human microbiomes. These findings are instrumental in understanding the antibiotic resistance landscape in the giant panda's gut, providing a framework for developing strategies to combat antibiotic resistance and safeguard the health of this endangered species.

The Impact of Bamboo Consumption on the Spread of Antibiotic Resistance Genes in Giant Pandas

The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.

The distribution variation of pathogens and virulence factors in different geographical populations of giant pandas

Intestinal diseases caused by opportunistic pathogens seriously threaten the health and survival of giant pandas. However, our understanding of gut pathogens in different populations of giant pandas, especially in the wild populations, is still limited. Here, we conducted a study based on 52 giant panda metagenomes to investigate the composition and distribution of gut pathogens and virulence factors (VFs) in five geographic populations (captive: GPCD and GPYA; wild: GPQIN, GPQIO, and GPXXL). The results of the beta-diversity analyzes revealed a close relationship and high similarity in pathogen and VF compositions within the two captive groups. Among all groups, Proteobacteria, Firmicutes, and Bacteroidetes emerged as the top three abundant phyla. By using the linear discriminant analysis effect size method, we identified pathogenic bacteria unique to different populations, such as Klebsiella in GPCD, Salmonella in GPYA, Hafnia in GPQIO, Pedobacter in GPXXL, and Lactococcus in GPQIN. In addition, we identified 12 VFs that play a role in the intestinal diseases of giant pandas, including flagella, CsrA, enterobactin, type IV pili, alginate, AcrAB, capsule, T6SS, urease, type 1 fimbriae, polar flagella, allantoin utilization, and ClpP. These VFs influence pathogen motility, adhesion, iron uptake, acid resistance, and protein regulation, thereby contributing to pathogen infection and pathogenicity. Notably, we also found a difference in virulence of Pseudomonas aeruginosa between GPQIN and non-GPQIN wild populations, in which the relative abundance of VFs (0.42%) of P. aeruginosa was the lowest in GPQIN and the highest in non-GPQIN wild populations (GPXXL: 23.55% and GPQIO: 10.47%). In addition to enhancing our understanding of gut pathogens and VFs in different geographic populations of giant pandas, the results of this study provide a specific theoretical basis and data support for the development of effective conservation measures for giant pandas.

Complete genome sequence of a blaNDM-5-producing Escherichia coli DC71 assigned as ST410-O8:H9 and recovered from a captive giant panda (Ailuropoda melanoleuca) in China

OBJECTIVES

In this study, we report the complete genome sequence of a multidrug-resistant Escherichia coli strain recovered from a fecal sample from a captive giant panda in China.

METHODS

Antimicrobial susceptibility testing was performed. Genomic DNA from E. coli DC71 was sequenced using a Nanopore PromethION sequencer instrument (Oxford Nanopore Technologies, UK) and MGI High-throughput Sequencing MGISEQ-2000 platforms. The clean reads were de novo assembled using SPAdes v3.11. The complete genome was annotated and analyzed using multilocus sequence typing, serotyping, plasmid replicons, fimH typing, chromosomal point mutations, acquired antimicrobial resistance, and virulence genes with web tools available at the Center for Genomic Epidemiology.

RESULTS

The complete genome, 4 991 906 bp in length and comprising 4677 protein-coding sequences, was generated. In silico analysis revealed that E. coli DC71 belonged to the ST410-O8:H9 subclone. A carbapenem resistance gene, bla_NDM-5, was located on the pDC71-2 plasmid, coproducing bla_TEM-1. Many other resistance determinants encoded by chromosomes and pDC71-3 were found. The virulence related genes carried by chromosomes were mostly related to enterohemorrhagic E. coli (EHEC) O157:H7.

CONCLUSIONS

To our knowledge, this is the first complete genome of an E. coli ST410-O8:H9 strain recovered from captive giant panda in China. This multidrug-resistant E. coli subclone may pose potential risks to human and animal health. The genome sequence will be helpful to understand the genomic structure, its diversity, and the molecular mechanism allowing bacteria to disseminate the resistance gene.