Biology subjects

Navab-Daneshmand, T.

Publications and source records attributed to Navab-Daneshmand, T..

3 recordsLinked to original sources

bioRxiv2024

Impact of biosolids amendment on the soil resistome and microbiome - a greenhouse study

The spread of antibiotic resistance poses a significant challenge to public health worldwide. Wastewater treatment utilities are reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). This study investigates the impact of biosolids amendment on the soil microbiome, resistome, virulence factors, and ESKAPE pathogens during carrot cultivation in a replicated greenhouse study. Metagenomic sequencing revealed that biosolids amendment increased the richness of microbial genera, ARGs, and virulence factors in soil. The relative abundance of ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter spp., was notably higher in biosolids-amended soils. These pathogens persisted throughout the 11-week cultivation period, raising concerns about the potential for horizontal gene transfer and the spread of antibiotic resistance. The study also identified significant co-occurrences between microbial genera and ARGs, which can suggest the possibility of the microbial taxa harboring the co-occurring ARGs. These findings highlight the importance of continued research and monitoring to ensure the safe and effective use of biosolids in agriculture.

molecular biology↗

bioRxiv2024

Resolved Genomes of Wastewater ESBL-Producing Escherichia coli and Metagenomic Analysis of Source Wastewater Samples

Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli pose a serious threat to human health because of their resistance to the most commonly prescribed antibiotics: penicillins and cephalosporins. In this study, we provide a genomic and metagenomic context for the determinant ESBL genes of E. coli isolated from various wastewater treatment utilities in Oregon, USA. Class A beta-lactamase genes on chromosomes (blaCTX-M, blaTEM) were clustered with antibiotic resistance genes associated with other classes of antibiotics (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such as blaCTX-M, blaTEM, and blaSHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One novel IncF plasmid (pSHV2A_ESBLF) was identified in which carried a multi-drug resistance genotype (blaSHV-2A, aadA22, aac(3), aph(6), tetA, and sul1) in addition to a mer (mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of the E. coli-originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in the E. coli genomes were below the detection limits. Other ESBL-associated genes (i.e., blaOXA.11, blaFOX.7, and blaGES.17) were identified in the wastewater samples and their occurrences were correlated with the core microbial genera (e.g., Paraprevotella). In both the E. coli genomes and the wastewater samples, tetracycline, aminoglycoside, and beta-lactam resistance determinants frequently co-occurred. The unique combination of whole-genome and metagenomic analysis provides a holistic description of ESBL-producing organisms and genes in the Oregonian wastewater system.

microbiology↗

bioRxiv2021

Impact of pH and removed filtrate on E. coli regrowth and microbial community during storage of electro-dewatered biosolids

Residual biosolids can be land applied if they meet microbiological requirements at the time of application. Electro-dewatering technology is shown to reduce biosolids bacterial counts to detection limits with little potential for bacterial regrowth during incubations. Here, we investigated the impacts on Escherichia coli regrowth and microbial communities of biosolids pH, removed nutrients via the filtrate, and inhibitory compounds produced in electro-dewatered biosolids. Findings suggest pH as the primary mechanism impacting E. coli regrowth in electro-dewatered biosolids. Propidium monoazide treatments were effective at removing DNA from dead cells, based on the removal of obligate anaerobes observed after anaerobic incubation. Analyses of high throughput sequenced data showed lower alpha-diversities associated with electro-dewatering treatment and incubation time. Moreover, biosolids pH and incubation period were the main factors contributing to the variations in microbial community compositions after incubation. Results highlight the role of electro-dewatered biosolids low pH on inhibiting the regrowth of culturable bacteria as well as reducing the microbial community variance.

microbiology↗