The emergence of antimicrobial resistance in environmental strains of the Bacteroides fragilis group

Niestępski, Sebastian; Harnisz, Monika; Korzeniewska, Ewa; Aguilera‐Arreola, Ma. Guadalupe; Contreras-Rodríguez, Araceli; Filipkowska, Zofia; Osińska, Adriana

doi:10.1016/j.envint.2018.12.056

Cited by 52 publications

(40 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Recent investigations have shown gut Cyanobacteria to be very conserved, but their 16S rRNA phylogenetic tree was different from the photosynthetic ones; this has led to the designation of a new putative class called Melainabacteria [47], whose members were able to ferment a variety of sugars in the gut [48]. Similar to other previous studies [21,39] neither Kraken 2 nor MG-RAST identified Melainabacteria in the samples, showing the need for further research to distinguish their role in the gut of cattle.…”

Section: Comparisons Of Microbial Composition and Abundancementioning

confidence: 69%

“…A typical characteristic of ecological Bacteroidetes is their capacity to break down complex glycans, for example, agarose, alginate, cellulose, chitin, and hemicellulose [38]. It has also been observed that Bacteroidetes are involved in the spread of antimicrobial resistance genes through horizontal gene transfer [39]. Firmicutes were the second most abundant taxonomic group.…”

Section: Comparisons Of Microbial Composition and Abundancementioning

confidence: 99%

See 1 more Smart Citation

A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle

Kibegwa

Bett

Gachuiri

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters. Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively. 933 species were detected by the two algorithms. Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample. This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. However, Kraken 2 generated a more accurate taxonomic identification given the higher number of “Unclassified” reads in MG-RAST. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.

show abstract

Section: Comparisons Of Microbial Composition and Abundancementioning

confidence: 69%

Section: Comparisons Of Microbial Composition and Abundancementioning

confidence: 99%

A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle

Kibegwa

Bett

Gachuiri

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

show abstract

“…Another study demonstrated the detection of MDR E. coli strains associated with neonatal meningitis, intestinal and extraintestinal serotypes in final effluents of WWTPs [52]. High levels of resistance were identified in BFG bacteria isolated from WWTPs compared to those that have been recovered from human faeces investigated [40]. Importantly, there is growing evidence that wastewater treatment does not have a profound impact on eliminating the ARGs present in hospital wastewater, with no significant difference in ARG abundance between influent and effluent hospital wastewater samples [54].…”

Section: Impact Of Wastewater Treatment Processes On Amr Disseminationmentioning

confidence: 99%

“…Generally, high levels of ARB, including MDR strains and diverse ARGs, have been detected in influent wastewater (untreated) collected from various sources, particularly low-income settings [41,44]; hospitals [36,39,40,42,46,47] and pharmaceutical waste [49,60]. However, many studies demonstrated that effluent samples collected from urban, hospital and pharmaceutical-treated wastewater still contain elevated levels of diverse ARGs, ARB and antimicrobial drugs [49,58,60,63].…”

Section: Selective Pressure Within Wastewater Environments Promote Thmentioning

confidence: 99%

See 1 more Smart Citation

The Contribution of Wastewater to the Transmission of Antimicrobial Resistance in the Environment: Implications of Mass Gathering Settings

et al. 2020

View full text Add to dashboard Cite

Antimicrobial resistance (AMR) is the major issue posing a serious global health threat. Low- and middle-income countries are likely to be the most affected, both in terms of impact on public health and economic burden. Recent studies highlighted the role of resistance networks on the transmission of AMR organisms, with this network being driven by complex interactions between clinical (e.g., human health, animal husbandry and veterinary medicine) and other components, including environmental factors (e.g., persistence of AMR in wastewater). Many studies have highlighted the role of wastewater as a significant environmental reservoir of AMR as it represents an ideal environment for AMR bacteria (ARB) and antimicrobial resistant genes (ARGs) to persist. Although the treatment process can help in removing or reducing the ARB load, it has limited impact on ARGs. ARGs are not degradable; therefore, they can be spread among microbial communities in the environment through horizontal gene transfer, which is the main resistance mechanism in most Gram-negative bacteria. Here we analysed the recent literature to highlight the contribution of wastewater to the emergence, persistence and transmission of AMR under different settings, particularly those associated with mass gathering events (e.g., Hajj and Kumbh Mela).

show abstract

Effects of sulfamethoxazole and copper on the natural microbial community from a fertilized soil

Narciso,

Grenni,

Spataro

et al. 2024

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Cattle manure or its digestate, which often contains antibiotic residues, can be used as an organic fertilizer and copper (Cu) as a fungicide in agriculture. Consequently, both antibiotics and Cu are considered soil contaminants. In this work, microcosms were performed with soil amended with either manure or digestate with Cu and an antibiotic (sulfamethoxazole, SMX) copresence and the planting of Lactuca sativa. After the addition of the organic amendments, a prompt increase in the microbial activity and at the same time of the sul1 and intI1 genes was observed, although ARGs generally decreased over time. In the amended and spiked microcosms, the microbial community was able to remove more than 99% of SMX in 36 days and the antibiotic did not bioaccumulate in the lettuce. Interestingly, where Cu and SMX were co-present, ARGs (particularly sul2) increased, showing how copper had a strong effect on resistance persistence in the soil. Copper also had a detrimental effect on the plant-microbiome system, affecting plant biomass and microbial activity in all conditions except in a digestate presence. When adding digestate microbial activity, biodiversity and lettuce biomass increased, with or without copper present. Not only did the microbial community favour plant growth, but lettuce also positively influenced its composition by increasing bacterial diversity and classes (e.g., Alphaproteobacteria) and genera (e.g., Bacillus), thus indicating a good-quality soil. Key points• Cattle digestate promoted the highest microbial activity, diversity, and plant growth • Cattle digestate counteracted detrimental contaminant effects • Cu presence promoted antibiotic cross-resistance in soil

show abstract

The emergence of antimicrobial resistance in environmental strains of the Bacteroides fragilis group

Cited by 52 publications

References 53 publications

A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle

A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle

The Contribution of Wastewater to the Transmission of Antimicrobial Resistance in the Environment: Implications of Mass Gathering Settings

Effects of sulfamethoxazole and copper on the natural microbial community from a fertilized soil

Contact Info

Product

Resources

About