Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India

Chakraborty, Jaya; Sapkale, Vibhavari; Rajput, Vinay; Shah, Manan; Kamble, Sanjay P.; Dharne, Mahesh

doi:10.1016/j.ecoenv.2020.110443

Cited by 26 publications

(15 citation statements)

References 64 publications

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“…In the present samples, a total of 402 ARGs were identified, which was significantly less than the 819 ARGs found in sediments near coral reefs of Xisha Island [49], and the 2354 ARGs from the Gulf of Khambat, India [50]. On the other hand, a study of the Lonar soda lake in India reported a mere 26 ARGs [51] in the surface sediments. The variation in ARG abundance can be related to the type and scale of anthropogenic pollution, as it can be a factor enhancing and disseminating ARGs in the surface sediments [52].…”

Section: Discussioncontrasting

confidence: 67%

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

et al. 2022

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Marine sediments are a sink for antibiotic resistance genes (ARGs) and antibiotic-resistant microbes (ARMs). Wastewater discharge into the aquatic environment is the dominant pathway for pharmaceuticals reaching aquatic organisms. Hence, the characterization of ARGs is a priority research area. This baseline study reports the presence of ARGs in 12 coastal sediment samples covering the urban coastline of Kuwait through whole-genome metagenomic sequencing. The presence of 402 antibiotic resistance genes (ARGs) were recorded in these samples; the most prevalent were patA, adeF, ErmE, ErmF, TaeA, tetX, mphD, bcrC, srmB, mtrD, baeS, Erm30, vanTE, VIM-7, AcrF, ANT4-1a, tet33, adeB, efmA, and rpsL, which showed resistance against 34 drug classes. Maximum resistance was detected against the beta-lactams (cephalosporins and penam), and 46% of genes originated from the phylum Proteobacteria. Low abundances of ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sps., and Escherichia coli) were also recorded. Approximately 42% of ARGs exhibited multiple drug resistance. All the ARGs exhibited spatial variations. The major mode of action was antibiotic efflux, followed by antibiotic inactivation, antibiotic target alteration, antibiotic target protection, and antibiotic target replacement. Our findings supported the occurrence of ARGs in coastal marine sediments and the possibility of their dissemination to surrounding ecosystems.

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Section: Discussioncontrasting

confidence: 67%

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

et al. 2022

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“…As for archaea, Euryarchaeota was the most abundant in the Bamucuo, which is similar to the observation in Lonar soda Lake in India (36), suggesting that the phylum Euryarchaeota could adapt to the most extreme environmental. However, Thaumarchaeota and Crenarchaeota were only identified from the soil sample in Bamucuo, indicating that there were differences between the soil and water microbial communities.…”

Section: Discussionsupporting

confidence: 83%

“…8) in the soil and water microbial communities in Bamucuo. However, studies in other regions reported that abundant ARGs have been found (36, 62). Therefore, we inferred that Bamucuo has not yet been extensively contaminated by the ARGs.…”

Section: Discussionmentioning

confidence: 92%

Metagenomics revealing molecular profiling of microbial community structure and metabolic capacity in Bamucuo, Tibet

Peng¹,

Wei²,

Sun

et al. 2022

Preprint

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We performed a survey of the microorganisms in Bamucuo, Tibet, resulting in 160,212 (soil) and 135,994 (water) contigs by shotgun metagenomic methods. We discovered 74 new bacterial species and reconstructed their draft genomes, which were obtained from the 75 reconstructed almost complete metagenomic assembly genomes (MAG) in the soil and water samples. Proteobacteria and Actinobacteria were found to be the most dominant bacterial phyla, while Euryarchaeota was the most dominant archaeal phylum. To our surprise, Pandoravirus salinus was found in the soil microbial community. We concluded that the microorganisms in Bamucuo fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway.

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“…Potential pathogenic bacteria and ARGs in hospital wastewater pose a considerable threat to public health. Metagenomic analysis revealed the complexity of the microbial communities and provided a functional profile of ARGs and patterns of co-occurrence between ARGs and potential host bacteria ( Chakraborty et al, 2020 ). Our study identified the distribution and prevalence of bacterial community and ARGs in the Eye and General hospital wastewater and attempted to evaluate the effects of the activated sludge treatment process and the direct chlorination disinfection treatment process in hospital wastewater.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic Analysis Reveals Changes in Bacterial Communities and Antibiotic Resistance Genes in an Eye Specialty Hospital and a General Hospital Before and After Wastewater Treatment

Cai

et al. 2022

Front. Microbiol.

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The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in hospital wastewater poses a great threat to public health, and wastewater treatment plants (WWTPs) play an important role in reducing the levels of ARB and ARGs. In this study, high-throughput metagenomic sequencing was used to analyze the bacterial community composition and ARGs in two hospitals exposed to different antibiotic use conditions (an eye specialty hospital and a general hospital) before and after wastewater treatment. The results showed that there were various potential pathogenic bacteria in the hospital wastewater, and the abundance and diversity of the influent ARGs in the general hospital were higher than those in the eye hospital. The influent of the eye hospital was mainly composed of Thauera and Pseudomonas, and sul1 (sulfonamide) was the most abundant ARG. The influent of the general hospital contained mainly Aeromonas and Acinetobacter, and tet39 (tetracycline) was the most abundant ARG. Furthermore, co-occurrence network analysis showed that the main bacteria carrying ARGs in hospital wastewater varied with hospital type; the same bacteria in wastewater from different hospitals could carry different ARGs, and the same ARG could also be carried by different bacteria. The changes in the bacterial community and ARG abundance in the effluent from the two hospitals showed that the activated sludge treatment and the direct chlorination disinfection can effectively remove some bacteria and ARGs in wastewater but have limitations. The species diversity increased significantly after the activated sludge treatment, while the direct chlorination disinfection did not increase the diversity. The activated sludge treatment has a better effect on the elimination of ARGs than the direct chlorination disinfection. In summary, we investigated the differences in bacterial communities and ARGs in wastewater from two hospitals exposed to different antibiotic usage conditions, evaluated the effects of different wastewater treatment methods on the bacterial communities and ARGs in hospital wastewater, and recommended appropriate methods for certain clinical environments.

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Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India

Cited by 26 publications

References 64 publications

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

Metagenomics revealing molecular profiling of microbial community structure and metabolic capacity in Bamucuo, Tibet

Metagenomic Analysis Reveals Changes in Bacterial Communities and Antibiotic Resistance Genes in an Eye Specialty Hospital and a General Hospital Before and After Wastewater Treatment

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