Biology subjects

Bagra, K.

Publications and source records attributed to Bagra, K..

4 recordsLinked to original sources

bioRxiv2024

Drivers of antibiotic resistance in two monsoon-impacted Indian urban rivers receiving untreated wastewater

Rivers in India receive 78.7% of untreated sewage from cities and towns making it a potential global "hotspot" for AMR. During monsoon, flooding is common in most Indian cities bringing in fecal contamination in storm runoff. Identifying the major driving factors contributing to the elevated levels of AMR in these rivers is essential to combat AMR proliferation. Determining whether the introduction of ARBs and ARGs through fecal pollution or subsequent (co-) selection for ARGs through chemical pollutants is responsible for the rise and spread of AMR is important in mitigation efforts. To achieve this, we targeted two rivers in northern India which received untreated wastewater and assessed the level of two fecal indicators (E. coli and intI1) and wastewater-associated ARGs (ermF, sul1, sul2, and tetW) along with heavy metals (Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn). Water and sediment samples were collected in triplicates at 5-6 locations for each river. Consequently, to evaluate how seasonality affects the ARG levels as well as their drivers in these heavily polluted rivers, sampling campaigns were carried out during three seasons: in summer (pre-monsoon), during monsoon, and post-monsoon in winter. We here demonstrate that the main source for the river resistome in the Bindal and Rispana is the constant inflow of untreated wastewater throughout the year and not the co-selection of ARGs due to the presence of heavy metals. This may be true for many Indian rivers that receive untreated or partially treated wastewater. The rainfall adds to the ARG abundance of the river instead of diluting it. MGE intI1 is more reliable than E. coli as an indicator for fecal pollution and horizontal gene transfer. Heavy metals, despite being present in the river in higher concentrations than the MCSC, no evidence for co-selection was observed.

molecular biology↗

bioRxiv2023

Tradeoffs of increasing temperatures for the spread of antimicrobial resistance in river biofilms

River microbial communities regularly act as the first defense barrier against the spread of antimicrobial resistance genes (ARG) that enter environmental microbiomes through wastewaters. However, how the invasion dynamics of wastewater-born ARGs into river biofilm communities will shift due to increasing average and peak temperatures worldwide through climate change remains unknown. Here we aimed at elucidating the effects of increasing temperatures on both, the natural river biofilm resistome, as well as the river biofilms invadability by foreign, wastewater-born ARGs. To achieve this, natural biofilms were grown in a pristine German river and transferred to artificial laboratory recirculation flume systems at three different temperatures (20{degrees}C, 25{degrees}C, 30{degrees}C). Already after one week of acclimatization to the temperatures, significant increases in the abundance of most naturally occurring ARGs were detected in the biofilms exposed to the highest temperature. Thereafter, biofilms were exposed to a single pulse of wastewater and the invasion dynamics of wastewater-born ARGs were analyzed over a period of two weeks. While initially after one day ARGs were able to invade all biofilms successfully and in equal proportions, the foreign invading ARGs were lost at a far increased rate at 30{degrees}C over time. ARG levels dropped to the initial natural levels at 30{degrees}C after 14 days. Contrary at the lower temperatures ARGs remained far elevated and certain ARGs were able to establish themselves in the biofilms. Overall, we here demonstrate tradeoffs of increasing temperature between increases in naturally occurring and faster loss dynamics of invading ARGs.

microbiology↗

bioRxiv2022

Exposure to environmental stress decreases the resistance of river microbial communities towards invasion by antimicrobial resistant bacteria

Environmental microbiomes are constantly exposed to invasion events through foreign, antibiotic resistant bacteria that were enriched in the anthropic sphere. However, the biotic and abiotic factors, as well as the natural barriers that determine the invasion success of these invader bacteria into the environmental microbiomes are poorly understood. A great example of such invasion events are river microbial communities constantly exposed to resistant bacteria originating from wastewater effluents. Here, we aim at gaining comprehensive insights into the key factors that determine their invasion success with a particular focus on the effects of environmental stressors, regularly co-released in wastewater effluents. Understanding invasion dynamics of resistant bacteria is crucial for limiting the environmental spread of antibiotic resistance. To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (E. coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress c the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.

microbiology↗

bioRxiv2022

Quantification of the mobility potential of antibiotic resistance genes through multiplexed ddPCR linkage analysis

Antibiotic resistance genes (ARGs) are widely disseminated within microbiomes of the human, animal, and environmental spheres. There is a clear need for global monitoring and risk assessment initiatives to evaluate the risks of ARGs towards human health. Therefore, not only ARG abundances within a given environment, but also their mobility, hence their ability to spread to human pathogenic bacteria needs to be quantified. Consequently, methods to accurately quantify the linkage of ARGs with mobile genetic elements are urgently needed. We developed a novel, sequencing-independent method for assessing ARG mobility by combining multiplexed droplet digital PCR (ddPCR) on DNA sheared into short fragments with statistical analysis. This allows quantifying the physical linkage between ARGs and mobile genetic elements, here demonstrated for the sulfonamide ARG sul1 and the Class1 integron integrase gene intI1. The methods efficiency is demonstrated using mixtures of model DNA fragments with either linked and unlinked target genes: Linkage of the two target genes can be accurately quantified based on high correlation coefficients between observed and expected values (R2) as well as low mean absolute errors (MAE) for both target genes, sul1 (R2=0.9997, MAE=0.71%, n=24) and intI1 (R2=0.9991, MAE=1.14%, n=24). Furthermore, we demonstrate that the chosen fragmentation length of DNA during shearing allows adjusting the rate of false positives and false negative detection of linkage. The applicability of the developed method for environmental samples is further demonstrated by assessing the mobility of sul1 across a wastewater treatment plant. The presented method allows rapidly obtaining reliable results within hours. It is labor- and costefficient and does not rely on sequencing technologies. Furthermore, it has a high potential to be scaled up to multiple targets. Consequently, it merits consideration to be included within global AMR surveillance initiatives for assessing ARG mobility. Author AbstractAntibiotic resistance represents a major problem in treating bacterial infections and endangers public health. Antibiotic resistant genes (ARGs) can spread among microbes in humans, animals, and the environment, thanks to mobile genetic elements. These are genetic structures involved in the mobility of genetic information and hence microbial traits. Methods that allow simultaneously quantifying the abundance of ARGs together with their association/linkage with mobile genetic elements are fundamental for assessing the risk they pose to human health, as mobility increases their likelihood to spread to human pathogens. Here we developed a novel method that allows to quantify the abundance and the linkage between ARGs and mobile genetic elements. The method relies on droplet digital PCR (ddPCR) technology performed on fragmented environmental DNA (of a chosen size), combined with statistical analysis. We found that the method accurately quantifies the linkage between the two targets in model and environmental DNA. The method is delivering rapid, labor- and cost-efficient results as it does not rely on technology that require prior bioinformatics knowledge and can be included in future monitoring frameworks.

microbiology↗