Biology subjects

Klumper, U.

Publications and source records attributed to Klumper, U..

5 recordsLinked to original sources

bioRxiv2025

Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol.

Antibiotic resistance poses a global public health threat. Cefiderocol, a recently introduced siderophore cephalosporin, employs a "Trojan Horse" mechanism by exploiting bacterial iron uptake systems for cell entry. Yet, resistant clinical isolates are already observed in clinics and resistance mechanisms are difficult to characterize. Here, we applied functional metagenomics to identify cefiderocol resistance genes. Functional metagenomic DNA libraries from diverse environmental samples collected across several countries were expressed in a cefiderocol-sensitive Escherichia coli host. This yielded four resistant clones with DNA originating from wastewater or freshwater DNA libraries. The identified antibiotic resistance genes (ARGs) causing an increase in cefiderocol minimum inhibitory concentrations encoded for beta-lactamases (VEB-3, OXA-372 homolog and YbxI homolog) and a partial penicillin binding protein homolog. Three of four shared closest homologs in pathogenic bacteria. One ARG was associated with a mobile genetic element and was broadly distributed across all wastewater samples from every country surveyed. This study underscores the critical importance of environmental surveillance for ARGs, particularly for novel agents like cefiderocol with limited understanding of resistance mechanisms.

microbiology↗

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↗

bioRxiv2022

The global groundwater resistome: core ARGs and their dynamics - an in silico re-analysis of publicly available groundwater metagenomes

Despite the importance of groundwater as a drinking water resource, currently, no comprehensive picture regarding the global levels of antibiotic resistance genes (ARGs) in groundwater environments exists. Moreover, the biotic and abiotic factors that shape the groundwater resistome on the global scale remain to be explored. Herein, we attempted to fill this knowledge gap through in silico re-analysis of publicly available global groundwater metagenomes. First, nine ARGs encoding resistance to aminoglycosides (aadA, aph(3), and ant(3)), sulfonamides (sul1 and sul2), {beta}-lactams (blaOXA and blaTEM), tetracyclines (tet(C)) and macrolides (msr(E)) were identified to constitute the core groundwater resistome with high detection and abundance levels. Second, the global drivers of groundwater resistome composition were identified by applying a structural equation model with mixed effects to disentangle the individual contributions of each abiotic and biotic factor. Most notably, global effects of the origin of groundwater samples on the resistome were detected with samples from high-income countries (HICs) constantly displaying lower ARG and mobile genetic element (MGE) abundances than those from low-and-middle-income countries (LMICs). While these effects were consistent across antibiotic classes, biotic factors such as interactions of the groundwater microbiome with fungal or bacterial natural producers of antibiotics, or the co-occurrence of ARGs on mobile genetic elements (MGEs) played significant roles in shaping abundance patterns of resistance towards individual antibiotic classes. Only few ARGs correlated to individual bacterial genera, with microbial community composition in general weakly associated with resistome composition. In conclusion, we provide a first global picture of the resistome of low-anthropogenic impacted groundwater environments and the underlying anthropogenic and biotic drivers shaping it, which can be used as a baseline in future surveillance of antibiotic resistance.

microbiology↗

bioRxiv2020

Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water.

In the present study, we investigated the impact of treated wastewater (TWW) irrigation on the prevalence of antibiotic resistance genes (ARGs) in subsoil pore-water, a so-far under-appreciated matrix. We hypothesized that TWW irrigation increases ARG prevalence in subsoil pore-water. This hypothesis was tested using a multiphase approach, which consisted of sampling percolated subsoil pore-water from lysimeter-wells of a real-scale TWW-irrigated field, operated for commercial farming practices, and controlled, laboratory mesocosms irrigated with freshwater or TWW. We monitored the abundance of six selected ARGs (sul1, blaOXA-58, tetM, qnrS, blaCTX-M-32 and blaTEM), the intI1 gene associated with mobile genetic elements and an indicator for anthropogenic pollution and bacterial abundance (16S rRNA gene) by qPCR. The bacterial load of subsoil pore water was independent of both, irrigation intensity in the field study and irrigation water type in the mesocosms. Among the tested genes in the field study, sul1 and intI1 exhibited constantly higher relative abundances. Their abundance was further positively correlated with increasing irrigation intensity. Controlled mesocosm experiments verified the observed field study results: the relative abundance of several genes, including sul1 and intI1, increased significantly when irrigating with TWW compared to freshwater irrigation. Overall, TWW irrigation promoted the spread of ARGs and intI1 in the subsoil pore-water, while the bacterial load was maintained. The combined results from the real-scale agricultural field and the controlled lab mesocosms indicate that the dissemination of ARGs in various subsurface environments needs to be taken into account during TWW irrigation scenarios. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/222497v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@19b130corg.highwire.dtl.DTLVardef@1ffb733org.highwire.dtl.DTLVardef@1548ff0org.highwire.dtl.DTLVardef@b60361_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITWW irrigation intensity and sul1 & intI1 abundance correlate in a real-scale field C_LIO_LIARGs & intI1 increase in subsoil pore-water during TWW irrigation in mesocosms C_LIO_LINo increase of ARGs & intI1 in freshwater irrigated mesocosms C_LIO_LITWW irrigation does not affect the bacterial load of subsoil pore-water C_LI

microbiology↗

bioRxiv2020

Impact of trimethoprim on the river microbiome and antimicrobial resistance.

Recent evidence suggests that anthropogenic activity can increase the levels of antimicrobial resistance (AMR) in the environment. Rivers and waterways are significant examples of environmental settings that have become repositories of antibiotics and antibiotic resistance genes (ARGs). Our recent study quantified drug concentrations in freshwater samples taken at a range of sites located on the Thames catchment; the highest levels of antibiotics and other drugs were recorded downstream of waste water treatment plants (WWTPs). One specific antibiotic: Trimethoprim (TMP) was shown at elevated concentrations reaching 2000ng/L at particular sites. We have also shown a correlative relationship between the residue of TMP and the prevalence of sulfonamide antibiotic resistance genes such as sul1. Despite this, there is still no evidence of a causative relationship between TMP concentrations and the prevalence of the ARGs at river sites. The aim of the current study was to conduct in-depth analysis using a combination of large metagenomic, geospatial and chemical datasets, in order to conduct a comparison between those sites with the highest TMP and lowest TMP levels across the Thames catchment. We aimed to establish the proximity of these sites to WWTPs, their population equivalence (PE) and land coverage. A secondary aim was to investigate seasonal variation in TMP and ARGs. Exploring these factors will help to decipher the clinical relevance of ARG accumulation at river sites. A significant correlation was shown between TMP levels at river sites and their distance downstream from a WWTP. Three sites located on the Rivers Cut and Ray showed significantly higher TMP concentrations in winter compared to summer. The population equivalence (PE) for sites with the highest TMP levels was significantly higher than those with the lowest levels. The land coverage of sites with the highest TMP levels was significantly more urban/suburban than sites with the lowest TMP concentrations, which were found to be significantly more arable. Five ARGs relevant to TMP and sulfonamides were identified across the Thames catchment. The most prevalent ARG was sul1, which was significantly more prevalent in winter compared to summer. By contrast sul2 was found to be significantly more prevalent in summer compared to winter at a site on the River Coln. The prevalence of the class 1 integron marker gene (inti1) did not differ significantly by season or between sites with the highest/lowest TMP levels.

microbiology↗