Biology subjects

Karkman, A.

Publications and source records attributed to Karkman, A..

3 recordsLinked to original sources

bioRxiv2025

Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts including clinically relevant species

The introduction of the first broad-spectrum antibiotics, sulfonamide drugs fundamentally revolutionized medicine in the 1930s. Shortly after and ever since sulfonamide resistance genes (sul genes) have been widely detected. Still, the most recent variant of these genes sul4, was first described only in 2017 and its host range and transmission mechanisms are still largely unknown. Here we applied PacBio long-read metagenomic sequencing and bacterial methylation signals to investigate the genetic contexts and bacterial carriage of the sul4 gene in wastewater. Furthermore, we extended our description of sul4 carriers to previously published data sets. Our results indicate that sul4 is prominently found in sludge and hosted by various bacteria such as the species from the phyla Myxococcota and Chloroflexota and genera Trichlorobacter, and Desulfobacillus, which are commonly found in activated sludge. Additionally, according to our results, sul4 has already spread into multiple strains of opportunistic human pathogens, such as Aeromonas and Moraxella in addition to the previously described Salmonella. The sequence region flanking sul4 included a truncated folK gene, and an ISCR28-element, and exhibited a high degree of conservation across the investigated sequences. Furthermore, the module was associated with various integron integrase genes. Also, other mobility-related elements that could further increase the likelihood of sul4 mobilization were detected. Altogether, our results describing the sul4 hosts of bacteria from distant lineages indicate the efficient mobility of sul4 by genetic elements that traverse both clinical and environmental bacteria. Finally, we suggest that wastewater may provide favorable conditions for such horizontal gene transfer events. ImportanceAntibiotic resistance is an ancient phenomenon and a common trait for many environmental bacteria. However, human activities in the post-antibiotic era, coupled with the bacterias ability to exchange genetic material across different lineages, have drastically increased the spread of resistance traits among bacteria from various niches. The primary concern is the resistance genes encoded by infections causing pathogens, already causing over one million deaths annually and indirectly contributing to nearly four million more. Therefore, understanding the bacteria that harbor ARGs and the genetic mechanisms driving their mobilization is crucial for understanding the dynamics and emerging trends of resistance. Here, we focus on revealing these crucial aspects of the newly discovered sulfonamide resistance gene sul4. Given the limitations of the metagenomic approach in linking the functional genes to their host genomes, the significance of our research lies in our workflow that allows this linkage by identification of shared methylation profiles.

microbiology↗

bioRxiv2023

Metagenomic assemblies tend to break around antibiotic resistance genes

BackgroundAssembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs), and inform interventions to prevent further spread of resistant bacteria. However, ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies. ResultsThe results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample. ConclusionsOur study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database might be necessary, at least as a complementary strategy, to get accurate ARG abundance and diversity measures.

bioinformatics↗

bioRxiv2018

Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments

Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. Such pollution can directly contribute to increased morbidity caused by the transmission of resistant fecal pathogens. Residual antibiotics in wastewaters have been speculated to select for resistant bacteria and thereby promote the evolution and emergence of new resistance factors. Increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments may, however, simply be a result of fecal contamination with resistant bacteria rather than caused by an on-site selection pressure. In this study we have disentangled these two alternative scenarios by relating the relative resistance gene abundance to the accompanying extent of fecal pollution in publicly available metagenomic data. This was possible by analyzing the abundance of a newly discovered phage which is exceptionally abundant in, and specific to, human feces. The presence of resistance genes could largely be explained by fecal pollution, with no clear signs of selection in the environment, the only exception being environments polluted by very high levels of antibiotics from manufacturing where selection is evident. Our results demonstrate the necessity to take in to account the fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance. The presence or absence of selection pressure has major implications for what the risk scenarios are (transmission versus evolution) and for what mitigations (reducing pathogenic bacteria or selective agents) should be prioritized to reduce health risks related to antibiotic resistance in the environment.

microbiology↗