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Chandan Pal
I'm a computational biologist with a background in microbiology. Currently, I'm working as a senior scientist in bioinformatics for the Biosecurity New Zealand of MPI in Auckland and applying NGS technologies in cutting-edge omics research in biosecurity and animal health areas.
I lead the bioinformatics core of the Ministry, perform admin duties for Linux servers and High-Performance Computing clusters, and lead a range of NGS-based research projects. I also work with diagnostic and incursion investigation teams at Plant health, Animal health labs, and marine biosecurity teams of the Ministry, and provide scientific advice in applying NGS-based technologies in biosecurity and disease investigations, and assist in analysing and interpreting large-scale NGS datasets generated from omics studies.
I obtained my PhD in medical sciences (bioinformatics) from the University of Gothenburg in Sweden. Previously, I received a master degree in Post-genomic science from the University of Liverpool in the United Kingdom and a bachelor degree in microbiology from Auckland University of Technology (AUT) in New Zealand. During my PhD, I studied the effects of antibacterial biocides (e.g. antiseptics, disinfectants) and metals (e.g. copper, silver) on antibiotic resistance using genomic and metagenomic approaches.
I have a deep interest in human and environmental microbiome research with a unique focus on microbial community structure and antimicrobial resistance. I also study bacterial, viral, fungal, insects and other animal genomics, metagenomics, metabarcoding, environmental DNA (eDNA), and microbial community ecology. I also have an interest in developing biological databases and bioinformatics software.
For more details visit
Personal website: https://chandanpal.weebly.com/
ResearchGate: https://www.researchgate.net/profile/Chandan_Pal
Google Scholar: https://scholar.google.se/citations?user=UnOky1QAAAAJ
Address: Guldhedsgatan 10
Gothenburg, Sweden
SE 413 46
I lead the bioinformatics core of the Ministry, perform admin duties for Linux servers and High-Performance Computing clusters, and lead a range of NGS-based research projects. I also work with diagnostic and incursion investigation teams at Plant health, Animal health labs, and marine biosecurity teams of the Ministry, and provide scientific advice in applying NGS-based technologies in biosecurity and disease investigations, and assist in analysing and interpreting large-scale NGS datasets generated from omics studies.
I obtained my PhD in medical sciences (bioinformatics) from the University of Gothenburg in Sweden. Previously, I received a master degree in Post-genomic science from the University of Liverpool in the United Kingdom and a bachelor degree in microbiology from Auckland University of Technology (AUT) in New Zealand. During my PhD, I studied the effects of antibacterial biocides (e.g. antiseptics, disinfectants) and metals (e.g. copper, silver) on antibiotic resistance using genomic and metagenomic approaches.
I have a deep interest in human and environmental microbiome research with a unique focus on microbial community structure and antimicrobial resistance. I also study bacterial, viral, fungal, insects and other animal genomics, metagenomics, metabarcoding, environmental DNA (eDNA), and microbial community ecology. I also have an interest in developing biological databases and bioinformatics software.
For more details visit
Personal website: https://chandanpal.weebly.com/
ResearchGate: https://www.researchgate.net/profile/Chandan_Pal
Google Scholar: https://scholar.google.se/citations?user=UnOky1QAAAAJ
Address: Guldhedsgatan 10
Gothenburg, Sweden
SE 413 46
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Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems.
Results
Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes.
Conclusions
This is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.
Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems.
Results
Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes.
Conclusions
This is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.