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Dr. Chandan Pal
Plant Health & Environment Laboratory (PHEL), Biosecurity New Zealand, Ministry for Primary Industries, Auckland, New Zealand

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0 Antimicrobial Resistance
0 Bioinformatics
0 Biosecurity
0 Food Safety
0 Pathogens

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Bioinformatics
Pathogens
virulence
high-throughput sequencing
Antimicrobial Resistance
Toxin-antitoxin systems

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Journal article
Published: 24 September 2020 in Microorganisms
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The acquisition of antibiotic resistance (AR) by foodborne pathogens, such as Salmonella enterica, has emerged as a serious public health concern. The relationship between the two key survival mechanisms (i.e., antibiotic resistance and virulence) of bacterial pathogens is complex. However, it is unclear if the presence of certain virulence determinants (i.e., virulence genes) and AR have any association in Salmonella. In this study, we report the prevalence of selected virulence genes and their association with AR in a set of phenotypically tested antibiotic-resistant (n = 117) and antibiotic-susceptible (n = 94) clinical isolates of Salmonella collected from Tennessee, USA. Profiling of virulence genes (i.e., virulotyping) in Salmonella isolates (n = 211) was conducted by targeting 13 known virulence genes and a gene for class 1 integron. The association of the presence/absence of virulence genes in an isolate with their AR phenotypes was determined by the machine learning algorithm Random Forest. The analysis revealed that Salmonella virulotypes with gene clusters consisting of avrA, gipA, sodC1, and sopE1 were strongly associated with any resistant phenotypes. To conclude, the results of this exploratory study shed light on the association of specific virulence genes with drug-resistant phenotypes of Salmonella. The presence of certain virulence genes clusters in resistant isolates may become useful for the risk assessment and management of salmonellosis caused by drug-resistant Salmonella in humans.

ACS Style

Daleniece Higgins; Nabanita Mukherjee; Chandan Pal; Irshad M. Sulaiman; Yu Jiang; Samir Hanna; John R. Dunn; Wilfried Karmaus; Pratik Banerjee. Association of Virulence and Antibiotic Resistance in Salmonella—Statistical and Computational Insights into a Selected Set of Clinical Isolates. Microorganisms 2020, 8, 1465 .

AMA Style

Daleniece Higgins, Nabanita Mukherjee, Chandan Pal, Irshad M. Sulaiman, Yu Jiang, Samir Hanna, John R. Dunn, Wilfried Karmaus, Pratik Banerjee. Association of Virulence and Antibiotic Resistance in Salmonella—Statistical and Computational Insights into a Selected Set of Clinical Isolates. Microorganisms. 2020; 8 (10):1465.

Chicago/Turabian Style

Daleniece Higgins; Nabanita Mukherjee; Chandan Pal; Irshad M. Sulaiman; Yu Jiang; Samir Hanna; John R. Dunn; Wilfried Karmaus; Pratik Banerjee. 2020. "Association of Virulence and Antibiotic Resistance in Salmonella—Statistical and Computational Insights into a Selected Set of Clinical Isolates." Microorganisms 8, no. 10: 1465.

Short report
Published: 27 June 2019 in Microbiome
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Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases. Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and blaRSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli. By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.

ACS Style

Nachiket Marathe; Fanny Berglund; Mohammad Razavi; Chandan Pal; Johannes Dröge; Sharvari Samant; Erik Kristiansson; D. G. Joakim Larsson. Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes. Microbiome 2019, 7, 1 -11.

AMA Style

Nachiket Marathe, Fanny Berglund, Mohammad Razavi, Chandan Pal, Johannes Dröge, Sharvari Samant, Erik Kristiansson, D. G. Joakim Larsson. Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes. Microbiome. 2019; 7 (1):1-11.

Chicago/Turabian Style

Nachiket Marathe; Fanny Berglund; Mohammad Razavi; Chandan Pal; Johannes Dröge; Sharvari Samant; Erik Kristiansson; D. G. Joakim Larsson. 2019. "Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes." Microbiome 7, no. 1: 1-11.

Journal article
Published: 01 March 2018 in Food Research International
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With the advent of high-throughput sequencing technologies, it is possible to comprehensively analyze the microbial community of foods without culturing them in the laboratory. The estimation of all microbes inhabiting a food commodity (food microbiota) therefore may shed light on the microbial quality and safety of foods. In this study, we utilized high-throughput pyrosequencing of 16S rRNA genes as well as traditional microbiological methods to evaluate the bacterial diversity and the predicted metabolic pathways associated with the bacterial communities of selected foods (romaine lettuce, cabbage, deli meat, and chicken legs, total 200 samples) procured from small and large retail outlets located in Memphis-Shelby County, Tennessee, USA. For high-throughput sequencing, microbial genomic DNA was directly extracted from the food products and subjected to genetic sequencing. Aerobic plate count of all food samples was also performed. Foods from small stores (such as corner stores) were found to contain higher bacterial counts as compared to large stores (such as supermarkets). High-throughput pyrosequencing in tandem with bioinformatics analyses revealed a comprehensive picture of the bacterial ecology of foods at different taxonomic levels. Firmicutes and Proteobacteria were the most abundant phyla across all products. At the genus level, Enterobacter and Pantoea in vegetables, and Bacillus and Aeromonas in animal products were found to be the most abundant. The bacterial predicted metabolic pathways such as inosine-5'-phosphate biosynthesis I, methylglyoxal (MG) degradation pathways, urea cycle, dTDP-l-rhamnose biosynthesis I, and mevalonate pathway I differed in foods procured from small stores as compared to large groceries or supermarkets. The results from this study revealed that the bacterial ecology (both in terms of numbers and types of bacteria) of food commodities might differ based on the vending outlet type (large vs. small) of retail stores. The overall estimation bacterial communities in foods by high-throughput sequencing method may be useful to identify potential taxa responsible for food spoilage. Moreover, the data from pyrosequencing of 16S rRNA genes can also be applied to infer major metabolic pathways in bacteria inhabiting different foods. This may reflect the role of these pathways in food-bacteria interaction and adaptation.

ACS Style

Daleniece Higgins; Chandan Pal; Irshad M. Sulaiman; Chunrong Jia; Tyler Zerwekh; Scot E. Dowd; Pratik Banerjee. Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study. Food Research International 2018, 105, 29 -40.

AMA Style

Daleniece Higgins, Chandan Pal, Irshad M. Sulaiman, Chunrong Jia, Tyler Zerwekh, Scot E. Dowd, Pratik Banerjee. Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study. Food Research International. 2018; 105 ():29-40.

Chicago/Turabian Style

Daleniece Higgins; Chandan Pal; Irshad M. Sulaiman; Chunrong Jia; Tyler Zerwekh; Scot E. Dowd; Pratik Banerjee. 2018. "Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study." Food Research International 105, no. : 29-40.

Journal article
Published: 01 November 2017 in Water Research
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Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India. Using shotgun metagenomics, we found a wide array (n = 175) of horizontally transferable antibiotic resistance genes (ARGs) including carbapenemases such as NDM, VIM, KPC, OXA-48 and IMP types. The relative abundance of total ARGs was 30-fold higher in river sediments within the city compared to upstream sites. Forty four ARGs, including the tet(X) gene conferring resistance to tigecycline, OXA-58 and GES type carbapenemases, were significantly more abundant in city sediments, while two ARGs were more common at upstream sites. The recently identified mobile colistin resistance gene mcr-1 was detected only in one of the upstream samples, but not in city samples. In addition to ARGs, higher abundances of various mobile genetic elements were found in city samples, including integron-associated integrases and ISCR transposases, as well as some biocide/metal resistance genes. Virulence toxin genes as well as bacterial genera comprising many pathogens were more abundant here; the genus Acinetobacter, which is often associated with multidrug resistance and nosocomial infections, comprised up to 29% of the 16S rRNA reads, which to our best knowledge is unmatched in any other deeply sequenced metagenome. There was a strong correlation between the abundance of Acinetobacter and the OXA-58 carbapenemase gene. Our study shows that uncontrolled discharge of untreated urban waste can contribute to an overall increase of the abundance and diversity of ARGs in the environment, including those conferring resistance to last-resort antibiotics.

ACS Style

Nachiket Marathe; Chandan Pal; Swapnil S. Gaikwad; Viktor Jonsson; Erik Kristiansson; D.G. Joakim Larsson. Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics. Water Research 2017, 124, 388 -397.

AMA Style

Nachiket Marathe, Chandan Pal, Swapnil S. Gaikwad, Viktor Jonsson, Erik Kristiansson, D.G. Joakim Larsson. Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics. Water Research. 2017; 124 ():388-397.

Chicago/Turabian Style

Nachiket Marathe; Chandan Pal; Swapnil S. Gaikwad; Viktor Jonsson; Erik Kristiansson; D.G. Joakim Larsson. 2017. "Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics." Water Research 124, no. : 388-397.

Journal article
Published: 01 July 2017 in Science of The Total Environment
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There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis. Plastic panels with one side painted with copper and zinc-containing antifouling paint were submerged in a Swedish marina and biofilms from both sides of the panels were harvested after 2.5-4weeks. DNA was isolated from the biofilms and subjected to metagenomic sequencing. Biofilm bacteria were cultured on marine agar supplemented with tetracycline, gentamicin, copper sulfate or zinc sulfate. Biofilm communities from painted surfaces displayed lower taxonomic diversity and enrichment of Gammaproteobacteria. Bacteria from these communities showed increased resistance to both heavy metals and tetracycline but not to gentamicin. Significantly higher abundance of metal and biocide resistance genes was observed, whereas mobile antibiotic resistance genes were not enriched in these communities. In contrast, we found an enrichment of chromosomal RND efflux system genes, including such with documented ability to confer decreased susceptibility to both antibiotics and biocides/heavy metals. This was paralleled by increased abundances of integron-associated integrase and ISCR transposase genes. The results show that the heavy metal-based antifouling paint exerts a strong selection pressure on marine bacterial communities and can co-select for certain antibiotic-resistant bacteria, likely by favoring species and strains carrying genes that provide cross-resistance. Although this does not indicate an immediate risk for promotion of mobile antibiotic resistance, the clear increase of genes involved in mobilizing DNA provides a foundation for increased opportunities for gene transfer in such communities, which might also involve yet unknown resistance mechanisms.

ACS Style

Carl-Fredrik Flach; Chandan Pal; Carl Johan Svensson; Erik Kristiansson; Marcus Östman; Johan Bengtsson-Palme; Mats Tysklind; D.G. Joakim Larsson. Does antifouling paint select for antibiotic resistance? Science of The Total Environment 2017, 590-591, 461 -468.

AMA Style

Carl-Fredrik Flach, Chandan Pal, Carl Johan Svensson, Erik Kristiansson, Marcus Östman, Johan Bengtsson-Palme, Mats Tysklind, D.G. Joakim Larsson. Does antifouling paint select for antibiotic resistance? Science of The Total Environment. 2017; 590-591 ():461-468.

Chicago/Turabian Style

Carl-Fredrik Flach; Chandan Pal; Carl Johan Svensson; Erik Kristiansson; Marcus Östman; Johan Bengtsson-Palme; Mats Tysklind; D.G. Joakim Larsson. 2017. "Does antifouling paint select for antibiotic resistance?" Science of The Total Environment 590-591, no. : 461-468.

Article
Published: 16 February 2017 in BioMetals
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Protists kill their bacterial prey using toxic metals such as copper. Here we hypothesize that the metalloid arsenic has a similar role. To test this hypothesis, we examined intracellular survival of Escherichia coli (E. coli) in the amoeba Dictyostelium discoideum (D. discoideum). Deletion of the E. coli ars operon led to significantly lower intracellular survival compared to wild type E. coli. This suggests that protists use arsenic to poison bacterial cells in the phagosome, similar to their use of copper. In response to copper and arsenic poisoning by protists, there is selection for acquisition of arsenic and copper resistance genes in the bacterial prey to avoid killing. In agreement with this hypothesis, both copper and arsenic resistance determinants are widespread in many bacterial taxa and environments, and they are often found together on plasmids. A role for heavy metals and arsenic in the ancient predator-prey relationship between protists and bacteria could explain the widespread presence of metal resistance determinants in pristine environments.

ACS Style

Xiuli Hao; Xuanji Li; Chandan Pal; Jon Hobman; D. G. Joakim Larsson; Quaiser Saquib; Hend A. Alwathnani; Barry P. Rosen; Yong-Guan Zhu; Christopher Rensing. Bacterial resistance to arsenic protects against protist killing. BioMetals 2017, 30, 307 -311.

AMA Style

Xiuli Hao, Xuanji Li, Chandan Pal, Jon Hobman, D. G. Joakim Larsson, Quaiser Saquib, Hend A. Alwathnani, Barry P. Rosen, Yong-Guan Zhu, Christopher Rensing. Bacterial resistance to arsenic protects against protist killing. BioMetals. 2017; 30 (2):307-311.

Chicago/Turabian Style

Xiuli Hao; Xuanji Li; Chandan Pal; Jon Hobman; D. G. Joakim Larsson; Quaiser Saquib; Hend A. Alwathnani; Barry P. Rosen; Yong-Guan Zhu; Christopher Rensing. 2017. "Bacterial resistance to arsenic protects against protist killing." BioMetals 30, no. 2: 307-311.

Review
Published: 01 January 2017 in Advances in Bacterial Pathogen Biology
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Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding

ACS Style

Chandan Pal; Karishma Asiani; Sankalp Arya; Christopher Rensing; Dov J. Stekel; D.G. Joakim Larsson; Jon L. Hobman. Metal Resistance and Its Association With Antibiotic Resistance. Advances in Bacterial Pathogen Biology 2017, 70, 261 -313.

AMA Style

Chandan Pal, Karishma Asiani, Sankalp Arya, Christopher Rensing, Dov J. Stekel, D.G. Joakim Larsson, Jon L. Hobman. Metal Resistance and Its Association With Antibiotic Resistance. Advances in Bacterial Pathogen Biology. 2017; 70 ():261-313.

Chicago/Turabian Style

Chandan Pal; Karishma Asiani; Sankalp Arya; Christopher Rensing; Dov J. Stekel; D.G. Joakim Larsson; Jon L. Hobman. 2017. "Metal Resistance and Its Association With Antibiotic Resistance." Advances in Bacterial Pathogen Biology 70, no. : 261-313.

Journal article
Published: 01 December 2016 in Science of The Total Environment
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Sewage treatment plants (STPs) have repeatedly been suggested as "hotspots" for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.

ACS Style

Johan Bengtsson-Palme; Rickard Hammarén; Chandan Pal; Marcus Östman; Berndt Björlenius; Carl-Fredrik Flach; Jerker Fick; Erik Kristiansson; Mats Tysklind; D.G. Joakim Larsson. Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Science of The Total Environment 2016, 572, 697 -712.

AMA Style

Johan Bengtsson-Palme, Rickard Hammarén, Chandan Pal, Marcus Östman, Berndt Björlenius, Carl-Fredrik Flach, Jerker Fick, Erik Kristiansson, Mats Tysklind, D.G. Joakim Larsson. Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Science of The Total Environment. 2016; 572 ():697-712.

Chicago/Turabian Style

Johan Bengtsson-Palme; Rickard Hammarén; Chandan Pal; Marcus Östman; Berndt Björlenius; Carl-Fredrik Flach; Jerker Fick; Erik Kristiansson; Mats Tysklind; D.G. Joakim Larsson. 2016. "Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics." Science of The Total Environment 572, no. : 697-712.

Journal article
Published: 07 October 2016 in Microbiome
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Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments. We provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event. Our study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.

ACS Style

Chandan Pal; Johan Bengtsson-Palme; Erik Kristiansson; D. G. Joakim Larsson. The structure and diversity of human, animal and environmental resistomes. Microbiome 2016, 4, 1 -15.

AMA Style

Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson, D. G. Joakim Larsson. The structure and diversity of human, animal and environmental resistomes. Microbiome. 2016; 4 (1):1-15.

Chicago/Turabian Style

Chandan Pal; Johan Bengtsson-Palme; Erik Kristiansson; D. G. Joakim Larsson. 2016. "The structure and diversity of human, animal and environmental resistomes." Microbiome 4, no. 1: 1-15.

Article
Published: 19 September 2016 in PROTEOMICS
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Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identification of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate postsubmission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.

ACS Style

Johan Bengtsson-Palme; Fredrik Boulund; Robert Edström; Amir Feizi; Anna Johnning; Viktor A. Jonsson; Fredrik H. Karlsson; Chandan Pal; Mariana Buongermino Pereira; Anna Rehammar; José Sanchez; Kemal Sanli; Kaisa Thorell; Paul A. Haynes; Stephen E. Stein; Michael P. Washburn. Strategies to improve usability and preserve accuracy in biological sequence databases. PROTEOMICS 2016, 16, 2454 -2460.

AMA Style

Johan Bengtsson-Palme, Fredrik Boulund, Robert Edström, Amir Feizi, Anna Johnning, Viktor A. Jonsson, Fredrik H. Karlsson, Chandan Pal, Mariana Buongermino Pereira, Anna Rehammar, José Sanchez, Kemal Sanli, Kaisa Thorell, Paul A. Haynes, Stephen E. Stein, Michael P. Washburn. Strategies to improve usability and preserve accuracy in biological sequence databases. PROTEOMICS. 2016; 16 (18):2454-2460.

Chicago/Turabian Style

Johan Bengtsson-Palme; Fredrik Boulund; Robert Edström; Amir Feizi; Anna Johnning; Viktor A. Jonsson; Fredrik H. Karlsson; Chandan Pal; Mariana Buongermino Pereira; Anna Rehammar; José Sanchez; Kemal Sanli; Kaisa Thorell; Paul A. Haynes; Stephen E. Stein; Michael P. Washburn. 2016. "Strategies to improve usability and preserve accuracy in biological sequence databases." PROTEOMICS 16, no. 18: 2454-2460.

Journal article
Published: 04 August 2016 in Bioinformatics
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Summary: With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets.

ACS Style

Rickard Hammarén; Chandan Pal; Johan Bengtsson-Palme. FARAO: the flexible all-round annotation organizer: Table 1. Bioinformatics 2016, 32, btw499 -3666.

AMA Style

Rickard Hammarén, Chandan Pal, Johan Bengtsson-Palme. FARAO: the flexible all-round annotation organizer: Table 1. Bioinformatics. 2016; 32 (23):btw499-3666.

Chicago/Turabian Style

Rickard Hammarén; Chandan Pal; Johan Bengtsson-Palme. 2016. "FARAO: the flexible all-round annotation organizer: Table 1." Bioinformatics 32, no. 23: btw499-3666.

Journal article
Published: 17 November 2015 in BMC Genomics
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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. 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. 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.

ACS Style

Chandan Pal; Johan Bengtsson-Palme; Erik Kristiansson; D. G. Joakim Larsson. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics 2015, 16, 1 -14.

AMA Style

Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson, D. G. Joakim Larsson. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics. 2015; 16 (1):1-14.

Chicago/Turabian Style

Chandan Pal; Johan Bengtsson-Palme; Erik Kristiansson; D. G. Joakim Larsson. 2015. "Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential." BMC Genomics 16, no. 1: 1-14.

Comparative study
Published: 23 March 2015 in Molecular Ecology Resources
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The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The metaxa software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to metaxa – metaxa2 – that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of metaxa2 was compared to other commonly used taxonomic classifiers, showing that metaxa2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. metaxa2 is freely available from http://microbiology.se/software/metaxa2/.

ACS Style

Johan Bengtsson-Palme; Martin Hartmann; Karl Eriksson; Chandan Pal; Kaisa Thorell; D.G. Joakim Larsson; Henrik Nilsson. metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources 2015, 15, 1403 -1414.

AMA Style

Johan Bengtsson-Palme, Martin Hartmann, Karl Eriksson, Chandan Pal, Kaisa Thorell, D.G. Joakim Larsson, Henrik Nilsson. metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources. 2015; 15 (6):1403-1414.

Chicago/Turabian Style

Johan Bengtsson-Palme; Martin Hartmann; Karl Eriksson; Chandan Pal; Kaisa Thorell; D.G. Joakim Larsson; Henrik Nilsson. 2015. "metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data." Molecular Ecology Resources 15, no. 6: 1403-1414.

Journal article
Published: 03 December 2013 in Nucleic Acids Research
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Antibiotic resistance has become a major human health concern due to widespread use, misuse and overuse of antibiotics. In addition to antibiotics, antibacterial biocides and metals can contribute to the development and maintenance of antibiotic resistance in bacterial communities through co-selection. Information on metal and biocide resistance genes, including their sequences and molecular functions, is, however, scattered. Here, we introduce BacMet (http://bacmet.biomedicine.gu.se)—a manually curated database of antibacterial biocide- and metal-resistance genes based on an in-depth review of the scientific literature. The BacMet database contains 470 experimentally verified resistance genes. In addition, the database also contains 25 477 potential resistance genes collected from public sequence repositories. All resistance genes in the BacMet database have been organized according to their molecular function and induced resistance phenotype.

ACS Style

Chandan Pal; Johan Bengtsson-Palme; Christopher Rensing; Erik Kristiansson; D. G. Joakim Larsson. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Research 2013, 42, D737 -D743.

AMA Style

Chandan Pal, Johan Bengtsson-Palme, Christopher Rensing, Erik Kristiansson, D. G. Joakim Larsson. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Research. 2013; 42 (D1):D737-D743.

Chicago/Turabian Style

Chandan Pal; Johan Bengtsson-Palme; Christopher Rensing; Erik Kristiansson; D. G. Joakim Larsson. 2013. "BacMet: antibacterial biocide and metal resistance genes database." Nucleic Acids Research 42, no. D1: D737-D743.