Fernanda Cristina Petersen

• Baker, Jonathon L.; Dahle, Ulf Reidar & Petersen, Fernanda Cristina (2026). mGem: Dentistry is strategically positioned yet underleveraged in the battle against antimicrobial resistance. mBio. ISSN 2161-2129. 17(9), p. e0064726–e0064726. doi: 10.1128/mbio.00647-26. Full text in Research Archive
• Kudowa, Evaristar; Tembo, Godwin; Chirwa, Anthony E.; Chikaonda, Tarsizio; Muyaya, Alfred & Makhaza, Lumbani [Show all 93 contributors for this article] (2026). Pooled analysis of PCV13 efficacy from controlled human infection trials in Malawi and the UK. npj Vaccines. 11. doi: 10.1038/s41541-026-01381-4. Full text in Research Archive Show summary

  We conducted the first pooled analysis of two randomised controlled vaccine trials on experimental pneumococcal serotype 6B carriage, registered in Malawi (PACTR202008503507113) and the UK (ISRCTN45340436). This post-hoc exploratory study examined the sex-based differences in carriage, vaccine efficacy and vaccine-induced responses. PCV-13 reduced colonisation by 76% (p < 0.001) with non-significant interaction by sex (RR = 1.549, p = 0.413). Females showed a higher carriage rate than males (28% vs. 19%, p = 0.066). Baseline anti-6B Capsular Polysaccharide Immunoglobulin G (IgG) titres were higher in females, significantly in Malawi (2.62 µg/ml vs males 2.05 µg/ml, p = 0.015). Post-vaccination titres did not differ by sex. The pooled fold change in IgG pre-post vaccination, was higher in vaccinated females (5.47 vs 3.30, p = 0.053). This analysis demonstrates the utility and challenges of integrating CHIM data between diverse settings to evaluate vaccine efficacy, describe inter-setting differences, investigate biological and immunological factors influencing protection against pneumococcal carriage and ultimately inform future vaccine development strategies.

• Rued, Britta E.; Dhariwal, Achal; Covington, Brett C.; Seyedsayamdost, Mohammad R.; Krivograd, Sophie A. & Pesavento, Russell P. [Show all 8 contributors for this article] (2025). Impact of the RaS-RiPP tryglysin and culturing conditions on ex-vivo oral microbiomes. npj Biofilms and Microbiomes. 11(1). doi: 10.1038/s41522-025-00794-8. Full text in Research Archive Show summary

  Abstract Natural products are ubiquitously produced by many species that we encounter during our daily lives. One genus, Streptococcus , can produce a wide array of quorum sensing linked natural products known as RaS-RiPPs (ribosomally synthesized and post-translationally modified peptides). Their production is triggered by the induction of an Rgg-SHP quorum sensing system, which senses the presence of SHPs (short hydrophobic peptides) and induces the gene expression of these operons. Previous work has found that streptococcal RaS-RiPPs modulate the growth of different streptococci and might play a role in antibiotic tolerance. This is of particular importance to the oral microbiome, where streptococci are a predominant genus. This study provides the first report on attempts to study the impact of the RaS-RiPP Tryglysin A on ex-vivo oral systems and explores important factors to consider when culturing these systems. We explore how medium selection, atmosphere, growth model, and saliva amount can impact the presence of both bacterial and fungal species. These studies provide the groundwork for determining how RaS-RiPP producing Streptococci might impact the composition and function of oral microbiome communities, as well as important aspects to consider when culturing ex-vivo oral systems.

• Farooq, Samiya; Talat, Absar; Dhariwal, Achal; Petersen, Fernanda Cristina & Khan, Asad U. (2025). Transgenerational gut dysbiosis: Unveiling the dynamics of antibiotic resistance through mobile genetic elements from mothers to infants. International Journal of Antimicrobial Agents. ISSN 0924-8579. 65(5). doi: 10.1016/j.ijantimicag.2025.107458. Full text in Research Archive
• Dhariwal, Achal; Shekhar, Sudhanshu & Petersen, Fernanda Cristina (2025). Nasal microbiota transplantation: a gateway to novel treatments. Trends in Microbiology. ISSN 0966-842X. doi: 10.1016/j.tim.2024.12.010. Full text in Research Archive Show summary

  Two recent studies have highlighted the potential of nasal microbiota transplantation (NMT) to treat chronic rhinosinusitis (CRS). Here we evaluate these findings and propose that lessons from fecal microbiota transplantation (FMT) could guide NMT development, with possible implications for combating antimicrobial resistance in respiratory infections.

• Brar, Navdeep Kaur; Dhariwal, Achal; Shekhar, Sudhanshu; Junges, Roger; Hakansson, Anders P. & Petersen, Fernanda Cristina (2024). HAMLET, a human milk protein-lipid complex, modulates amoxicillin induced changes in an ex vivo biofilm model of the oral microbiome. Frontiers in Microbiology. 15. doi: 10.3389/fmicb.2024.1406190. Full text in Research Archive Show summary

  Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work in conjunction with antibiotics and minimize resistance risk. In this study we investigated the composite effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using an ex vivo oral biofilm model with pooled saliva samples. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and low concentrations of amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination promoted a remarkable shift in overall microbial composition compared to the untreated samples. A large proportion of the bacterial species in the combined treatment were Lactobacillus crispatus, a species with probiotic effects, whereas it was only detected in a minor fraction in untreated samples. Although resistome analysis indicated no major shifts in alpha-diversity, the results showed the presence of TEM beta-lactamase genes in low proportions in all treated samples but absence in untreated samples. Our study illustrates HAMLET’s capability to alter the effects of amoxicillin on the oral microbiome and potentially favor the growth of selected probiotic bacteria when in combination. The findings extend previous knowledge on the combined effects of HAMLET and antibiotics against target pathogens to include potential modulatory effects on polymicrobial biofilms of human origin.

• Brar, Navdeep Kaur; Dhariwal, Achal; Åmdal, Heidi Aarø; Junges, Roger; Salvadori, Gabriela & Baker, J.L. [Show all 8 contributors for this article] (2024). Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. npj Biofilms and Microbiomes. 10(1). doi: 10.1038/s41522-024-00507-7. Full text in Research Archive Show summary

  Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.

• Xavier-Queiroz, Mateus; Hamann, Pedro Ricardo Vieira; Åmdal, Heidi Aarø; Polikarpov, Igor; Petersen, Fernanda Cristina & Ricomini-Filho, Antônio Pedro (2024). Absence of inhibitory effects of two new glucanases on streptococcus mutans growth. Brazilian Journal of Oral Sciences. ISSN 1677-3217. 23. doi: 10.20396/BJOS.V23I00.8676163. Full text in Research Archive Show summary

  Glucanohydrolases have shown promise in degrading exopolysaccharides in cariogenic biofilms, making them a potential strategy for biofilm control without disrupting the oral microbiota. However, their direct antimicrobial effects remain unclear. Aim: To determine the antimicrobial activity on S. mutans of two newly discovered glucanases characterized by our group, PmGH87 (mutanase) from Prevotella melaninogenica and CoGH66 (dextranase) from Capnocytophaga ochracea, using a commercial dextranase from Penicillum sp. as a control. Methods: Their effects on growth were assessed using a luciferase reporter system coupled with the promoter of the ldh gene in Streptococcus mutans. Results: Quantification of optical density and luminescence over a 10-hour growth period revealed that the commercial dextranase exhibited inhibitory effects on S. mutans growth. However, these effects were neutralized by heat treatment, suggesting the presence of a heat-sensitive contaminant or an additional antimicrobial property associated with the commercial dextranase from Penicillum sp. On the other hand, the purified mutanase and dextranase enzymes had no inhibitory effect on S. mutans growth. Conclusion: In conclusion, the absence of inhibitory effects on S. mutans growth by the newly discovered enzymes emphasizes their potential for biofilm control while preserving the delicate balance of the oral microbiota and preventing the emergence of resistance.

• Dhariwal, Achal; Rajar, Polona; Silva, Gabriela Salvadori Da; Åmdal, Heidi Aarø; Berild, Dag & Saugstad, Ola Didrik [Show all 11 contributors for this article] (2024). Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Nature Communications. 15(1). doi: 10.1038/s41467-024-50433-7. Full text in Research Archive Show summary

  Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8–10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.

• Anderl, Florian Nicolas; Salvadori, Gabriela; Veletic, Mladen; Petersen, Fernanda Cristina & Balasingham, Ilangko (2024). Quantitative Aspects, Engineering and Optimization of Bacterial Sensor Systems. IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. 10(4), p. 517–533. doi: 10.1109/TMBMC.2024.3452066. Full text in Research Archive
• Dornelas-Figueira, Louise Morais; Filho, Antonio Pedro Ricomini; Junges, Roger; Åmdal, Heidi Aarø; Cury, Altair Antoninha Del Bel & Petersen, Fernanda Cristina (2023). In Vitro Impact of Fluconazole on Oral Microbial Communities, Bacterial Growth, and Biofilm Formation. Antibiotics. 12(9). doi: 10.3390/antibiotics12091433. Full text in Research Archive Show summary

  Antifungal agents are widely used to specifically eliminate infections by fungal pathogens. However, the specificity of antifungal agents has been challenged by a few studies demonstrating antibacterial inhibitory effects against Mycobacteria and Streptomyces species. Here, we evaluated for the first time the potential effect of fluconazole, the most clinically used antifungal agent, on a human oral microbiota biofilm model. The results showed that biofilm viability on blood and mitis salivarius agar media was increased over time in the presence of fluconazole at clinically relevant concentrations, despite a reduction in biomass. Targeted PCR revealed a higher abundance of Veillonella atypica, Veillonella dispar, and Lactobacillus spp. in the fluconazole-treated samples compared to the control, while Fusobacterium nucleatum was reduced and Streptococcus spp were not significantly affected. Further, we tested the potential impact of fluconazole using single-species models. Our results, using Streptococcus mutans and Streptococcus mitis luciferase reporters, showed that S. mutans planktonic growth was not significantly affected by fluconazole, whereas for S. mitis, planktonic growth, but not biofilm viability, was inhibited at the highest concentration. Fluconazole’s effects on S. mitis biofilm biomass were concentration and time dependent. Exposure for 48 h to the highest concentration of fluconazole was associated with S. mitis biofilms with the most increased biomass. Potential growth inhibitory effects were further tested using four non-streptococcal species. Among these, the planktonic growth of both Escherichia coli and Granulicatella adiacens was inhibited by fluconazole. The data indicate bacterial responses to fluconazole that extend to a broader range of bacterial species than previously anticipated from the literature, with the potential to disturb biofilm communities.

• Junges, Roger; Khan, Rabia; Tovpeko, Yanina; Åmdal, Heidi Aarø; Petersen, Fernanda Cristina & Morrison, Donald A. (2023). Markerless Genome Editing in Competent Streptococci, Oral Biology. Molecular Techniques and Applications. Springer. ISSN 9781071627792. p. 201–216. doi: 10.1007/978-1-0716-2780-8_13. Full text in Research Archive
• Shekhar, Sudhanshu; Brar, Navdeep Kaur; Håkansson, Anders P. & Petersen, Fernanda Cristina (2023). Treatment of Mouse Infants with Amoxicillin, but Not the Human Milk-Derived Antimicrobial HAMLET, Impairs Lung Th17 Responses. Antibiotics. 12(2). doi: 10.3390/antibiotics12020423. Full text in Research Archive Show summary

  Emerging evidence suggests differential effects of therapeutic antibiotics on infant T cell responses to pathogens. In this study, we explored the impact of the treatment of mouse infants with amoxicillin and the human milk-derived antimicrobial HAMLET (human alpha-lactalbumin made lethal to tumor cells) on T cell responses to Streptococcus pneumoniae. Lung cells and splenocytes were isolated from the infant mice subjected to intranasal administration of amoxicillin, HAMLET, or a combination of HAMLET and amoxicillin, and cultured with S. pneumoniae to measure T cell responses. After in-vitro stimulation with S. pneumoniae, lung cells from amoxicillin- or amoxicillin plus HAMLET-treated mice produced lower levels of Th17 (IL-17A), but not Th1 (IFN-γ), cytokine than mice receiving HAMLET or PBS. IL-17A/IFN-γ cytokine levels produced by the stimulated splenocytes, on the other hand, revealed no significant difference among treatment groups. Further analysis of T cell cytokine profiles by flow cytometry showed that lung CD4+, but not CD8+, T cells from amoxicillin- or HAMLET plus amoxicillin-treated mice expressed decreased levels of IL-17A compared to those from HAMLET-exposed or control mice. Collectively, these results indicate that exposure of infant mice to amoxicillin, but not HAMLET, may suppress lung Th17 responses to S. pneumoniae.

• Dhariwal, Achal; Bråten, Lars Christian Haugli; Sturød, Kjersti; Silva, Gabriela Salvadori Da; Bargheet, Ahmed & Åmdal, Heidi Aarø [Show all 11 contributors for this article] (2023). Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome. Gut microbes. ISSN 1949-0976. 15(1). doi: 10.1080/19490976.2022.2157200. Full text in Research Archive Show summary

  The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including anti- biotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composi- tion were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health- associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.

• Rajar, Polona; Dhariwal, Achal; Silva, Gabriela Salvadori Da; Junges, Roger; Åmdal, Heidi Aarø & Berild, Dag [Show all 12 contributors for this article] (2022). Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies. Frontiers in Microbiology. 13, p. 1–15. doi: 10.3389/fmicb.2022.1038120. Full text in Research Archive Show summary

  Introduction Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Methods Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. Results The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness. Discussion Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.

• Shekhar, Sudhanshu; Brar, Navdeep Kaur & Petersen, Fernanda Cristina (2022). Suppressive effect of therapeutic antibiotic regimen on antipneumococcal Th1/Th17 responses in neonatal mice. Pediatric Research. ISSN 0031-3998. doi: 10.1038/s41390-022-02115-7. Full text in Research Archive
• Bajalan, Aya; Bui, Tiina; Salvadori, Gabriela; Marques, Dalton; Schumacher, Alison & Rösing, Cassiano Kuchenbecker [Show all 11 contributors for this article] (2022). Awareness regarding antimicrobial resistance and confidence to prescribe antibiotics in dentistry: a cross-continental student survey. Antimicrobial Resistance & Infection Control. 11(1). doi: 10.1186/s13756-022-01192-x. Full text in Research Archive Show summary

  Background The antimicrobial resistance (AMR) crisis is a major global threat and one of its biggest drivers is the overuse of antibiotics in humans. Dentists are responsible for 5–10% antibiotic prescriptions worldwide and recent data suggest that knowledge and prescribing practices need improvement. Methods A cross-sectional web-survey was sent to dental students from six universities in Norway, Canada, and Brazil. Topics addressed covered awareness, confidence to prescribe antibiotics, and education needs. Data were presented descriptively and statistical testing was employed to compare group means when applicable. Results In total, 562 responses were collected across the three countries with a response rate of 28.6%. ‘Antibiotic resistance’ was among the highest priorities (scale 1–10) with an average of 8.86 (SEM ± 0.05), together with ‘Gender inequality’ (8.68 ± 0.07) and ‘Climate change’ (8.68 ± 0.07). Only 28.8% thought that Dentistry was engaged in national/international campaigns promoting awareness on the topic and 8.9% stated to have heard about the ‘One Health’ concept. Final year dental students showed an average confidence to prescribe antibiotics of 7.59 (± 0.14). Most students demonstrated interest in receiving additional education on all topics listed, with the three most pressing being ‘antibiotic prescription for treatment of infections’ (82.9%), ‘drug interactions’ (80.9%), and ‘spread of antibiotic resistance’ (79.6%). A trend was observed between higher awareness regarding the topic and higher confidence to prescribe. Conclusions There is a need to revisit dental education on antibiotic resistance with a global perspective and to create more stewardship initiatives that promote awareness on the topic.

• Lekang, Katrine; Shekhar, Sudhanshu; Berild, Dag; Petersen, Fernanda Cristina & Winther-Larsen, Hanne Cecilie (2022). Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut. PLOS ONE. 17(10), p. e0275737–e0275737. doi: 10.1371/journal.pone.0275737. Full text in Research Archive Show summary

  Antibiotics seize an effect on bacterial composition and diversity and have been demonstrated to induce disruptions on gut microbiomes. This may have implications for human health and wellbeing, and an increasing number of studies suggest a link between the gut microbiome and several diseases. Hence, reducing antibiotic treatments may be beneficial for human health status. Further, antimicrobial resistance (AMR) is an increasing global problem that can be counteracted by limiting the usage of antibiotics. Longer antibiotic treatments have been demonstrated to increase the development of AMR. Therefore, shortening of antibiotic treatment durations, provided it is safe for patients, may be one measure to reduce AMR. In this study, the objective was to investigate effects of standard and reduced antibiotic treatment lengths on gut microbiomes using a murine model. Changes in the murine gut microbiome was assessed after using three different treatment durations of amoxicillin (3, 7 or 14 days) as well as a control group not receiving amoxicillin. Fecal samples were collected before and during the whole experiment, until three weeks past end of treatment. These were further subject for 16S rRNA Illumina MiSeq sequencing. Our results demonstrated significant changes in bacterial diversity, richness and evenness during amoxicillin treatment, followed by a reversion in terms of alpha-diversity and abundance of major phyla, after end of treatment. However, a longer restitution time was indicated for mice receiving amoxicillin for 14 days, and phylum Patescibacteria did not fully recover. In addition, an effect on the composition of Firmicutes was indicated to last for at least three weeks in mice treated with amoxicillin for 14 days. Despite an apparently reversion to a close to original state in overall bacterial diversity and richness, the results suggested more durable changes in lower taxonomical levels. We detected several families, genera and ASVs with significantly altered abundance three weeks after exposure to amoxicillin, as well as bacterial taxa that appeared significantly affected by amoxicillin treatment length. This may strengthen the argument for shorter antibiotic treatment regimens to both limit the emergence of antibiotic resistance and risk of gut microbiome disturbance.

• Weber, Florian; Figueira, Louise Morais Dornelas; Hafiane, Nora; Zaytseva-Zotova, Daria; Bautista, Alejandro Barrantes & Petersen, Fernanda Cristina [Show all 7 contributors for this article] (2022). Can polyphenolic surface modifications prevent fungal colonization of titanium dental implants? Colloids and Surfaces B: Biointerfaces. ISSN 0927-7765. 219. doi: 10.1016/j.colsurfb.2022.112813. Full text in Research Archive Show summary

  Oral biofilms can be a major health problem causing infections and chronic inflammation of mucosal tissue. While much effort is put in the investigation of bacteria in biofilms, the role of fungi is often neglected, despite Candida albicans playing a key role in the formation of multispecies oral biofilms. With the rise of antibiotic resistance, new strategies to reduce microbial growth need to be found. Therefore, plant derived polyphenolic molecules have been suggested to reduce both adhesion and growth of pathogenic bacteria and fungi. In this study, we investigated the use of polyphenolic coatings to reduce adhesion and biofilm formation of C. albicans BWP17 on titanium implants. Tannic acid and pyrogallol coatings altered the hydrophobic and charge properties of titanium surfaces, and both compounds were gradually released as active molecules over time. Despite such effects, we found no significant inhibition on growth and biofilm formation of C. Albicans, indicating that the release of active molecules from the coatings did not reach relevant inhibitory concentrations. However, a potential antibiofilm effect was observed by the pH-dependent disassembly of the polyphenolic layer, which caused the biofilm to detach. Hence, further efforts are required to create tailored implant surfaces, which sustainably reduce microbial growth and adhesion.

• Marshall, Helina; José, Ricardo J.; Kilian, Mogens; Petersen, Fernanda Cristina & Brown, Jeremy S. (2021). Effects of Expression of Streptococcus pneumoniae PspC on the Ability of Streptococcus mitis to Evade Complement-Mediated Immunity. Frontiers in Microbiology. 12, p. 1–12. doi: 10.3389/fmicb.2021.773877. Full text in Research Archive Show summary

  Streptococcus pneumoniae and Streptococcus mitis are genetically closely related and both frequently colonise the naso-oropharynx, yet S. pneumoniae is a common cause of invasive infections whereas S. mitis is only weakly pathogenic. We hypothesise that sensitivity to innate immunity may underlie these differences in virulence phenotype. We compared the sensitivity of S. pneumoniae and S. mitis strains to complement-mediated immunity, demonstrating S. mitis strains were susceptible to complement-mediated opsonophagocytosis. S. pneumoniae resistance to complement is partially dependent on binding of the complement regulator Factor H by the surface protein PspC. However, S. mitis was unable to bind factor H. The S. pneumoniae TIGR4 strain pspC was expressed in the S. mitis SK142 strain to create a S. mitis pspC + strain. Immunoblots demonstrated the S. mitis pspC + strain expressed PspC, and flow cytometry confirmed this resulted in Factor H binding to S. mitis , reduced susceptibility to complement and improved survival in whole human blood compared to the wild-type S. mitis strain. However, in mouse models the S. mitis pspC + strain remained unable to establish persistent infection. Unlike S. pneumoniae strains, culture in serum or blood did not support increased CFU of the S. mitis strains. These results suggest S. mitis is highly sensitive to opsonisation with complement partially due to an inability to bind Factor H, but even when complement sensitivity was reduced by expression of pspC , poor growth in physiological fluid limited the virulence of S. mitis in mice.

• Dhariwal, Achal; Junges, Roger; Chen, Tsute & Petersen, Fernanda Cristina (2021). ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data. NAR Genomics and Bioinformatics. 3. doi: 10.1093/nargab/lqab018. Full text in Research Archive Show summary

  The study of resistomes using whole metagenomic sequencing enables high-throughput identification of resistance genes in complex microbial communities, such as the human microbiome. Over recent years, sophisticated and diverse pipelines have been established to facilitate raw data processing and annotation. Despite the progress, there are no easy-to-use tools for comprehensive visual, statistical and functional analysis of resistome data. Thus, exploration of the resulting large complex datasets remains a key bottleneck requiring robust computational resources and technical expertise, which creates a significant hurdle for advancements in the field. Here, we introduce ResistoXplorer, a user-friendly tool that integrates recent advancements in statistics and visualization, coupled with extensive functional annotations and phenotype collection, to enable high-throughput analysis of common outputs generated from metagenomic resistome studies. ResistoXplorer contains three modules—the ‘Antimicrobial Resistance Gene Table’ module offers various options for composition profiling, functional profiling and comparative analysis of resistome data; the ‘Integration’ module supports integrative exploratory analysis of resistome and microbiome abundance profiles derived from metagenomic samples; finally, the ‘Antimicrobial Resistance Gene List’ module enables users to intuitively explore the associations between antimicrobial resistance genes and the microbial hosts using network visual analytics to gain biological insights. ResistoXplorer is publicly available at http://www.resistoxplorer.no.

• Shekhar, Sudhanshu; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina (2021). Vaccination With the Commensal Streptococcus mitis Expressing Pneumococcal Serotype 5 Capsule Elicits IgG/IgA and Th17 Responses Against Streptococcus pneumoniae. Frontiers in Immunology. doi: 10.3389/fimmu.2021.676488. Full text in Research Archive Show summary

  Recent studies have identified a clinical isolate of the commensal Streptococcus mitis that expresses Streptococcus pneumoniae serotype 5 capsule (S. mitis serotype 5) and shows serospecificity toward pneumococcal serotype 5. However, it remains unknown whether S. mitis serotype 5 induces protective immunity against pneumococcal serotype 5. In this study, we evaluated the ability of S. mitis serotype 5 to generate protective immunity in a mouse model of lung infection with pneumococcal serotype 5. Upon challenge infection with S. pneumoniae serotype 5, mice intranasally immunized with S. mitis serotype 5 exhibited reduced pneumococcal loads in the lungs, nasal wash, and bronchoalveolar lavage fluid compared with those receiving PBS (control). The immunized mice displayed significantly higher levels of IgG and IgA antibodies reactive to S. mitis serotype 5, S. pneumoniae serotype 5 or S. pneumoniae serotype 4 than the antibody levels in control mice. In vaccinated mice, the IgG/IgA antibody levels reactive to S. mitis serotype 5 or S. pneumoniae serotype 5 were higher than the levels reactive to S. pneumoniae serotype 4. Furthermore, in-vitro restimulation of the lung-draining mediastinal lymph node cells and splenocytes from immunized mice with killed S. mitis serotype 5, S. pneumoniae serotype 5 or S. pneumoniae serotype 4 showed enhanced Th17, but not Th1 and Th2, responses. Overall, our findings show that mucosal immunization with S. mitis serotype 5 protects against S. pneumoniae serotype 5 infection and induces Th17 and predominant serotype-specific IgG/IgA antibody responses against pneumococcal infection.

• Pandey, Sushma; Søland, Tine Merete; Bjerkli, Inger-Heidi; Sand, Lars Peter; Petersen, Fernanda Cristina & Costea, Daniela Elena [Show all 8 contributors for this article] (2021). Combined loss of expression of involucrin and cytokeratin 13 is associated with poor prognosis in squamous cell carcinoma of mobile tongue. Head and Neck. ISSN 1043-3074. 43(11), p. 3374–3385. doi: 10.1002/hed.26826. Full text in Research Archive Show summary

  Background This study aimed to evaluate the prognostic significance of expression levels of involucrin (IVL), cytokeratin (CK)-10 and -13 at different intratumor sites (tumor center and invading area) of oral tongue squamous cell carcinoma (OTSCC). Methods IVL, CK13 and CK10 expression levels were examined in a multicenter cohort of 146 OTSCCs using immunohistochemistry. External mRNA datasets were used for expression analysis and/or to validate survival associations. Results External transcriptomic datasets showed downregulation of IVL and KRT13 in oral malignancies including OTSCC as compared to normal controls. The combined loss of IVL and CK13 expression at the invading core but not at the center core was significantly associated with poor differentiation and reduced 5-year overall survival. Multivariate Cox analysis confirmed the loss of CK13 and IVL expression to be an independent prognostic factor. Transcriptomic dataset corroborated immunohistochemistry results. Conclusions Combined expression levlels of IVL and CK13 might be useful as prognostic biomarkers in OTSCC.

• Dhariwal, Achal; Junges, Roger; Chen, Tsute & Petersen, Fernanda Cristina (2020). ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data. BioRxiv. ISSN 0362-4331. doi: 10.1101/2020.08.14.250837. Full text in Research Archive
• Shekhar, Sudhanshu & Petersen, Fernanda Cristina (2020). The Dark Side of Antibiotics: Adverse Effects on the Infant Immune Defense against Infection. Frontiers in Pediatrics. doi: 10.3389/fped.2020.544460. Full text in Research Archive Show summary

  Although antibiotics confer significant health benefits in treating or preventing bacterial infections, an accumulating wealth of evidence illustrates their detrimental effect on host-microbiota homeostasis, posing a serious menace to the global public health. In recent years, it is becoming evident that infants, who are subjected to frequent antibiotic exposures due to their vulnerability to infection, reflect increased susceptibility to a wide spectrum of diseases, including infection, in later life. Antibiotics induce perturbations of the microbiota or dysbiosis, which in turn alters the host immune responses against pathogens. In comparison with adults, antibiotic treatments in infants have disproportionate consequences because the infant microbiota represents an evolving system that is unstable and immature until 2–3 years of age. However, relatively less knowledge is available on how antibiotics affect the infant microbiota and immunity. In this review article, we focus on how antibiotic treatment regimens influence the infant innate and adaptive immunity to pathogens in humans and animal models, and make the host susceptible to infections in later life. There is a critical need to better understand the effect of antibiotics on infant immune function, which may have implications for developing effective prophylactics and therapeutics against diseases in infants and adults.

• Petersen, Fernanda Cristina; Dahle, Ulf R; Nicolau, Belinda & Casals-Pascual, Climent (2020). COVID-19: Looking Into the Overlooked. Frontiers in Molecular Biosciences. 7. doi: 10.3389/fmolb.2020.00165. Full text in Research Archive
• Rajar, Polona; Saugstad, Ola Didrik; Berild, Dag; Dutta, Anirban; Greisen, Gorm & Lausten-Thomsen, Ulrik [Show all 11 contributors for this article] (2020). Antibiotic stewardship in premature infants: a systematic review. Neonatology. ISSN 1661-7800. 117(6), p. 673–686. doi: 10.1159/000511710. Full text in Research Archive Show summary

  &lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; Antibiotic treatment in premature infants is often empirically prescribed, and practice varies widely among otherwise comparable neonatal intensive care units. Unnecessary and prolonged antibiotic treatment is documented in numerous studies. Recent research shows serious side effects and suggests long-term adverse health effects in prematurely born infants exposed to antibiotics in early life. One preventive measure to reduce unnecessary antibiotic exposure is implementation of antibiotic stewardship programs. Our objective was to review the literature on implemented antibiotic stewardship programs including premature infants with gestational age ≤34 weeks. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; Six academic databases (PubMed [Medline], McMaster PLUS, Cochrane Database of Systematic Reviews, UpToDate, Cochrane Central Register of Controlled Trials, and National Institute for Health and Care Excellence) were systematically searched. PRISMA guidelines were applied. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; The search retrieved 1,212 titles of which 12 fitted inclusion criteria (11 observational studies and 1 randomized clinical trial). Included articles were critically appraised. We grouped the articles according to common area of implemented stewardship actions: (1) focus on reducing initiation of antibiotic therapy, (2) focus on shortening duration of antibiotic therapy, (3) various organizational stewardship implementations. The heterogeneity of cohort composition, of implemented actions and of outcome measures made meta-analysis inappropriate. We provide an overview of the reduction in antibiotic use achieved. &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; Antibiotic stewardship programs can be effective for premature newborns especially when multifactorial and tailored to this population, focusing on reducing initiation or on shortening the duration of antibiotic therapy. Programs without specific measures were less effective.

• Rørvik, Gro Herredsvela; Liskiewicz, Krystyna Anna; Kryuchkov, Fedor; Naemi, Ali-Oddin; aasheim, Hans-Christian & Petersen, Fernanda Cristina [Show all 8 contributors for this article] (2020). Cyclic di-adenosine monophosphate regulates metabolism and growth in the oral commensal streptococcus mitis. Microorganisms. 8:1269(9), p. 1–21. doi: 10.3390/microorganisms8091269. Full text in Research Archive Show summary

  Cyclic di-adenosine monophosphate (c-di-AMP) has emerged as an important bacterial signaling molecule that functions both as an intracellular second messenger in bacterial cells and an extracellular ligand involved in bacteria-host cross-talk. In this study, we identify and characterize proteins involved in controlling the c-di-AMP concentration in the oral commensal and opportunistic pathogen Streptococcusmitis (S. mitis). We identified three known types of c-di-AMP turnover proteins in the genome of S. mitis CCUG31611: a CdaA-type diadenylate cyclase as well as GdpP-, and DhhP-type phosphodiesterases. Biochemical analyses of purified proteins demonstrated that CdaA synthesizes c-di-AMP from ATP whereas both phosphodiesterases can utilize c-di-AMP as well as the intermediary metabolite of c-di-AMP hydrolysis 5′-phosphadenylyl-adenosine (pApA) as substrate to generate AMP, albeit at different catalytic efficiency. Using deletion mutants of each of the genes encoding c-di-AMP turnover proteins, we show by high resolution MS/MS that the intracellular concentration of c-di-AMP is increased in deletion mutants of the phosphodiesterases and non-detectable in the cdaA-mutant. We also detected pApA in mutants of the DhhP-type phosphodiesterase. Low and high levels of c-di-AMP were associated with longer and shorter chains of S. mitis, respectively indicating a role in regulation of cell division. The deletion mutant of the DhhP-type phosphodiesterase displayed slow growth and reduced rate of glucose metabolism.

• Marshall, Helina; Aguayo, Sebastian; Kilian, Mogens; Petersen, Fernanda Cristina; Bozec, Laurent & Brown, Jeremy S. (2020). In Vivo Relationship between the Nano-Biomechanical Properties of Streptococcal Polysaccharide Capsules and Virulence Phenotype. ACS Nano. ISSN 1936-0851. 14(1), p. 1070–1083. doi: 10.1021/acsnano.9b08631. Full text in Research Archive
• Pandey, Sushma; Follin-Arbelet, Benoit; Pun, Chin Bahadur; Gautam, Dej K.; Johannessen, Anne Christine & Petersen, Fernanda Cristina [Show all 8 contributors for this article] (2020). Helicobacter pylori was not detected in oral squamous cell carcinomas from cohorts of Norwegian and Nepalese patients. Scientific Reports. 10. doi: 10.1038/s41598-020-65694-7. Full text in Research Archive Show summary

  Helicobacter pylori (HP) infection is an established causative agent for gastric cancer. Although the oral cavity is a part of the gastrointestinal system, the presence and possible causative role of HP in oral squamous cell carcinoma (OSCC) is a subject of controversy. Therefore, the current study aimed to investigate HP infection in two cohorts of OSCC patients with different demographic characteristics, lifestyles and habitual risk factors. A total of 242 formalin-fixed paraffin-embedded OSCC specimens from two different patient cohorts (Norway, n = 171 and Nepal, n = 71) were used to examine HP using immunohistochemistry (IHC) and quantitative polymerase chain reaction (qPCR). Two different HP specific genes (23S rRNA and ureA) were used for TaqMan-based qPCR, and for subsequent verification using HP specific RIDAGENE HP kit and SYBR Green based qPCR. All of the OSCC specimens from both cohorts were found to be negative for HP infection with IHC and qPCR, although the positive control specimens tested positive. Our findings suggest that HP is absent in the examined OSCC cohorts, irrespective of race, lifestyle and habitual risk factors. This indicates that, in contrast to gastric cancer, HP is an unlikely contributing factor for OSCC pathogenesis.

• Shekhar, Sudhanshu; Khan, Rabia; Schenck, Karl & Petersen, Fernanda Cristina (2019). Intranasal Immunization with the Commensal Streptococcus mitis Confers Protective Immunity against Pneumococcal Lung Infection. Applied and Environmental Microbiology. ISSN 0099-2240. 85(6). doi: 10.1128/AEM.02235-18. Full text in Research Archive
• Junges, Roger; Sturød, Kjersti; Salvadori, Gabriela; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina (2019). Characterization of a Signaling System in Streptococcus mitis That Mediates Interspecies Communication with Streptococcus pneumoniae. Applied and Environmental Microbiology. ISSN 0099-2240. 85(2). doi: 10.1128/AEM.02297-18. Full text in Research Archive
• Junges, Roger; Salvadori, Gabriela; Chen, Tsute; Morrison, Donald A. & Petersen, Fernanda Cristina (2019). Hidden Gems in the Transcriptome Maps of Competent Streptococci. Frontiers in Molecular Biosciences. 5, p. 1–7. doi: 10.3389/fmolb.2018.00116. Full text in Research Archive Show summary

  Natural transformation is regarded as an important mechanism in bacteria that allows for adaptation to different environmental stressors by ensuring genome plasticity. Since the discovery of this phenomenon in Streptococcus pneumoniae, remarkable progress has been made in the understanding of the molecular mechanisms and pathways coordinating this process. Recently, the advent of high-throughput sequencing allows the posing of questions that address the system at a larger scale but also allow for the creation of high-resolution maps of transcription. Thus, while much is already known about genetic competence in streptococci, recent studies continue to reveal intricate novel regulation pathways and components. In this perspective article, we highlight the use of transcriptional profiling and mapping as a valuable resource in the identification and characterization of “hidden gems” pertinent to the natural transformation system. Such strategies have recently been employed in a variety of different species. In S. mutans, for example, genome editing combined with the power of promoter mapping and RNA-Seq allowed for the identification of a link between the ComCDE and the ComRS systems, a ComR positive feedback loop mediated by SigX, and the XrpA peptide, encoded within sigX, which inhibits competence. In S. pneumoniae, a novel member of the competence regulon termed BriC was found to be directly under control of ComE and to promote biofilm formation and nasopharyngeal colonization but not competence. Together these new technologies enable us to discover new links and to revisit old pathways in the compelling study of natural genetic transformation.

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• Petersen, Fernanda Cristina (2026). Beyond the gut, beyond borders: Uncovering the genetic potential of the respiratory microbiome. Full text in Research Archive
• Petersen, Fernanda Cristina (2026). Beyond the gut: Insights from the nasopharyngeal microbiome. Full text in Research Archive
• Ma, Siyao; Hong, Quan Nha; Levine, Alissa; Benali, Safaë; Petersen, Fernanda Cristina & Dawson, Aimee [Show all 11 contributors for this article] (2026). Antimicrobial Resistance Awareness and One Health Understanding among Dental Students in Quebec. Full text in Research Archive
• Dhariwal, Achal; Salvadori, Gabriela; Åmdal, Heidi Aarø; Dutta, Anirban; Mande, Sharmila & Nangia, Sushma [Show all 7 contributors for this article] (2026). Exploring Resistomes in Low-Microbial-Biomass Airway Microbiomes Using Functional Metagenomics. Full text in Research Archive
• Petersen, Fernanda Cristina (2025). Nasopharyngeal Metagenomics Reveals Trajectories Shaped by Antibiotics and a Specific Outbreak in Preterm Infants. Full text in Research Archive
• Petersen, Fernanda Cristina (2025). Early-Life Perturbations and the Shaping of the Infant Airway Microbiome. Full text in Research Archive
• Petersen, Fernanda Cristina & Dahle, Ulf R (2025). Antimicrobial resistance: “Wake-up call” or “Dream on”? - Faculty of Dentistry. Full text in Research Archive Show summary

  This crucial question framed the recent symposium organized by the NORSE and RESISFORCE networks in collaboration with the AMR Centre at the Norwegian Institute of Public Health (NIPH). The symposium was initiated by Fernanda Petersen, Professor at the faculty of Dentistry and the head of the RESISFORCE network and Ulf Dahle, the project leader of the NORSE-network and Head of the AMR Centre at NIPH.

• Petersen, Fernanda Cristina & Dahle, Ulf R (2025). The RESISFORCE Network. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2025). Early-life Antibiotics and Hospitalization Influence Nasopharyngeal Microbiome Dynamics in preterm infants. Full text in Research Archive
• Petersen, Fernanda Cristina; Nicolau, Belinda Farias & Junges, Roger (2025). Antimicrobial Resistance in Oral Health Care: A Global Call to Action. Full text in Research Archive
• Shekhar, Sudhanshu; Šrůtková, Dagmar; Dhariwal, Achal; Petersen, Fernanda Cristina & Schwarzer, Martin (2025). Human Nasal Microbiota Transplantation in Germ-Free Mice: A Model for Therapeutic Exploration. Full text in Research Archive
• Petersen, Fernanda Cristina & Dahle, Ulf R (2024). The RESISFORCE Network 2024. Full text in Research Archive
• Petersen, Fernanda Cristina & Dhariwal, Achal (2024). Antibiotic use: Microbial aftermath. Full text in Research Archive
• Petersen, Fernanda Cristina & Dahle, Ulf R (2024). Antimicrobial resistance: "Wake-up call" or "Dream on"? Full text in Research Archive
• Dhariwal, Achal; Dahle, Ulf R; Baker, Jonathon; Filho, Antonio Pedro Ricomini; Tabchoury, Cinthia & Petersen, Fernanda Cristina (2024). Collaborative Approaches to Antimicrobial Resistance Research in Dentistry. Full text in Research Archive
• Sagen, Andreas Solberg; Shawrob, Kazi Shefaul Mulk; Petersen, Fernanda Cristina & Junges, Roger (2024). Horizontal gene transfer and antibiotic resistance: activation of the competence system for DNA uptake in Streptococcus constellatus. Full text in Research Archive
• Shawrob, Kazi; Dhariwal, Achal; Silva, Gabriela Salvadori Da; Petersen, Fernanda Cristina & Junges, Roger (2024). Mapping antibiotic resistance patterns in Streptococcus pneumoniae. Full text in Research Archive
• Shawrob, Kazi Shefaul Mulk; Dhariwal, Achal; Silva, Gabriela Salvadori Da; Petersen, Fernanda Cristina & Junges, Roger (2024). Mapping antibiotic resistance patterns in Streptococcus pneumoniae. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2024). Impacts of Population-Level Antibiotic Consumption on Antimicrobial Resistance: A One-Health Approach. Full text in Research Archive
• Rogala, Agnes; Zaytseva-Zotova, Daria; Baran, Anna; Petersen, Fernanda Cristina & Tiainen, Hanna (2024). Inactivated probiotics on tannic acid nanocoating - enhancing bioactivity for improved bone and soft tissue integration. Full text in Research Archive
• Sagen, Andreas Solberg; Shawrob, Kazi Shefaul Mulk; Petersen, Fernanda Cristina & Junges, Roger (2024). Incorporating antibiotic resistance through natural transformation in Streptococcus constellatus. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2024). Exploring the antibiotic resistance gene profiles in the nasopharynx of Preterm Infants: Longitudinal impact of hospitalization and antibiotic exposure. Full text in Research Archive Show summary

  Introducing our research, we address the urgent need to understand antibiotic resistance within respiratory microbial communities, which are significant contributors to antimicrobial resistance-related mortality. Utilizing shotgun metagenomics, our study investigates the nasopharynx resistome development in preterm infants, particularly focusing on the impact of early antibiotic exposure and its association with clinical factors. Our comprehensive analysis reveals widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) and dynamic changes in resistome composition, diversity, and abundance following antibiotic administration. Notably, persistent ARGs linked with Serratia marcescens underscore the enduring impact of hospitalization. These findings emphasize the critical importance of further exploring this reservoir of pathogens and ARGs, shedding light on the collateral effects of antibiotics and prolonged hospital stays.

• Dhariwal, Achal & Petersen, Fernanda Cristina (2024). ResistoXplorer 2.0: an improved bioinformatics tool for comprehensive statistical, visual and integrative analysis of AMR metagenomic sequencing data. Full text in Research Archive Show summary

  Background and Aim: Antimicrobial resistance (AMR) is considered as one of the most urgent threats to global public health, and metagenomic-based investigations featuring high-throughput analysis of sequence data are increasingly common and important across human, animal, agricultural and environmental sectors. The resulting large and complex datasets often require powerful, yet user-friendly bioinformatics tools to unveil key patterns, identify significant biomarkers, and explore potential activities. Method: We previously introduced ResistoXplorer, a user-friendly web-based tool for bench researchers and clinicians to perform comprehensive downstream analysis on AMR genes (resistome) abundance profiles. ResistoXplorer is developed using three open-source programming languages: Java, R, and JavaScript. Results: Compared to the previous version, ResistoXplorer 2.0 features three new modules: (i) a raw data processing module for metagenomic sequencing data processing and ARGs annotation that connects directly with the ARG Table module for comprehensive visual, statistical and exploratory analysis; (ii) a time series analysis module that incorporates robust, powerful as well as more advanced statistical and visualization approaches tailored for longitudinal studies; and (iii) an interactive 2D/3D network-based visual analytics system providing the topological view of public ARG databases to discover and gain novel biological insights. Other significant improvements include interactive visualizations for common graphical outputs, updated statistical methods to perform integrative analysis of paired microbiome and resistome datasets. The underlying ResistoXplorerR package will also be released to enable transparent and reproducible analysis. Applications: ResistoXplorer will be a one stop shop that allows AMR researchers to thoroughly explore their metagenomic data via intuitive web interfaces. Development of such bioinformatics tool suite promotes the application of metagenomics-based investigations for surveillance, enhance our understanding of AMR and its dynamics in humans, animals, and environmental microbial communities. ResistoXplorer 2.0 will be publicly available at resistoxplorer.no.

• Dhariwal, Achal; Petersen, Fernanda Cristina & Salvadori, Gabriela (2024). Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Full text in Research Archive
• Shawrob, Kazi Shefaul Mulk; Dhariwal, Achal; Silva, Gabriela Salvadori Da; Petersen, Fernanda Cristina & Junges, Roger (2024). Insights into multidrug resistance in Streptococcus pneumoniae. Full text in Research Archive
• Dhariwal, Achal; Petersen, Fernanda Cristina & Salvadori, Gabriela (2024). Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2024). Hands-on Bioinformatics on AMR data. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2024). Bioinformatics (Upstream) analysis of metagenomic resistome data. Full text in Research Archive
• Petersen, Fernanda Cristina; Soni, Nancy; Rued, Britta; Sribasgaran, Biramitha & Ghafoor, Saba (2023). Resisforce: an international partnership bringing together research and education on biofilm and antimicrobial resistance. Full text in Research Archive
• Petersen, Fernanda Cristina (2023). Experiences from the FutureLearn Online Course Exploring the Landscape of Antibiotic Resistance in Microbiomes. Full text in Research Archive
• Dahle, Ulf R & Petersen, Fernanda Cristina (2023). Antimicrobial resistance: A challenge that crosses borders. Full text in Research Archive Show summary

  https://www.uio.no/om/aktuelt/universitetsplassen/domus-bibliotheca/arrangementer/2023/resisforce-norse-program-db-english.pdf

• Dhariwal, Achal; Petersen, Fernanda Cristina; Chen, Tsute & Baker, Jonathon (2023). Introduction to Resistome: key concepts and hands-on analysis. Full text in Research Archive
• Smith, Clay; Nicolau, Belinda Farias; Junges, Roger; Petersen, Fernanda Cristina & Levine, Alissa (2023). Perceptions, Attitudes, Beliefs, and Recommendations Regarding Antimicrobial Resistance and Antibiotic Prescriptions: A Qualitative Study Among McGill DMD Students. Full text in Research Archive
• McLaughlin, Kendra J.; Junges, Roger; Levine, Alissa; Petersen, Fernanda Cristina & Nicolau, Belinda Farias (2023). Exploring Dental Professionals' Attitudes Toward Antimicrobial Resistance and Their Role in Mitigating Health Risks. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2022). Using ResistoXplorer for comprehensive visual, statistical, and exploratory analysis of AMR metagenomic data. Full text in Research Archive
• Brar, Navdeep Kaur; Junges, Roger; Hakansson, Anders P. & Petersen, Fernanda Cristina (2022). General IADR conference. The Impact of HAMLET, a Human-Milk Protein Complex, on the Ecology of the Oral Microbiome. Full text in Research Archive
• Ghafoor, Saba; Salvadori, Gabriela; Ricomini-Filho, Antônio Pedro; Marques, Dalton; Petersen, Fernanda Cristina & Nicolau, Belinda Farias [Show all 8 contributors for this article] (2022). Dental education on antibiotic resistance: a qualitative analysis of the educators’ perspectives. Full text in Research Archive
• Ghafoor, Saba; Salvadori, Gabriela; Ricomini-Filho, Antônio Pedro; Marques, Dalton; Petersen, Fernanda Cristina & Nicolau, Belinda Farias [Show all 8 contributors for this article] (2022). Dental education on antibiotic resistance. Full text in Research Archive
• Brar, Navdeep Kaur; Dhariwal, Achal; Junges, Roger; Håkansson, Anders & Petersen, Fernanda Cristina (2022). Potential of HAMLET, a human milk protein-lipid complex, to modulate ecological changes in the oral microbiome induced by amoxicillin. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2022). Impact of Long-Term Amoxicillin Treatment on the Gut Microbiome and Resistome. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2022). ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data. Full text in Research Archive
• Petersen, Fernanda Cristina (2022). Antimicrobial resistance: challenges and prospects Closing remarks. Full text in Research Archive
• Petersen, Fernanda Cristina (2022). Antimicrobial resistance: challenges and prospects Opening remarks. Full text in Research Archive
• Petersen, Fernanda Cristina (2022). Collateral effects of antibiotics on the human microbiome: does it matter? Full text in Research Archive
• Brar, Navdeep Kaur; Dhariwal, Achal; Åmdal, Heidi Aarø; Junges, Roger; Salvadori, Gabriela & Petersen, Fernanda Cristina (2022). The Impact of Ampicillin on the Oral Microbiome and Resistome. Full text in Research Archive
• Rajar, Polona; Dhariwal, Achal; Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø & Berild, Dag [Show all 12 contributors for this article] (2022). Microbial DNA extraction of high-host content and low biomass samples: optimized protocol for nasopharynx metagenomic studies. Full text in Research Archive Show summary

  Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirates from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). PCR results were indicative of achieved microbial enrichment. Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.

• Petersen, Fernanda Cristina (2022). Antibiotic exposure: the growing concern about off-target effects. Full text in Research Archive
• Petersen, Fernanda Cristina (2022). Off-target impact of antibiotics on the microbiome. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2021). Resistoxplorer: A web-based tool for visual, statistical and exploratory analysis of resistome data. Full text in Research Archive
• Ghafoor, Saba; Petersen, Fernanda Cristina & Junges, Roger (2021). The global challenge of dental education on antibiotic resistance: a qualitative interview study. Full text in Research Archive
• Shekhar, Sudhanshu; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina (2021). Vaccination with the commensal Streptococcus mitis expressing pneumococcal serotype 5 capsule elicits IgG/IgA and Th17 responses against Streptococcus pneumoniae. Full text in Research Archive
• Petersen, Fernanda Cristina (2021). Let's talk about microbiomes. Full text in Research Archive
• Petersen, Fernanda Cristina (2021). Off-target impact of antibiotics. Full text in Research Archive Show summary

  For almost every drug, there is a trade-off between benefits and risks. For antibiotics, prescription to humans has been largely based on a «better safe than sorry» or «just in case» approach, with little attention paid to risks. In the awake of the antibiotic crisis and the increased focus on a balanced microbiome for health, our attention is now turning to risks, including the unwanted collateral effects on the microbiome. Although antibiotics are used to target specific bacteria in the site of infection, off-target effects are virtually unavoidable. What happens when you take antibiotics is that your microbiome is hit by different antibiotic concentrations. Although these are usually lower than in the targeted infection sites, these concentrations can affect the microbiome, and select for and promote the development of antibiotic resistance. Recent studies driven by advancements in metagenomics are already revealing the impact of antibiotics in enriching for antibiotic resistance among commensals and major pathogens found at off-target sites. As the field moves forward, we expect novel approaches to reduce collateral effects, and an increase in studies providing high quality evidence on the off-target impact of antibiotics.

• Brar, Navdeep Kaur; Junges, Roger; Hakansson, Anders P. & Petersen, Fernanda Cristina (2021). The Impact of HAMLET, a Human-Milk Protein Complex, on the Ecology of the Oral Microbiome. Full text in Research Archive
• Petersen, Fernanda Cristina; Dhariwal, Achal; Bråten, Lars Christian Haugli; Sturød, Kjersti; Junges, Roger & Salvadori, Gabriela [Show all 10 contributors for this article] (2021). Off-target impact of long-term amoxicillin treatment. Full text in Research Archive
• Rajar, Polona & Petersen, Fernanda Cristina (2020). Born in the twilight of antibiotics: Implications of antibiotic use to the preterm infant respiratory microbiome and resistome development. Full text in Research Archive
• Petersen, Fernanda Cristina (2020). Metagenomic approaches for analysis of AMR in microbiomes. Full text in Research Archive
• Shekhar, Sudhanshu & Petersen, Fernanda Cristina (2020). Neonatal exposure to therapeutic antibiotic regimens suppresses peripheral and mucosal T cell responses. Full text in Research Archive
• Petersen, Fernanda Cristina; Dhariwal, Achal; Sturød, Kjersti & Nickelsen, Trine (2020). Babyer får penicillin ? og uheldige bakterier blusser opp. [Internet]. Apollon. Full text in Research Archive
• Figueira, Louise Morais Dornelas & Petersen, Fernanda Cristina (2020). Cross-Kingdom Impact of Antimicrobial. Full text in Research Archive
• Dhariwal, Achal; Petersen, Fernanda Cristina; Junges, Roger & Chen, Tsute (2020). ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data. Full text in Research Archive
• Petersen, Fernanda Cristina (2020). Towards epi-omic approaches in the study of microbiomes. Full text in Research Archive
• Bergersen, Linda Hildegard; Petersen, Fernanda Cristina & Dahle, Ulf R (2020). Kort sagt, fredag 27. mars. [Journal]. Aftenposten. Full text in Research Archive
• Petersen, Fernanda Cristina (2019). No time to wait: living in the twilight of antibiotics. Full text in Research Archive
• Pandey, Sushma; Follin-Arbelet, Benoit; Pun, Chin Babadur; Gautam, Dej K.; Johannessen, Anne C. & Petersen, Fernanda Cristina [Show all 8 contributors for this article] (2019). Helicobacter pylori is not present in oral squamous cell carcinomas from cohorts of Norwegian and Nepalese patients. Full text in Research Archive
• Dhariwal, Achal & Petersen, Fernanda Cristina (2019). Visual exploration and network-based analysis of resistome data. Full text in Research Archive
• Pagotto, LL; Junges, Roger; Salvadori, Gabriela; Petersen, Fernanda Cristina & Filho, AP Ricomini (2019). Inhibition of Streptococcus mutans competence by chlorhexidine gluconate. Full text in Research Archive

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