This page has only limited features, please log in for full access.

Unclaimed
Lotta-Riina Sundberg
University of Jyvaskyla, Department of Biological and Environmental Science and Nanoscience Center

Honors and Awards

The user has no records in this section


Career Timeline

The user has no records in this section.


Short Biography

The user biography is not available.
Following
Followers
Co Authors
The list of users this user is following is empty.
Following: 0 users

Feed

Article
Published: 10 August 2021
Reads 0
Downloads 0

Parasitism by bacteriophages has led to the evolution of a variety of defense mechanisms in their host bacteria. However, it is unclear what factors lead to specific defenses being deployed upon phage infection. To explore this question, we exposed the bacterial fish pathogen Flavobacterium columnare to its virulent phage V156 in the presence of a eukaryotic host signal (mucin). All tested conditions led to some level of innate immunity, but the presence of mucin led to a dramatic increase in CRISPR spacer acquisition, especially in low nutrient conditions where over 60% of colonies had obtained at least one new spacer. Additionally, we show that the presence of a competitor bacterium further increases CRISPR spacer acquisition in F. columnare. These results suggest that ecological factors are important in determining defense strategies against phages, and that the concentration of phages on metazoan surfaces may select for the diversification of bacterial immune systems.

ACS Style

Gabriel Mf Almeida; Ville Hoikkala; Janne Ravantti; Noora Rantanen; Lotta-Riina Sundberg. Mucin induces CRISPR-Cas defence in an opportunistic pathogen. 2021, 1 .

AMA Style

Gabriel Mf Almeida, Ville Hoikkala, Janne Ravantti, Noora Rantanen, Lotta-Riina Sundberg. Mucin induces CRISPR-Cas defence in an opportunistic pathogen. . 2021; ():1.

Chicago/Turabian Style

Gabriel Mf Almeida; Ville Hoikkala; Janne Ravantti; Noora Rantanen; Lotta-Riina Sundberg. 2021. "Mucin induces CRISPR-Cas defence in an opportunistic pathogen." , no. : 1.

Article
Published: 27 July 2021 in Applied and Environmental Microbiology
Reads 0
Downloads 0

Phage resistance of infectious bacteria is a common phenomenon posing challenges for the development of phage therapy. Along with a growing world population and the need for increased food production, constantly intensifying animal farming has to face increasing problems of infectious diseases.

ACS Style

Heidi M. T. Kunttu; Anniina Runtuvuori-Salmela; Krister Sundell; Tom Wiklund; Mathias Middelboe; Lotta Landor; Roghaieh Ashrafi; Ville Hoikkala; Lotta-Riina Sundberg. Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and the Type IX Secretion System. Applied and Environmental Microbiology 2021, 87, AEM0081221 .

AMA Style

Heidi M. T. Kunttu, Anniina Runtuvuori-Salmela, Krister Sundell, Tom Wiklund, Mathias Middelboe, Lotta Landor, Roghaieh Ashrafi, Ville Hoikkala, Lotta-Riina Sundberg. Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and the Type IX Secretion System. Applied and Environmental Microbiology. 2021; 87 (16):AEM0081221.

Chicago/Turabian Style

Heidi M. T. Kunttu; Anniina Runtuvuori-Salmela; Krister Sundell; Tom Wiklund; Mathias Middelboe; Lotta Landor; Roghaieh Ashrafi; Ville Hoikkala; Lotta-Riina Sundberg. 2021. "Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and the Type IX Secretion System." Applied and Environmental Microbiology 87, no. 16: AEM0081221.

Journal article
Published: 27 July 2021 in Antibiotics
Reads 0
Downloads 0

Viruses of bacteria, bacteriophages, specifically infect their bacterial hosts with minimal effects on the surrounding microbiota. They have the potential to be used in the prevention and treatment of bacterial infections, including in the field of food production. In aquaculture settings, disease-causing bacteria are often transmitted through the water body, providing several applications for phage-based targeting of pathogens, in the rearing environment, and in the fish. We tested delivery of phages by different methods (via baths, in phage-coated material, and via oral delivery in feed) to prevent and treat Flavobacterium columnare infections in rainbow trout fry using three phages (FCOV-S1, FCOV-F2, and FCL-2) and their hosts (FCO-S1, FCO-F2, and B185, respectively). Bath treatments given before bacterial infection and at the onset of the disease symptoms were the most efficient way to prevent F. columnare infections in rainbow trout, possibly due to the external nature of the disease. In a flow-through system, the presence of phage-coated plastic sheets delayed the onset of the disease. The oral administration of phages first increased disease progression, although total mortality was lower at the end of the experiment. When analysed for shelf-life, phage titers remained highest when maintained in bacterial culture media and in sterile lake water. Our results show that successful phage therapy treatment in the aquaculture setting requires optimisation of phage delivery methods in vivo.

ACS Style

Heidi Kunttu; Anniina Runtuvuori-Salmela; Mathias Middelboe; Jason Clark; Lotta-Riina Sundberg. Comparison of Delivery Methods in Phage Therapy against Flavobacterium columnare Infections in Rainbow Trout. Antibiotics 2021, 10, 914 .

AMA Style

Heidi Kunttu, Anniina Runtuvuori-Salmela, Mathias Middelboe, Jason Clark, Lotta-Riina Sundberg. Comparison of Delivery Methods in Phage Therapy against Flavobacterium columnare Infections in Rainbow Trout. Antibiotics. 2021; 10 (8):914.

Chicago/Turabian Style

Heidi Kunttu; Anniina Runtuvuori-Salmela; Mathias Middelboe; Jason Clark; Lotta-Riina Sundberg. 2021. "Comparison of Delivery Methods in Phage Therapy against Flavobacterium columnare Infections in Rainbow Trout." Antibiotics 10, no. 8: 914.

Journal article
Published: 30 April 2021 in Microorganisms
Reads 0
Downloads 0

The microbial community surrounding fish eyed eggs can harbor pathogenic bacteria. In this study we focused on rainbow trout (Oncorhynchus mykiss) eyed eggs and the potential of bacteriophages against the pathogenic bacteria Flavobacterium psychrophilum and F. columnare. An infection bath method was first established, and the effects of singular phages on fish eggs was assessed (survival of eyed eggs, interaction of phages with eyed eggs). Subsequently, bacteria-challenged eyed eggs were exposed to phages to evaluate their effects in controlling the bacterial population. Culture-based methods were used to enumerate the number of bacteria and/or phages associated with eyed eggs and in the surrounding environment. The results of the study showed that, with our infection model, it was possible to re-isolate F. psychrophilum associated with eyed eggs after the infection procedure, without affecting the survival of the eggs in the short term. However, this was not possible for F. columnare, as this bacterium grows at higher temperatures than the ones recommended for incubation of rainbow trout eyed eggs. Bacteriophages do not appear to negatively affect the survival of rainbow trout eyed eggs and they do not seem to strongly adhere to the surface of eyed eggs either. Finally, the results demonstrated a strong potential for short term (24 h) phage control of F. psychrophilum. However, further studies are needed to explore if phage control can be maintained for a longer period and to further elucidate the mechanisms of interactions between Flavobacteria and their phages in association with fish eggs.

ACS Style

Valentina Donati; Inger Dalsgaard; Anniina Runtuvuori-Salmela; Heidi Kunttu; Johanna Jørgensen; Daniel Castillo; Lotta-Riina Sundberg; Mathias Middelboe; Lone Madsen. Interactions between Rainbow Trout Eyed Eggs and Flavobacterium spp. Using a Bath Challenge Model: Preliminary Evaluation of Bacteriophages as Pathogen Control Agents. Microorganisms 2021, 9, 971 .

AMA Style

Valentina Donati, Inger Dalsgaard, Anniina Runtuvuori-Salmela, Heidi Kunttu, Johanna Jørgensen, Daniel Castillo, Lotta-Riina Sundberg, Mathias Middelboe, Lone Madsen. Interactions between Rainbow Trout Eyed Eggs and Flavobacterium spp. Using a Bath Challenge Model: Preliminary Evaluation of Bacteriophages as Pathogen Control Agents. Microorganisms. 2021; 9 (5):971.

Chicago/Turabian Style

Valentina Donati; Inger Dalsgaard; Anniina Runtuvuori-Salmela; Heidi Kunttu; Johanna Jørgensen; Daniel Castillo; Lotta-Riina Sundberg; Mathias Middelboe; Lone Madsen. 2021. "Interactions between Rainbow Trout Eyed Eggs and Flavobacterium spp. Using a Bath Challenge Model: Preliminary Evaluation of Bacteriophages as Pathogen Control Agents." Microorganisms 9, no. 5: 971.

Journal article
Published: 27 April 2021 in mBio
Reads 0
Downloads 0

CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader’s genome.

ACS Style

Ville Hoikkala; Janne Ravantti; César Díez-Villaseñor; Marja Tiirola; Rachel A. Conrad; Mark J. McBride; Sylvain Moineau; Lotta-Riina Sundberg. Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System. mBio 2021, 12, 1 .

AMA Style

Ville Hoikkala, Janne Ravantti, César Díez-Villaseñor, Marja Tiirola, Rachel A. Conrad, Mark J. McBride, Sylvain Moineau, Lotta-Riina Sundberg. Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System. mBio. 2021; 12 (2):1.

Chicago/Turabian Style

Ville Hoikkala; Janne Ravantti; César Díez-Villaseñor; Marja Tiirola; Rachel A. Conrad; Mark J. McBride; Sylvain Moineau; Lotta-Riina Sundberg. 2021. "Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System." mBio 12, no. 2: 1.

Journal article
Published: 22 March 2021 in Antibiotics
Reads 0
Downloads 0

Environmental heterogeneity is a central component influencing the virulence and epidemiology of infectious diseases. The number and distribution of susceptible hosts determines disease transmission opportunities, shifting the epidemiological threshold between the spread and fadeout of a disease. Similarly, the presence and diversity of other hosts, pathogens and environmental microbes, may inhibit or accelerate an epidemic. This has important applied implications in farming environments, where high numbers of susceptible hosts are maintained in conditions of minimal environmental heterogeneity. We investigated how the quantity and quality of aquaculture enrichments (few vs. many stones; clean stones vs. stones conditioned in lake water) influenced the severity of infection of a pathogenic bacterium, Flavobacterium columnare, in salmonid fishes. We found that the conditioning of the stones significantly increased host survival in rearing tanks with few stones. A similar effect of increased host survival was also observed with a higher number of unconditioned stones. These results suggest that a simple increase in the heterogeneity of aquaculture environment can significantly reduce the impact of diseases, most likely operating through a reduction in pathogen transmission (stone quantity) and the formation of beneficial microbial communities (stone quality). This supports enriched rearing as an ecological and economic way to prevent bacterial infections with the minimal use of antimicrobials.

ACS Style

Anssi Karvonen; Ville Räihä; Ines Klemme; Roghaieh Ashrafi; Pekka Hyvärinen; Lotta-Riina Sundberg. Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics. Antibiotics 2021, 10, 335 .

AMA Style

Anssi Karvonen, Ville Räihä, Ines Klemme, Roghaieh Ashrafi, Pekka Hyvärinen, Lotta-Riina Sundberg. Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics. Antibiotics. 2021; 10 (3):335.

Chicago/Turabian Style

Anssi Karvonen; Ville Räihä; Ines Klemme; Roghaieh Ashrafi; Pekka Hyvärinen; Lotta-Riina Sundberg. 2021. "Quantity and Quality of Aquaculture Enrichments Influence Disease Epidemics and Provide Ecological Alternatives to Antibiotics." Antibiotics 10, no. 3: 335.

Journal article
Published: 02 December 2020 in Microorganisms
Reads 0
Downloads 0

The role of prophages in the evolution, diversification, or virulence of the fish pathogen Flavobacterium columnare has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the F. columnare type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of F. columnare Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between F. columnare strains and the fF4 phage, and another putative prophage in the F. columnare strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen F. columnare ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese F. columnare strains. Second, CRISPR analysis revealed four F. columnare strains that contain unique spacers targeting different regions of the putative prophage p49512 in the F. columnare strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the F. columnare prophages and different host strains.

ACS Style

Elina Laanto; Janne J. Ravantti; Lotta-Riina Sundberg. Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen. Microorganisms 2020, 8, 1919 .

AMA Style

Elina Laanto, Janne J. Ravantti, Lotta-Riina Sundberg. Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen. Microorganisms. 2020; 8 (12):1919.

Chicago/Turabian Style

Elina Laanto; Janne J. Ravantti; Lotta-Riina Sundberg. 2020. "Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen." Microorganisms 8, no. 12: 1919.

Preprint content
Published: 02 October 2020
Reads 0
Downloads 0

Increasing problems with antibiotic resistance has directed interest towards phages as tools to treat bacterial infections in the aquaculture industry. However, phage resistance evolves rapidly in bacteria posing a challenge for successful phage therapy. To investigate phage resistance in the fish pathogenic bacterium Flavobacterium columnare, two phage-sensitive, virulent wild-type isolates, FCO-F2 and FCO-F9, were exposed to phages and subsequently analyzed for bacterial viability and colony morphology. Twenty-four phage-exposed isolates were further characterized for phage resistance, antibiotic susceptibility, motility, adhesion and biofilm formation on polystyrene surface, protease activity, whole genome sequencing and virulence against rainbow trout fry. Bacterial viability first decreased in the exposure cultures, subsequently increasing after 1-2 days. Simultaneously, the colony morphology of the phage-exposed isolates changed from original rhizoid to rough. The rough isolates arising in phage exposure were phage-resistant with low virulence, whereas rhizoid isolates maintained phage sensitivity, though reduced, and high virulence. Gliding motility and protease activity were also related to the phage sensitivity. Observed genetic mutations in phage-resistant isolates were mostly located in genes coding for type IX secretion system, a component of the flavobacterial gliding motility machinery. However, there were mutational differences between individual isolates, and not all phage-resistant isolates had genetic mutations. This indicates that development of phage resistance in F. columnare probably is a multifactorial process including both genetic mutations and changes in gene expression. Phage resistance may not, however, be a challenge for development of phage therapy against F. columnare infections, since phage resistance is associated with decrease in bacterial virulence. Importance: Phage resistance of infectious bacteria is a common phenomenon posing challenges for development of phage therapy. Along with growing World population and need for increased food production, constantly intensifying animal farming has to face increasing problems of infectious diseases. Columnaris disease, caused by F. columnare, is a worldwide threat for salmonid fry and juvenile farming. Without antibiotic treatments, infections can lead to 100% mortality in a fish stock. Phage therapy of columnaris disease would reduce a development of antibiotic-resistant bacteria and antibiotic loads by the aquaculture industry, but phage-resistant bacterial isolates may become a risk. However, phenotypic and genetic characterization of phage-resistant F. columnare isolates in this study revealed that they are less virulent than phage-sensitive isolates and thus not a challenge for phage therapy against columnaris disease. This is a valuable information for the fish farming industry globally when considering phage-based prevention and curing methods for F. columnare infections.

ACS Style

Heidi Mt Kunttu; Anniina Runtuvuori-Salmela; Krister Sundell; Tom Wiklund; Mathias Middelboe; Lotta Landor; Roghaieh Ashrafi; Ville Hoikkala; Lotta-Riina Sundberg. Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System. 2020, 1 .

AMA Style

Heidi Mt Kunttu, Anniina Runtuvuori-Salmela, Krister Sundell, Tom Wiklund, Mathias Middelboe, Lotta Landor, Roghaieh Ashrafi, Ville Hoikkala, Lotta-Riina Sundberg. Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System. . 2020; ():1.

Chicago/Turabian Style

Heidi Mt Kunttu; Anniina Runtuvuori-Salmela; Krister Sundell; Tom Wiklund; Mathias Middelboe; Lotta Landor; Roghaieh Ashrafi; Ville Hoikkala; Lotta-Riina Sundberg. 2020. "Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System." , no. : 1.

Preprint content
Published: 23 September 2020
Reads 0
Downloads 0

Intensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage-based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 phages against F. columnare from Finland and Sweden. Bacterial isolates were virulent on rainbow trout (Oncorhynchus mykiss) and fell into four previously described genetic groups A, C, E and G, with genetic groups C and E being the most virulent. Phage host range studied against a collection of 228 bacterial isolates demonstrated modular infection patterns based on host genetic group. Phages infected contemporary and previously isolated bacterial hosts, but bacteria isolated most recently were generally resistant to previously isolated phages. Despite large differences in geographical origin, isolation year or host range of the phages, whole genome sequencing of 56 phages showed high level of genetic similarity to previously isolated F. columnare phages (Ficleduovirus, Myoviridae). Altogether, this phage collection demonstrates a potential to be used in phage therapy.

ACS Style

Anniina Runtuvuori-Salmela; Heidi Mt Kunttu; Elina Laanto; Gabriel Mdf Almeida; Kati Makela; Mathias Middelboe; Lotta-Riina Sundberg. Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control. 2020, 1 .

AMA Style

Anniina Runtuvuori-Salmela, Heidi Mt Kunttu, Elina Laanto, Gabriel Mdf Almeida, Kati Makela, Mathias Middelboe, Lotta-Riina Sundberg. Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control. . 2020; ():1.

Chicago/Turabian Style

Anniina Runtuvuori-Salmela; Heidi Mt Kunttu; Elina Laanto; Gabriel Mdf Almeida; Kati Makela; Mathias Middelboe; Lotta-Riina Sundberg. 2020. "Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control." , no. : 1.

Preprint content
Published: 12 June 2020 in bioRxiv
Reads 0
Downloads 0

SummaryPhenotypic variation allows adaptation of opportunistic pathogens to variable conditions in the outside-host environment with strong effects on their epidemiology and pathogenicity in hosts. Here we found that the isolates of an opportunistic fish pathogen Flavobacterium columnare from fish farming environment had higher phenotypic variation between two morphotypes in growth, as compared to the isolates from the natural water environment. The rough morphotypes had higher growth rate than the rhizoid morphotypes especially in the higher resource concentrations and in the higher temperature, but only if the isolate was originating from the fish farms. Rhizoid morphotype was more virulent than the rough type regardless of their origin. However, the virulence of the rough type increased sharply with the size of the fish, and the bacterial isolates from the gills of diseased fish were rhizoid type, indicating a reversal of the rough morphotype into rhizoid in contact with the fish. The high growth rate of the rough morphotype combined with the morphotype reversibility could increase the probability of columnaris epidemics at fish farms. Our findings suggest that intensive farming imposes different selection pressures on bacterial survival in the outside-host environment and its transmission compared to the natural water environment.

ACS Style

Katja Pulkkinen; Tarmo Ketola; Jouni Laakso; Johanna Mappes; Lotta-Riina Sundberg. Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen. bioRxiv 2020, 1 .

AMA Style

Katja Pulkkinen, Tarmo Ketola, Jouni Laakso, Johanna Mappes, Lotta-Riina Sundberg. Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen. bioRxiv. 2020; ():1.

Chicago/Turabian Style

Katja Pulkkinen; Tarmo Ketola; Jouni Laakso; Johanna Mappes; Lotta-Riina Sundberg. 2020. "Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen." bioRxiv , no. : 1.

Journal article
Published: 29 May 2020 in Antibiotics
Reads 0
Downloads 0

Phage therapy is becoming a widely recognized alternative for fighting pathogenic bacteria due to increasing antibiotic resistance problems. However, one of the common concerns related to the use of phages is the evolution of bacterial resistance against the phages, putatively disabling the treatment. Experimental adaptation of the phage (phage training) to infect a resistant host has been used to combat this problem. Yet, there is very little information on the trade-offs of phage infectivity and host range. Here we co-cultured a myophage FCV-1 with its host, the fish pathogen Flavobacterium columnare, in lake water and monitored the interaction for a one-month period. Phage resistance was detected within one day of co-culture in the majority of the bacterial isolates (16 out of the 18 co-evolved clones). The primary phage resistance mechanism suggests defense via surface modifications, as the phage numbers rose in the first two days of the experiment and remained stable thereafter. However, one bacterial isolate had acquired a spacer in its CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas locus, indicating that also CRISPR-Cas defense was employed in the phage-host interactions. After a week of co-culture, a phage isolate was obtained that was able to infect 18 out of the 32 otherwise resistant clones isolated during the experiment. Phage genome sequencing revealed several mutations in two open reading frames (ORFs) likely to be involved in the regained infectivity of the evolved phage. Their location in the genome suggests that they encode tail genes. Characterization of this evolved phage, however, showed a direct cost for the ability to infect several otherwise resistant clones—adsorption was significantly lower than in the ancestral phage. This work describes a method for adapting the phage to overcome phage resistance in a fish pathogenic system.

ACS Style

Elina Laanto; Kati Mäkelä; Ville Hoikkala; Janne J. Ravantti; Lotta-Riina Sundberg. Adapting a Phage to Combat Phage Resistance. Antibiotics 2020, 9, 1 .

AMA Style

Elina Laanto, Kati Mäkelä, Ville Hoikkala, Janne J. Ravantti, Lotta-Riina Sundberg. Adapting a Phage to Combat Phage Resistance. Antibiotics. 2020; 9 (6):1.

Chicago/Turabian Style

Elina Laanto; Kati Mäkelä; Ville Hoikkala; Janne J. Ravantti; Lotta-Riina Sundberg. 2020. "Adapting a Phage to Combat Phage Resistance." Antibiotics 9, no. 6: 1.

Journal article
Published: 13 May 2020 in Water
Reads 0
Downloads 0

Presence of antimicrobial cocktails in the hydrological cycles is of interest because of their potential to mediate antimicrobial resistance within the natural environment. In this study, we determined the concentrations of selected antibiotics and antiretroviral drugs (ARVDs) in wastewater treatment plant (WWTP) effluent, effluent suspended particulate matter (SPM), surface waters and river sediments in Kenya in order to determine the extent of pollution within the sampled environment. Target analysis for the most common antibiotics and ARVDs was done. Sulfamethoxazole (SMX), ciprofloxacin (CIP), trimethoprim (TMP), norfloxacin (NOR), zidovidine (ZDV), lamivudine (3TC) and nevirapine (NVP) were analyzed using LC-ESI-MS/MS. Effluent aqueous phase had concentrations ranging between 1.2 µg L−1 to 956.4 µg L−1 while the effluent SPM showed higher concentrations, ranging between 2.19 mg Kg−1 and 82.26 mg Kg−1. This study shows emission of active pharmaceutical ingredients (APIs) from WWTP to the environment mainly occurs via the SPM phase, which is usually overlooked in environmental analyses. Concentrations in surface waters and river sediments ranged between 1.1 µg L−1 to 228 µg L−1 and 11 µg Kg−1 to 4125 µg Kg−1 respectively. ARVDs occurred at consistently higher concentrations than antibiotics in both the aqueous and solid samples. The wastewater treatment plants and lagoons where sludge degradation should occur, are sources of active pharmaceutical ingredients (APIs) including transformational products, nutrients and organic matter that are released back to the aqueous phase.

ACS Style

Pius Kairigo; Elijah Ngumba; Lotta-Riina Sundberg; Anthony Gachanja; Tuula Tuhkanen. Contamination of Surface Water and River Sediments by Antibiotic and Antiretroviral Drug Cocktails in Low and Middle-Income Countries: Occurrence, Risk and Mitigation Strategies. Water 2020, 12, 1376 .

AMA Style

Pius Kairigo, Elijah Ngumba, Lotta-Riina Sundberg, Anthony Gachanja, Tuula Tuhkanen. Contamination of Surface Water and River Sediments by Antibiotic and Antiretroviral Drug Cocktails in Low and Middle-Income Countries: Occurrence, Risk and Mitigation Strategies. Water. 2020; 12 (5):1376.

Chicago/Turabian Style

Pius Kairigo; Elijah Ngumba; Lotta-Riina Sundberg; Anthony Gachanja; Tuula Tuhkanen. 2020. "Contamination of Surface Water and River Sediments by Antibiotic and Antiretroviral Drug Cocktails in Low and Middle-Income Countries: Occurrence, Risk and Mitigation Strategies." Water 12, no. 5: 1376.

Preprint content
Published: 20 February 2020
Reads 0
Downloads 0

CRISPR-Cas immune systems adapt to new threats by acquiring spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition, despite apparent variation in spacer content between strains. It has been suggested that such loci may use acquisition machinery from co-occurring CRISPR-Cas systems. Here, using a lytic dsDNA phage, we observe spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient subtype VI-B locus and a complete subtype II-C locus. We characterize acquisition events in both loci and show that the RNA-targeting VI-B locus acquires spacers in trans using acquisition machinery from the DNA-targeting II-C locus. Our observations reinforce the concept of modularity in CRISPR-Cas systems and raise further questions regarding plasticity of adaptation modules.

ACS Style

Ville Hoikkala; Janne J Ravantti; César Díez-Villaseñor; Marja Tiirola; Rachel A. Conrad; Mark J. McBride; Lotta-Riina Sundberg. Cooperation between CRISPR-Cas types enables adaptation in an RNA-targeting system. 2020, 1 .

AMA Style

Ville Hoikkala, Janne J Ravantti, César Díez-Villaseñor, Marja Tiirola, Rachel A. Conrad, Mark J. McBride, Lotta-Riina Sundberg. Cooperation between CRISPR-Cas types enables adaptation in an RNA-targeting system. . 2020; ():1.

Chicago/Turabian Style

Ville Hoikkala; Janne J Ravantti; César Díez-Villaseñor; Marja Tiirola; Rachel A. Conrad; Mark J. McBride; Lotta-Riina Sundberg. 2020. "Cooperation between CRISPR-Cas types enables adaptation in an RNA-targeting system." , no. : 1.

Journal article
Published: 24 December 2019 in mBio
Reads 0
Downloads 0

The mucosal surfaces of animals are habitat for microbes, including viruses. Bacteriophages—viruses that infect bacteria—were shown to be able to bind to mucus. This may result in a symbiotic relationship in which phages find bacterial hosts to infect, protecting the mucus-producing animal from bacterial infections in the process. Here, we studied phage binding on mucus and the effect of mucin on phage-bacterium interactions. The significance of our research is in showing that phage adhesion to mucus results in preventive protection against bacterial infections, which will serve as basis for the development of prophylactic phage therapy approaches. Besides, we also reveal that exposure to mucus upregulates bacterial virulence and that this is exploited by phages for infection, adding one additional layer to the metazoan-bacterium-phage biological interactions and ecology. This phenomenon might be widespread in the biosphere and thus crucial for understanding mucosal diseases, their outcome and treatment.

ACS Style

Gabriel M. F. Almeida; Elina Laanto; Roghaieh Ashrafi; Lotta-Riina Sundberg. Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria. mBio 2019, 10, 1 .

AMA Style

Gabriel M. F. Almeida, Elina Laanto, Roghaieh Ashrafi, Lotta-Riina Sundberg. Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria. mBio. 2019; 10 (6):1.

Chicago/Turabian Style

Gabriel M. F. Almeida; Elina Laanto; Roghaieh Ashrafi; Lotta-Riina Sundberg. 2019. "Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria." mBio 10, no. 6: 1.

Article
Published: 05 December 2019 in Microbiology Resource Announcements
Reads 0
Downloads 0

We report a complete genome sequence of a Finnish isolate of the fish pathogen Flavobacterium columnare . Using PacBio RS II sequencing technology, the complete circular genome of F. columnare strain B185 with 3,261,404 bp was obtained.

ACS Style

Janne J. Ravantti; Elina Laanto; Petri Papponen; Lotta-Riina Sundberg. Complete Genome Sequence of Fish Pathogen Flavobacterium columnare Strain B185, Originating from Finland. Microbiology Resource Announcements 2019, 8, 1 .

AMA Style

Janne J. Ravantti, Elina Laanto, Petri Papponen, Lotta-Riina Sundberg. Complete Genome Sequence of Fish Pathogen Flavobacterium columnare Strain B185, Originating from Finland. Microbiology Resource Announcements. 2019; 8 (49):1.

Chicago/Turabian Style

Janne J. Ravantti; Elina Laanto; Petri Papponen; Lotta-Riina Sundberg. 2019. "Complete Genome Sequence of Fish Pathogen Flavobacterium columnare Strain B185, Originating from Finland." Microbiology Resource Announcements 8, no. 49: 1.

Journal article
Published: 24 October 2019 in Antibiotics
Reads 0
Downloads 0

Aquaculture production has increased tremendously during the last decades, and new techniques have been developed, e.g., recirculating aquaculture systems (RAS). In RAS, the majority of water volume is circulated via mechanical and biological filters and reused in the tanks. However, the prevention and treatment of diseases in these systems are challenging, as the pathogens spread throughout the system, and the addition of chemicals and antibiotics disrupts the microbiome of the biofilters. The increasing antibiotic resistance has made phage therapy a relevant alternative for antibiotics in food production. Indeed, as host-specific and self-replicating agent they might be optimal for targeted pathogen eradication in RAS. We tested the survival and spread of Flavobacterium columnare -infecting phage FCL-2 in recirculating aquaculture fish farm with rainbow trout (Oncorhynchus mykiss) in a fully controlled study. After a single addition, phage persisted in water samples collected from tank, fixed bed, moving bed, and aeration unit up to 14 days, and in the water of rearing tanks, rainbow trout mucus, and bioreactor carrier media from the fixed and moving bed biofilters for 21 days. Furthermore, phage adsorbed preferentially to moving bed carrier media, which contained biofilm attached and from which higher phage numbers were recovered. This study shows phages as a potent strategy for maintaining biosecurity in RAS systems.

ACS Style

Gabriel M.F. Almeida; Kati Mäkelä; Elina Laanto; Jani Pulkkinen; Jouni Vielma; Lotta-Riina Sundberg. The Fate of Bacteriophages in Recirculating Aquaculture Systems (RAS)—Towards Developing Phage Therapy for RAS. Antibiotics 2019, 8, 192 .

AMA Style

Gabriel M.F. Almeida, Kati Mäkelä, Elina Laanto, Jani Pulkkinen, Jouni Vielma, Lotta-Riina Sundberg. The Fate of Bacteriophages in Recirculating Aquaculture Systems (RAS)—Towards Developing Phage Therapy for RAS. Antibiotics. 2019; 8 (4):192.

Chicago/Turabian Style

Gabriel M.F. Almeida; Kati Mäkelä; Elina Laanto; Jani Pulkkinen; Jouni Vielma; Lotta-Riina Sundberg. 2019. "The Fate of Bacteriophages in Recirculating Aquaculture Systems (RAS)—Towards Developing Phage Therapy for RAS." Antibiotics 8, no. 4: 192.

Research article
Published: 08 October 2019 in ACS Applied Bio Materials
Reads 0
Downloads 0

Control of bacterial diseases by bacteriophages (phages) is gaining more interest due to increasing antibiotic resistance. This has led to technologies to attach phages on surfaces to form a biomaterial that can functionally display phages that interact with bacteria, to carry out successful infection cycles. Such a material could be applied in many environments, where the target pathogens are expected. Although this approach has been applied successfully in a few studies already, the basis of the antibacterial effect by the immobilized phages is unclear, and the interpretation of the results depends on the study. Here, we studied the phage attachment density, their detachment rate and infectivity on five different surfaces: silicon, amine-treated silicon, gold, carboxylate-treated gold and crosslinker-activated carboxylate-treated gold. The density of attached phages varied between the different surfaces and was highest on the crosslinker-activated carboxylate-treated gold. To understand whether the antibacterial effect is caused by the attached or the detached phages, the strength of the immobilization was analyzed by performing 3-12 washing steps. The detachment rates differed between the materials, with the amine treated silicon surface generating the highest release of phages and maintaining the highest infectivity, even after extensive washing. On the other hand, covalent crosslinking seemed to interfere with the infectivity. Our results suggest that the detachment of the phages from the surface is a possible mechanism for the antibacterial effect. Furthermore, we introduce a measure of the infectivity by comparing the bacterial growth reductions produced by the phage-treated materials to the effect caused by a known number of free phages, resulting in a unit “Effective PFU/surface area”, a comparable standard between different studies.

ACS Style

Miika Leppänen; Ilari J. Maasilta; Lotta-Riina Sundberg. Antibacterial Efficiency of Surface-Immobilized Flavobacterium-Infecting Bacteriophage. ACS Applied Bio Materials 2019, 2, 4720 -4727.

AMA Style

Miika Leppänen, Ilari J. Maasilta, Lotta-Riina Sundberg. Antibacterial Efficiency of Surface-Immobilized Flavobacterium-Infecting Bacteriophage. ACS Applied Bio Materials. 2019; 2 (11):4720-4727.

Chicago/Turabian Style

Miika Leppänen; Ilari J. Maasilta; Lotta-Riina Sundberg. 2019. "Antibacterial Efficiency of Surface-Immobilized Flavobacterium-Infecting Bacteriophage." ACS Applied Bio Materials 2, no. 11: 4720-4727.

Journal article
Published: 14 August 2019 in Evolutionary Applications
Reads 0
Downloads 0

Hosts are typically infected with multiple strains or genotypes of one or several parasite species. These infections can take place simultaneously, but also at different times, i.e. sequentially, when one of the parasites establishes first. Sequential parasite dynamics are common in nature, but also in intensive farming units such as aquaculture. However, knowledge of effects of previous exposures on virulence of current infections in intensive farming is very limited. This is critical as consecutive epidemics and infection history of a host could underlie failures in management practices and medical intervention of diseases. Here, we explored effects of timing of multiple infections on virulence in two common aquaculture parasites, the bacterium Flavobacterium columnare and the fluke Diplostomum pseudospathaceum. We exposed fish hosts first to flukes and then to bacteria in two separate experiments, altering timing between the infections from few hours to several weeks. We found that both short-term and long-term differences in timing of the two infections resulted in significant, genotype-specific decrease in bacterial virulence. Second, we developed a mathematical model, parameterized from our experimental results, to predict the implications of sequential infections for epidemiological progression of the disease, and levels of fish population suppression, in an aquaculture setting. Predictions of the model showed that sequential exposure of hosts can decrease the population-level impact of the bacterial epidemic, primarily through the increased recovery rate of sequentially infected hosts, thereby substantially protecting the population from the detrimental impact of infection. However, these effects depended on bacterial strain-fluke genotype combinations, suggesting the genetic composition of the parasite populations can greatly influence the degree of host suppression. Overall, these results suggest that host infection history can have significant consequences for the impact of infection at host population level, potentially shaping parasite epidemiology, disease dynamics and evolution of virulence in farming environments.

ACS Style

Anssi Karvonen; Andy Fenton; Lotta‐Riina Sundberg. Sequential infection can decrease virulence in a fish-bacterium-fluke interaction: Implications for aquaculture disease management. Evolutionary Applications 2019, 12, 1900 -1911.

AMA Style

Anssi Karvonen, Andy Fenton, Lotta‐Riina Sundberg. Sequential infection can decrease virulence in a fish-bacterium-fluke interaction: Implications for aquaculture disease management. Evolutionary Applications. 2019; 12 (10):1900-1911.

Chicago/Turabian Style

Anssi Karvonen; Andy Fenton; Lotta‐Riina Sundberg. 2019. "Sequential infection can decrease virulence in a fish-bacterium-fluke interaction: Implications for aquaculture disease management." Evolutionary Applications 12, no. 10: 1900-1911.

Research article
Published: 03 April 2019 in Journal of Applied Ecology
Reads 0
Downloads 0

1.Parasitic diseases represent one of the greatest challenges for aquaculture worldwide and there is an increasing emphasis on ecological solutions to prevent infections. One proposed solution is enriched rearing, where traditional stimulus‐poor rearing tanks are equipped with different types of structures to increase habitat complexity. Such spatial enrichment is known to increase survival of fish during parasite epidemics, but the underlying mechanisms are still unclear. 2.We studied whether enriched rearing affected infection of an important fish pathogen Flavobacterium columnare in young Atlantic salmon (Salmo salar) and sea‐migrating brown trout (Salmo trutta). First, we used natural bacterial exposures and multiple fish populations in a common garden experiment to address the role of host genetic background in effects of enriched rearing. Second, fish from standard and enriched rearing were experimentally exposed to controlled bacterial doses in standard and enriched environments in a full factorial design to explore the relative roles of rearing background and environment of exposure on survival of fish. 3.Enriched rearing significantly increased survival of fish during the natural bacterial outbreak. This effect was also fairly consistent and observed in eight of the ten fish populations. In the controlled exposure, fish exposed in enriched environment had higher survival regardless of their rearing background, suggesting a stronger impact of the environment on the disease progression. Additionally, the survival in the enriched environment was highest among the fish of enriched rearing background, supporting the idea of their higher resistance. 4.Synthesis and applications. Our result suggests that the enhanced survival of fish in enriched rearing results from a combined effect of the environment and improved fish condition, and to a lesser degree from host genetic background. This has important implications for when and how environmental enrichment should be applied. Overall, these results indicate that environmental enrichment has the potential to improve survival of fish during parasitic epidemics and thus reduce use of antibiotics in aquaculture. This article is protected by copyright. All rights reserved.

ACS Style

Ville Räihä; Lotta-Riina Sundberg; Roghaieh Ashrafi; Pekka Hyvärinen; Anssi Karvonen. Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak. Journal of Applied Ecology 2019, 56, 1741 -1750.

AMA Style

Ville Räihä, Lotta-Riina Sundberg, Roghaieh Ashrafi, Pekka Hyvärinen, Anssi Karvonen. Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak. Journal of Applied Ecology. 2019; 56 (7):1741-1750.

Chicago/Turabian Style

Ville Räihä; Lotta-Riina Sundberg; Roghaieh Ashrafi; Pekka Hyvärinen; Anssi Karvonen. 2019. "Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak." Journal of Applied Ecology 56, no. 7: 1741-1750.

Preprint
Published: 28 March 2019
Reads 0
Downloads 0

Metazoan mucosal surfaces are major interfaces between the organism and environment. These surfaces have been proposed to host bacteriophages in a symbiotic relationship with metazoans. Considering the so far poorly understood phage–mucus interaction and its role in ecological interactions and for mucosal bacterial infections, empirical evidence and model systems need to be established. Here, using the fish pathogen Flavobacterium columnare and rainbow trout (Oncorhynchus mykiss), we show that phages infecting the pathogen are capable of binding to primary mucus layers and protecting fish from infections. Furthermore, exposure to mucus changes the bacterial phenotype by increasing bacterial virulence and susceptibility to phage infections. Tests using other phage–bacterium pairs suggest that the relevance of mucus for bacteria and phages may be widespread in the biosphere. Therefore, interactions of bacteria and phages inside the mucus environment may be important for disease and evolution, and this phenomenon has significant potential to be exploited for preventive phage therapy approaches.

ACS Style

Gabriel Mf Almeida; Elina Laanto; Roghaieh Ashrafi; Lotta-Riina Sundberg. Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria. 2019, 592097 .

AMA Style

Gabriel Mf Almeida, Elina Laanto, Roghaieh Ashrafi, Lotta-Riina Sundberg. Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria. . 2019; ():592097.

Chicago/Turabian Style

Gabriel Mf Almeida; Elina Laanto; Roghaieh Ashrafi; Lotta-Riina Sundberg. 2019. "Bacteriophage adherence to mucus mediates preventive protection against pathogenic bacteria." , no. : 592097.