| 1. |
- Holmgren, Jan, 1944, et al.
(författare)
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Mucosal adjuvants and anti-infection and anti-immunopathology vaccines based on cholera toxin, cholera toxin B subunit and CpG DNA
- 2005
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Ingår i: Immunology Letters. - : Elsevier. - 0165-2478 .- 1879-0542. ; 97:2, s. 181-8
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Tidskriftsartikel (refereegranskat)abstract
- Mucosal immunisation may be used both to protect the mucosal surfaces against infections and as a means for immunological treatment of peripheral immunopathological disorders through the induction of systemic antigen-specific tolerance ('oral tolerance'). The development of mucosal vaccines, whether for prevention of infectious diseases or for oral tolerance immunotherapy, requires efficient antigen delivery and adjuvant systems that can help to present the appropriate vaccine or immunotherapy antigens to the mucosal immune system. The most potent (but also toxic) mucosal adjuvants are cholera toxin (CT) and the closely related Escherichia coli heat-labile enterotoxin (LT), and much effort and significant progress have been made recently to generate toxicologically acceptable derivatives of these toxins with retained adjuvant activity. Among these are the non-toxic, recombinantly produced cholera toxin B-subunit (CTB). CTB is a specific protective antigen component of a widely registered oral cholera vaccine as well as a promising vector for either giving rise to mucosal anti-infective immunity or for inducing peripheral anti-inflammatory tolerance to chemically or genetically linked foreign antigens administered mucosally. CT and CTB have also recently been used as combined vectors and adjuvants for markedly promoting ex vivo dendritic cell (DC) vaccination with different antigens and also steering the immune response to the in vivo-reinfused DCs towards either broad Th1 + Th2 + CTL immunity (CT) or Th2 or tolerance (CTB). Another type of mucosal adjuvants is represented by bacterial DNA or synthetic oligodeoxynucleotides containing CpG-motifs, which especially when linked to CTB have been found to effectively stimulate both innate and adaptive mucosal immune responses. The properties and clinical potential of these different classes of adjuvants are being discussed. © 2004 Elsevier B.V. All rights reserved.
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| 2. |
- Boulund, Fredrik, 1985, et al.
(författare)
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Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets
- 2017
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 18:1, s. Art 682-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are increasingly encountered in clinical settings. Over the last decade, several families of qnr genes have been discovered and characterized, but their true prevalence and diversity still remain unclear. In particular, environmental and host-associated bacterial communities have been hypothesized to maintain a large and unknown collection of qnr genes that could be mobilized into pathogens. Results: In this study we used computational methods to screen genomes and metagenomes for novel qnr genes. In contrast to previous studies, we analyzed an almost 20-fold larger dataset comprising almost 13 terabases of sequence data. In total, 362,843 potential qnr gene fragments were identified, from which 611 putative qnr genes were reconstructed. These gene sequences included all previously described plasmid-mediated qnr gene families. Fifty-two of the 611 identified qnr genes were reconstructed from metagenomes, and 20 of these were previously undescribed. All of the novel qnr genes were assembled from metagenomes associated with aquatic environments. Nine of the novel genes were selected for validation, and six of the tested genes conferred consistently decreased susceptibility to ciprofloxacin when expressed in Escherichia coli. Conclusions: The results presented in this study provide additional evidence for the ubiquitous presence of qnr genes in environmental microbial communities, expand the number of known qnr gene variants and further elucidate the diversity of this class of resistance genes. This study also strengthens the hypothesis that environmental bacterial communities act as sources of previously uncharacterized qnr genes.
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| 3. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Does antifouling paint select for antibiotic resistance?
- 2017
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 590, s. 461-468
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Tidskriftsartikel (refereegranskat)abstract
- There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis. Plastic panels with one side painted with copper and zinc-containing antifouling paint were submerged in a Swedish marina and biofilms from both sides of the panels were harvested after 2.5-4 weeks. DNA was isolated from the biofilms and subjected to metagenomic sequencing. Biofilm bacteria were cultured on marine agar supplemented with tetracycline, gentamicin, copper sulfate or zinc sulfate. Biofilm communities from painted surfaces displayed lower taxonomic diversity and enrichment of Gammaproteobacteria. Bacteria from these communities showed increased resistance to both heavy metals and tetracycline but not to gentamicin. Significantly higher abundance of metal and biocide resistance genes was observed, whereas mobile antibiotic resistance genes were not enriched in these communities. In contrast, we found an enrichment of chromosomal RND efflux system genes, including such with documented ability to confer decreased susceptibility to both antibiotics and biocides/heavy metals. This was paralleled by increased abundances of integron-associated integrase and ISCR transposase genes. The results show that the heavy metal-based antifouling paint exerts a strong selection pressure on marine bacterial communities and can co-select for certain antibiotic-resistant bacteria, likely by favoring species and strains carrying genes that provide cross-resistance. Although this does not indicate an immediate risk for promotion of mobile antibiotic resistance, the clear increase of genes involved in mobilizing DNA provides a foundation for increased opportunities for gene transfer in such communities, which might also involve yet unknown resistance mechanisms.
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| 4. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Functional verification of computationally predicted qnr genes
- 2013
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Ingår i: Annals of Clinical Microbiology and Antimicrobials. - : Springer Science and Business Media LLC. - 1476-0711. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Background The quinolone resistance (qnr) genes are widely distributed among bacteria. We recently developed and applied probabilistic models to identify tentative novel qnr genes in large public collections of DNA sequence data including fragmented metagenomes. Findings: By using inducible recombinant expressions systems the functionality of four identified qnr candidates were evaluated in Escherichia coli. Expression of several known qnr genes as well as two novel candidates provided fluoroquinolone resistance that increased with elevated inducer concentrations. The two novel, functionally verified qnr genes are termed Vfuqnr and assembled qnr 1. Co-expression of two qnr genes suggested non-synergistic action. Conclusion The combination of a computational model and recombinant expression systems provides opportunities to explore and identify novel antibiotic resistance genes in both genomic and metagenomic datasets.
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| 5. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics
- 2016
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 572, s. 697-712
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Tidskriftsartikel (refereegranskat)abstract
- Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.
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| 6. |
- Berglund, Fanny, 1988, et al.
(författare)
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Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic data
- 2017
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5:1, s. 134-134
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Tidskriftsartikel (refereegranskat)abstract
- Background: Metallo-beta-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-beta-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-beta-lactamases of class B1, the most clinically important subclass of these enzymes. Results: Based on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-beta-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-beta-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-beta-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-beta-lactamases. Phylogenetic analysis showed that B1 metallo-beta-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 beta-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species. Conclusions: This study more than doubles the number of known B1 metallo-beta-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.
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| 7. |
- Berglund, Fanny, et al.
(författare)
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The resistome and microbiome of wastewater treatment plant workers - The AWARE study.
- 2023
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Ingår i: Environment international. - 0160-4120 .- 1873-6750. ; 180
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Tidskriftsartikel (refereegranskat)abstract
- Urban wastewater treatment plants harbor a large collection of antibiotic resistant enteric bacteria. It is therefore reasonable to hypothesize that workers at such plants would possess a more diverse set of resistant enteric bacteria, compared to the general population. To address this hypothesis, we have compared the fecal microbiome and resistome of 87 workers at wastewater treatment plants (WWTPs) from Romania and the Netherlands to those of 87 control individuals, using shotgun metagenomics. Controlling for potential confounders, neither the total antibiotic resistance gene (ARG) abundance, nor the overall bacterial composition were significantly different between the two groups. If anything, the ARG richness was slightly lower in WWTP workers, and in a stratified analysis the total ARG abundance was significantly lower in Dutch workers compared to Dutch control participants. We identified country of residence, together with recent antibiotic intake in the Dutch population, as the largest contributing factors to the total abundance of ARGs. A striking side-finding was that sex was associated with carriage of disinfectant resistance genes, with women in both Romania and the Netherlands having significantly higher abundance compared to men. A follow up investigation including an additional 313 publicly available samples from healthy individuals from three additional countries showed that the difference was significant for three genes conferring resistance to chemicals commonly used in cosmetics and cleaning products. We therefore hypothesize that the use of cosmetics and, possibly, cleaning products leads to higher abundance of disinfectant resistance genes in the microbiome of the users. Altogether, this study shows that working at a WWTP does not lead to a higher abundance or diversity of ARGs and no large shifts in the overall gut microbial composition in comparison to participants not working at a WWTP. Instead, other factors such as country of residence, recent antibiotic intake and sex seem to play a larger role.
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| 8. |
- Bobis Camacho, Julián, 1997, et al.
(författare)
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Evaluation of culture conditions for sewage-based surveillance of antibiotic resistance in Klebsiella pneumoniae.
- 2024
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Ingår i: Journal of global antimicrobial resistance. - 2213-7173.
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have shown promise in predicting clinical antibiotic resistance rates from sewage data. Few have focused on Klebsiella pneumoniae, despite its virulence and importance as carrier of antibiotic resistance. Several media have been suggested for the isolation of K. pneumoniae from complex samples. However, comprehensive evaluations of culture protocols for isolation of K. pneumoniae from sewage are lacking.Here, influent samples from a major Swedish sewage treatment plant were used to evaluate ten culture conditions in parallel: cultivation on Brilliant green containing Inositol-Nitrate-Deoxycholate agar (BIND), Bruce agar, Klebsiella ChromoSelect Selective agar®, MacConkey-Inositol-Carbenicillin, or Simmons Citrate Agar with Inositol (SCAI) incubated at either 37˚C or 42˚C for 44 h. The culture conditions were compared based on colony counts of presumed K. pneumoniae and identification precision assessed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.The sensitivity was lowest for BIND, whereas it was similar for the other media irrespective of incubation temperature. For four media, a better precision was observed after incubation at 42˚C compared to 37˚C, to a large extent explained by a lower frequency of captured Klebsiella oxytoca. SCAI incubated at 42˚C showed the highest precision (84.4%). By combining this protocol with subsequent antibiotic resistance screening of collected isolates, low resistance rates in sewage K. pneumoniae were revealed, potentially reflecting the local resistance landscape.When combined with downstream analyses, SCAI incubated at 42˚C could be a valuable culture protocol for sewage-based studies on various aspects of K. pneumoniae epidemiology including antibiotic resistance prevalence.
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| 9. |
- Böhm, Maria-Elisabeth, et al.
(författare)
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A novel, integron-regulated, class c β-lactamase
- 2020
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Ingår i: Antibiotics. - : MDPI AG. - 2079-6382. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- © 2020 by the authors. Licensee MDPI, Basel, Switzerland. AmpC-type β-lactamases severely impair treatment of many bacterial infections, due to their broad spectrum (they hydrolyze virtually all β-lactams, except fourth-generation cephalosporins and carbapenems) and the increasing incidence of plasmid-mediated versions. The original chromosomal AmpCs are often tightly regulated, and their expression is induced in response to exposure to β-lactams. Regulation of mobile ampC expression is in many cases less controlled, giving rise to constitutively resistant strains with increased potential for development or acquisition of additional resistances. We present here the identification of two integron-encoded ampC genes, blaIDC-1 and blaIDC-2 (integron-derived cephalosporinase), with less than 85% amino acid sequence identity to any previously annotated AmpC. While their resistance pattern identifies them as class C β-lactamases, their low isoelectric point (pI) values make differentiation from other β-lactamases by isoelectric focusing impossible. To the best of our knowledge, this is the first evidence of an ampC gene cassette within a class 1 integron, providing a mobile context with profound potential for transfer and spread into clinics. It also allows bacteria to adapt expression levels, and thus reduce fitness costs, e.g., by cassette-reshuffling. Analyses of public metagenomes, including sewage metagenomes, show that the discovered ampCs are primarily found in Asian countries.
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| 10. |
- Böhm, Maria-Elisabeth, et al.
(författare)
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Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities.
- 2020
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics.We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now.To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.
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| 11. |
- Dai, D. J., et al.
(författare)
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Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge
- 2022
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is concern that the microbially rich activated sludge environment of wastewater treatment plants (WWTPs) may contribute to the dissemination of antibiotic resistance genes (ARGs). We applied long-read (nanopore) sequencing to profile ARGs and their neighboring genes to illuminate their fate in the activated sludge treatment by comparing their abundance, genetic locations, mobility potential, and bacterial hosts within activated sludge relative to those in influent sewage across five WWTPs from three continents. Results: The abundances (gene copies per Gb of reads, aka gc/Gb) of all ARGs and those carried by putative pathogens decreased 75-90% from influent sewage (192-605 gc/Gb) to activated sludge (31-62 gc/Gb) at all five WWTPs. Long reads enabled quantification of the percent abundance of ARGs with mobility potential (i.e., located on plasmids or co-located with other mobile genetic elements (MGEs)). The abundance of plasmid-associated ARGs decreased at four of five WWTPs (from 40-73 to 31-68%), and ARGs co-located with transposable, integrative, and conjugative element hallmark genes showed similar trends. Most ARG-associated elements decreased 0.35-13.52% while integrative and transposable elements displayed slight increases at two WWTPs (1.4-2.4%). While resistome and taxonomic compositions both shifted significantly, host phyla for chromosomal ARG classes remained relatively consistent, indicating vertical gene transfer via active biomass growth in activated sludge as the key pathway of chromosomal ARG dissemination. Conclusions: Overall, our results suggest that the activated sludge process acted as a barrier against the proliferation of most ARGs, while those that persisted or increased warrant further attention.
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| 12. |
- Eriksson, Anders, 1957, et al.
(författare)
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Five mucosal transcripts of interest in ulcerative colitis identified by quantitative real-time PCR: a prospective study.
- 2008
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Ingår i: BMC gastroenterology. - 1471-230X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The cause and pathophysiology of ulcerative colitis are both mainly unknown. We have previously used whole-genome microarray technique on biopsies obtained from patients with ulcerative colitis to identify 5 changed mucosal transcripts. The aim of this study was to compare mucosal expressions of these five transcripts in ulcerative colitis patients vs. controls, along with the transcript expression in relation to the clinical ulcerative colitis status. METHODS: Colonic mucosal specimens from rectum and caecum were taken at ambulatory colonoscopy from ulcerative colitis patients (n = 49) with defined inflammatory activity and disease extension, and from controls (n = 67) without inflammatory bowel disease. The five mucosal transcripts aldolase B, elafin, MST-1, simNIPhom and SLC6A14 were analyzed using quantitative real-time PCR. RESULTS: Significant transcript differences in the rectal mucosa for all five transcripts were demonstrated in ulcerative colitis patients compared to controls. The grade of transcript expression was related to the clinical disease activity. CONCLUSION: The five gene transcripts were changed in patients with ulcerative colitis, and were related to the disease activity. The known biological function of some of the transcripts may contribute to the inflammatory features and indicate a possible role of microbes in ulcerative colitis. The findings may also contribute to our pathophysiological understanding of ulcerative colitis.
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| 13. |
- Eriksson, Anders, 1957, et al.
(författare)
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Real-time PCR quantification analysis of five mucosal transcripts in patients with Crohn's disease.
- 2008
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Ingår i: European journal of gastroenterology & hepatology. - 0954-691X. ; 20:4, s. 290-6
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Crohn's disease has a genetic background. Onset of the clinical manifestations, however, is suggested to be triggered by environmental factors. Microarray analysis has shown that the expression of transcripts aldolase B, elafin, MST-1, simNIPhom and SLC6A14 are altered in patients with ulcerative colitis. The primary aim of this study was to explore the expressions of these five transcripts in macroscopically inflamed and noninflamed mucosa in patients with Crohn's disease. METHODS: Mucosal specimens obtained from colon in consecutive patients with Crohn's disease (n=23) and controls (n=67) undergoing colonoscopy were analyzed using real-time PCR technique. RESULTS: The expressions of the transcripts aldolase B, elafin, simNIPhom and SLC6A14 were increased, whereas the expression of MST-1 was decreased in noninflamed rectal mucosa in patients with Crohn's disease compared with controls. The expression of aldolase B was increased and the expressions of elafin and simNIPhom were decreased in inflamed colonic mucosa compared with noninflamed rectal mucosa in patients with Crohn's disease. No correlation, between the clinical activity of Crohn's disease (Mayo score or=6) and transcript expression was detected. CONCLUSION: The mucosal transcript pattern in Crohn's disease may, based on the known biological function of the transcripts, explain some of the typical features of Crohn's disease and indicate a possible pathophysiological role of microbes. Our results may thereby contribute to the understanding of the pathogenesis and manifestations of Crohn's disease.
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| 14. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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A Comprehensive Screening of Escherichia coli Isolates from Scandinavia's Largest Sewage Treatment Plant Indicates No Selection for Antibiotic Resistance.
- 2018
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Ingår i: Environmental science & technology. - : American Chemical Society (ACS). - 1520-5851 .- 0013-936X. ; 52:19, s. 11419-11428
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Tidskriftsartikel (refereegranskat)abstract
- There is concern that sewage treatment plants (STPs) serve as hotspots for emergence and selection of antibiotic resistant bacteria. However, field studies investigating resistance selection by comparing bacterial populations in influents and effluents have produced variable and sometimes contradictive results. Also, large taxonomic changes between influents and effluents make interpretation of studies measuring relative gene abundances ambiguous. The aim here was to investigate whether within-species selection occurs by conducting a comprehensive screening of Escherichia coli isolated from composite influent and effluent samples collected at Scandinavia's largest STP, accompanied by analyses of antibiotics residues. In total, 4028 isolates, collected on eight occasions during 18 months, were screened for resistance to seven antibiotics. Although differences in proportions of resistant E. coli between influent and effluent samples were detected for a few antibiotics on two occasions, aggregated data over time showed no such differences for any of the investigated antibiotics. Neither was there any enrichment of multiresistant or extended-spectrum beta-lactamase-producing isolates through the treatment process. Despite some antibiotics were detected at or close to concentrations predicted to provide some selective pressure, field observations of resistance profiles in E. coli do not provide support for systematic selection in the investigated STP.
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| 15. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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A truncated form of HpaA is a promising antigen for use in a vaccine against Helicobacter pylori.
- 2011
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Ingår i: Vaccine. - : Elsevier BV. - 1873-2518 .- 0264-410X. ; 29:6, s. 1235-1241
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Tidskriftsartikel (refereegranskat)abstract
- HpaA is a Helicobacter pylori-specific lipoprotein that has been shown to be an effective protective antigen for mucosal vaccination against H. pylori infection in mice. However, detergents are needed for the purification of full-length HpaA (HpaA(full)), which might confer toxicity, thus making HpaA(full) unsuitable for use in a human vaccine. We here describe a recombinantly produced truncated version of HpaA (HpaA(trunc)), which is easily purified without the use of detergents. Evaluation in the murine H. pylori infection model showed that sublingual immunization with HpaA(trunc) was equally immunogenic and protective as immunization with HpaA(full). Immunization with a combination of HpaA(trunc) and recombinant UreB protein induced strong immune responses to both antigens and importantly had a strong synergistic effect on protection, associated with synergistically increased expression of IL-17 in the stomach. Notably, sublingual immunization with HpaA(trunc) and UreB was superior to corresponding intragastric immunization with regard to the level of protection induced. In conclusion, HpaA(trunc) is a promising, readily produced, non-toxic recombinant antigen for inclusion in a mucosal vaccine against H. pylori infection, which may preferably be given sublingually together with UreB.
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| 16. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Broad up-regulation of innate defense factors during acute cholera.
- 2007
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Ingår i: Infection and immunity. - 0019-9567. ; 75:5, s. 2343-50
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Tidskriftsartikel (refereegranskat)abstract
- We used a whole-genome microarray screening system (Affymetrix human GeneChips covering 47,000 different transcripts) to examine the gene expression in duodenal mucosa during acute cholera. Biopsies were taken from the duodenal mucosa of seven cholera patients 2 and 30 days after the onset of diarrhea, and the gene expression patterns in the acute- and convalescent-phase samples were compared pairwise. Of about 21,000 transcripts expressed in the intestinal epithelium, 29 were defined as transcripts that were up-regulated and 33 were defined as transcripts that were down-regulated during acute cholera. The majority of the up-regulated genes characterized were found to have an established or possible role in the innate defense against infections; these genes included the LPLUNC1, LF, VCC1, TCN1, CD55, SERPINA3, MMP1, MMP3, IL1B, LCN2, SOCS3, GDF15, SLPI, CXCL13, and MUC1 genes. The results of confirmative PCR correlated well with the microarray data. An immunohistochemical analysis revealed increased expression of lactoferrin in lamina propria cells and increased expression of CD55 in epithelial cells, whereas increased expression of the SERPINA3 protein (alpha1-antichymotrypsin) was detected in both lamina propria and epithelial cells during acute cholera. The expression pattern of CD55 and SERPINA3 in cholera toxin (CT)-stimulated Caco-2 cells was the same as the pattern found in the intestinal mucosa during acute cholera, indicating that the activation of the CD55 and SERPINA3 genes in intestinal epithelium was induced by CT. In conclusion, during acute cholera infection, innate defense mechanisms are switched on to an extent not described previously. Both direct effects of CT on the epithelial cells and changes in the lamina propria cells contribute to this up-regulation.
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| 17. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Cholera toxin induces a transient depletion of CD8+ intraepithelial lymphocytes in the rat small intestine as detected by microarray and immunohistochemistry.
- 2005
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Ingår i: Infection and immunity. - 0019-9567. ; 73:9, s. 5595-602
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Tidskriftsartikel (refereegranskat)abstract
- Cholera toxin (CT), besides causing intestinal hypersecretion after intragastric administration or during cholera infection, affects a multitude of regulatory mechanisms within the gut mucosal network, including T cells. By use of microarray screening, real-time PCR, and immunohistochemistry, we demonstrate here a rapid depletion of jejunal CD8(+) intraepithelial lymphocytes (IEL) in rats after intragastric CT challenge. This depletion may depend on CT-induced migration of IEL, since it was associated with a progressive decrease of CD8(+) cells in the epithelium and a contemporary transient increase of such cells, preferentially at the base of the villi, in the lamina propria. A significant decrease in the total number of villous CD8(+) cells at 6 and 18 h after CT challenge was detected; this possibly reflects an efflux from the jejunal mucosa. The kinetics of the CD8(+) IEL demonstrate the return to normal intraepithelial position at original numbers already 72 h after the single CT dose. The induced migration seems to be dependent on the enzymatic A-subunit of CT, since challenge with neither sorbitol nor CT B-subunit did mimic the effects of CT on CD8(+) IEL. Furthermore, a decrease in the level of both RANTES transcript and protein was detected, most likely as a consequence of the CT-induced migration of CD8(+) IEL. These results point to a complex interaction between CT, epithelial cells, and IEL, resulting in a disturbance of the gut homeostasis, which might have relevance for the strong immunomodulatory effects of intragastrically administered CT.
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| 18. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Cholera toxin induces expression of ion channels and carriers in rat small intestinal mucosa.
- 2004
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Ingår i: FEBS letters. - 0014-5793. ; 561:1-3, s. 122-6
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Tidskriftsartikel (refereegranskat)abstract
- Cholera toxin causes cyclic adenosine monophosphate (cAMP)-induced electrolyte and water secretion in the small intestine. The toxin-induced change in gene expression in rat small intestine was evaluated with microarray technique and the results were confirmed by semiquantitative polymerase chain reaction (PCR). The transporter CNT2 for nucleosides was upregulated between 6 and 18 h after challenge, whereas the level of GLUT1 transporter for glucose became elevated at 6 h. Both changes probably facilitate uptake of these nutrients in the gut. At 18 h, the major chloride channel in the villus, ClC2, was upregulated. Aquaporin 8 was downregulated at 6 h and two mucin-producing genes were upregulated 18 h after toxin challenge. The expression was back to normal after 72 h, which is the turnover time for intestinal epithelial cells.
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| 19. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Detection of elafin as a candidate biomarker for ulcerative colitis by whole-genome microarray screening.
- 2006
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Ingår i: Inflammatory bowel diseases. - : Oxford University Press (OUP). - 1078-0998. ; 12:9, s. 837-42
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Tidskriftsartikel (refereegranskat)abstract
- The cause of ulcerative colitis (UC) is largely unknown. Microarray studies are an efficient way of investigating the various genes involved. Here, we have used whole-genome microarrays to clarify the clinical picture and to identify new biomarkers for improved diagnosis. Rectal biopsies were taken from five UC patients and five matched controls, and RNA transcripts were prepared. After labeling, each sample was individually applied to the microarray chips. All transcripts that were more than 10-fold up-regulated in all five patients were analyzed further in seven additional patients and seven controls using quantitative polymerase chain reaction. Of 47,000 transcripts examined, 4 were highly up-regulated in all patients: those encoding elafin, a secreted protease inhibitor, the ion and amino acid transporter B (SLC6A14), and the metabolic enzyme aldolase B, as well as a recently identified transcript named similar to numb-interacting homolog. The up-regulation of these transcripts appears to follow the progression of the disease because elevated expression was detected in the proximal part of the colon in patients with total colitis but not in patients with left-sided colitis. Immunohistologic examination showed very distinct differences in the expression of elafin. Extensive expression was detected in enterocytes and goblet cells of the affected mucosa, whereas there was no detectable expression in unaffected mucosa and in healthy controls. The results implicate four transcripts and proteins of special interest as possible targets for pharmacologic interference and as biomarkers in UC. Of these, elafin may be of special interest because it is a secreted protein that may be measured in body fluids.
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| 20. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Differential expression of intestinal membrane transporters in cholera patients.
- 2007
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Ingår i: FEBS letters. - : Wiley. - 0014-5793. ; 581:17, s. 3183-8
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Tidskriftsartikel (refereegranskat)abstract
- Vibrio cholerae causes the cholera disease through secretion of cholera toxin (CT), resulting in severe diarrhoea by modulation of membrane transporters in the intestinal epithelium. Genes encoding membrane-spanning transporters identified as being differentially expressed during cholera disease in a microarray screening were studied by real-time PCR, immunohistochemistry and in a CaCo-2 cell model. Two amino acid transporters, SLC7A11 and SLC6A14, were upregulated in acute cholera patients compared to convalescence. Five other transporters were downregulated; aquaporin 10, SLC6A4, TRPM6, SLC23A1 and SLC30A4, which have specificity for water, serotonin (5-HT), magnesium, vitamin C and zinc, respectively. The majority of these changes appear to be attempts of the host to counteract the secretory response. Our results also support the concept that epithelial cells are involved in 5-HT signalling during acute cholera.
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| 21. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake
- 2015
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Ingår i: Journal of Antimicrobial Chemotherapy. - : Oxford University Press (OUP). - 0305-7453 .- 1460-2091. ; 70:10, s. 2709-2717
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Tidskriftsartikel (refereegranskat)abstract
- Objectives Antibiotic-polluted environments may function as reservoirs for novel resistance plasmids not yet encountered in pathogens. The aims of this study were to assess the potential of resistance transfer between bacteria from such environments and Escherichia coli, and to characterize the conjugative elements involved. Methods Sediment samples from Kazipally lake and Asanikunta tank, two Indian lakes with a history of severe pollution with fluoroquinolones, were investigated. Proportions of resistant bacteria were determined by selective cultivation, while horizontal gene transfer was studied using a GFP-tagged E. coli as recipient. Retrieved transconjugants were tested for susceptibility by Etest® and captured conjugative resistance elements were characterized by WGS. Results The polluted lakes harboured considerably higher proportions of ciprofloxacin-resistant and sulfamethoxazole-resistant bacteria than did other Indian and Swedish lakes included for comparison (52% versus 2% and 60% versus 7%, respectively). Resistance plasmids were captured from Kazipally lake, but not from any of the other lakes; in the case of Asanikunta tank because of high sediment toxicity. Eight unique IncA/C and IncN resistance plasmids were identified among 11 sequenced transconjugants. Five plasmids were fully assembled, and four of these carried the quinolone resistance gene qnrVC1, which has previously only been found on chromosomes. Acquired resistance genes, in the majority of cases associated with class 1 integrons, could be linked to decreased susceptibility to several different classes of antibiotics. Conclusions Our study shows that environments heavily polluted with antibiotics contain novel multiresistance plasmids transferrable to E. coli.
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| 22. |
- Flach, Carl-Fredrik, 1977
(författare)
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Microarray analyses of the small intestinal mucosa during experimental and clinical cholera
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Vibrio cholerae is a Gram-negative bacterium and the causative agent of cholera. The bacteria infect humans via contaminated water and food, and colonize the upper parts of the small intestine to cause disease. The disease is characterized by watery diarrhoea and most of its clinical features can be attributed to the secreted cholera toxin (CT). CT binds to the surface of epithelial cells by its B-subunit homopentamer and after internalization, the enzymatic active A-subunit catalyses the ADP-ribosylation of Gsá leading to the activation of adenylate cyclase. The following increase in cAMP modulates transporters in the epithelial cells resulting in the massive net secretion of electrolytes and water. Besides its toxic effect, CT is also known to be a strong mucosal adjuvant, causing augmented immune responses against co-administered antigens.We have here used the microarray technique to study how the gene expression is modulated in the small intestinal mucosa, both in rats after oral challenge with CT and in cholera patients during the acute stage of the disease. Observed differences in expression have to a large extent been confirmed with real-time PCR and/or immunohistochemistry.In rats it was shown that CT affected the expression of four different membrane transporters, of which at least three most likely counteract the secretory response. CT also induced the upregulation of two mucin genes, probably as a consequence of the CT-induced release of mucus from goblet cells. The microarray screening of the rat small intestinal mucosa also revealed the co-ordinated downregulation of a number of transcripts associated with CD8+ intraepithelial lymphocytes after CT challenge. Immunohistochemistry revealed that the decrease in the level of these transcripts in samples taken from the upper parts of the villi can be explained by a CT-induced migration of CD8+ cells from the epithelium to the lamina propria compartment, preferentially to the lower parts of the villi, and possibly also out from the villi.The whole genome screening of cholera patients showed a broad upregulation of innate defence factors, including genes encoding antibacterial proteins, as well as genes that contribute to the general protection of the mucosa, during the acute phase of the disease. In contrast, among the identified downregulated genes, a significant proportion is involved in metabolism and transport of lipids. Further, the screening revealed the differential expression of seven membrane transporters, two upregulated and five downregulated, suggesting changes that both counteract, as well as potentiate the secretory response. The two identified upregulated transporters encode two amino acid transporters, indicating a broad uptake of amino acids during cholera. Thus, the addition of amino acids to the oral rehydration solutions used for treatment of cholera should be reconsidered, since this may increase the absorption of cotransported electrolytes. Five of the genes encoding membrane transporters, which were shown to be differentially expressed during acute cholera, did show the same expression pattern in CT-stimulated CaCo-2 cells, a human intestinal epithelial cell line, pointing to direct effects of CT on the epithelial cells in these cases.In this work, we have, for the first time, applied the microarray technique to examine changes induced during cholera in vivo. The screening of thousands of genes revealed previously unknown modulations of transporters, the immune system, and the innate defence during experimental and clinical cholera. The results may add new clues to the secretory response during cholera, and how it is counteracted by the host, as well as suggesting new mechanisms that contribute to the immunomodulatory properties of CT.
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| 23. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Monitoring of hospital sewage shows both promise and limitations as an early-warning system for carbapenemase-producing Enterobacterales in a low-prevalence setting
- 2021
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Ingår i: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 200
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Tidskriftsartikel (refereegranskat)abstract
- Carbapenemase-producing Enterobacterales (CPE) constitute a significant threat to healthcare systems. Continuous surveillance is important for the management and early warning of these bacteria. Sewage monitoring has been suggested as a possible resource-efficient complement to traditional clinical surveillance. It should not least be suitable for rare forms of resistance since a single sewage sample contains bacteria from a large number of individuals. Here, the value of sewage monitoring in early warning of CPE was assessed at the Sahlgrenska University Hospital in Gothenburg, Sweden, a setting with low prevalence of CPE. Twenty composite hospital sewage samples were collected during a two-year period. Carbapenemase genes in the complex samples were analyzed by quantitative PCR and the CPE loads were assessed through cultures on CPE-selective agar followed by species determination as well as phenotypic and genotypic tests targeting carbapenemases of presumed CPE. The findings were related to CPE detected in hospitalized patients. A subset of CPE isolates from sewage and patients were subjected to whole genome sequencing. For three of the investigated carbapenemase genes, bla(NDM), bla(OXA-48-like) and bla(KPC), there was concordance between gene levels and abundance of corresponding CPE in sewage. For the other two analyzed genes, bla(VIM) and bla(IMP), there was no such concordance, most likely due to the presence of those genes in non-Enterobacterales populating the sewage samples. In line with the detection of OXA-48-like- and NDM-producing CPE in sewage, these were also the most commonly detected CPE in patients. NDM-producing CPE were detected on a single occasion in sewage and isolated strains were shown to match strains detected in a patient. A marked peak in CPE producing OXA-48-like enzymes was observed in sewage during a few months. When levels started to increase there were no known cases of such CPE at the hospital but soon after a few cases were detected in samples from patients. The OXA-48-like-producing CPE from sewage and patients represented different strains, but they carried similar bla(OXA-48-like)-harbouring mobile genetic elements. In conclusion, sewage analyses show both promise and limitations as a complement to traditional clinical resistance surveillance for early warning of rare forms of resistance. Further evaluation and careful interpretation are needed to fully assess the value of such a sewage monitoring system. (C) 2021 The Authors. Published by Elsevier Ltd.
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| 24. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Mucosal vaccination increases local chemokine production attracting immune cells to the stomach mucosa of Helicobacter pylori infected mice.
- 2012
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Ingår i: Vaccine. - : Elsevier BV. - 1873-2518 .- 0264-410X. ; 30:9, s. 1636-1643
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Tidskriftsartikel (refereegranskat)abstract
- Background: Vaccination is an attractive approach for the prevention of Helicobacter pylori infection and disease. In a mouse model, infection induces an accumulation of dendritic cells, macrophages, granulocytes, and B- and T cells to the stomach mucosa, which is further heightened when the infection is preceded by a mucosal immunization. We have studied the chemokines and chemokine receptors guiding infection- and vaccination-induced immune cells to the stomach and their relation to protection against H. pylori infection in mice. Materials and methods: C57BL/6 mice were immunized sublingually with H. pylori lysate antigens and cholera toxin adjuvant or left unimmunized, and then challenged with live H. pylori bacteria. Stomach tissue was taken at 3, 7, 14 and 21 days after challenge and bacterial colonization, chemokine and chemokine receptor gene expression, and influx of cells into the stomach mucosa were evaluated. Results: RT-PCR array screening revealed differential expression of a broad range of chemokine and chemokine receptor genes between immunized and unimmunized mice. A significant upregulation of chemokines known to attract, among other cells, eosinophils (CCL8), T cells (CXCL10, CXCL11) and neutrophils (CXCL2, CXCL5) and of their cognate receptors CCR3, CXCR3 and CXCR2, preceded or coincided with vaccine-induced protection, which was first evident 7 days after infection and was then sustained at the later time-points. Consistent with the increase in chemokines and chemokine receptors flow cytometric analysis indicated a sequential accumulation of CD4+ T cells, eosinophils, neutrophils and CD103+ dendritic cells in the gastric lamina propria of immunized mice. Conclusions: This study provides insights into vaccination-induced chemokines that guide the influx of protective immune cells into the stomach of H. pylori infected mice.
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| 25. |
- Flach, Carl-Fredrik, 1977, et al.
(författare)
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Pro-inflammatory cytokine gene expression in the stomach correlates with vaccine-induced protection against Helicobacter pylori infection in mice: an important role for interleukin-17 during the effector phase. : Immune correlates to H. pylori protection
- 2011
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Ingår i: Infection and immunity. - 1098-5522. ; 79:2, s. 879-886
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Tidskriftsartikel (refereegranskat)abstract
- CD4(+) T cells have been shown to be essential for vaccine-induced protection against Helicobacter pylori infection in mice. Less is known about relative contributions of individual cell subpopulations, such as TH1 and TH17 cells, and their associated cytokines. The aim of the present study was to find immune correlates to vaccine-induced protection and further study their role in protection against H. pylori infection. Immunized and unimmunized mice were challenged with H. pylori and immune responses were compared. Vaccine-induced protection was assessed by measuring H. pylori colonization in the stomach. Gastric gene expression of TH1- and/or TH17-associated cytokines was analyzed by quantitative PCR and contributions of individual cytokines to protection were evaluated by antibody-mediated in vivo neutralization. By analyzing immunized and unimmunized mice a significant inverse correlation could be demonstrated between levels of interleukin (IL)-12p40, tumor necrosis factor α (TNF), interferon γ (IFNγ) and IL-17 gene expression and number of H. pylori in the stomach of individual animals after challenge. In a kinetic study, up-regulation of TNF, IFNγ and IL-17 coincided with vaccine-induced protection 7 days after H. pylori challenge and was sustained for at least 21 days. In vivo neutralization of these cytokines during the effector phase of the immune response revealed a significant role for IL-17, but not for IFNγ or TNF, in vaccine-induced protection. In conclusion, although both TH1- and TH17-associated gene expression in the stomach correlate with vaccine-induced protection against H. pylori infection, our study indicates that mainly TH17 effector mechanisms are of critical importance to protection.
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