| 1. |
- Alaridah, Nader, et al.
(författare)
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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden
- 2019
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.
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| 2. |
- Johnning, Anna, 1985, et al.
(författare)
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The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis
- 2018
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Ingår i: Microbial Genomics. - : Microbiology Society. - 2057-5858. ; 4:11
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Tidskriftsartikel (refereegranskat)abstract
- Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia colt, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7-18 different genes per isolate), including the following encoding carbapenemases: bla(KPC-2), bla(OXA-48), bla(OXA-72), bla(NDM-1), bla(NDm-7) and bla(VIM-1). In addition, a novel version of bla(SHv) was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were colocalized on these and other plasmids, suggesting a risk for coselection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance - based on acquired resistance determinants - was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
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| 3. |
- Salvà-Serra, Francisco, 1989, et al.
(författare)
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Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.
- 2016
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Ingår i: Genome Announcements. - 2169-8287. ; 4:2
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Tidskriftsartikel (refereegranskat)abstract
- Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41 contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.
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| 4. |
- Tång Hallbäck, Erika, 1973, et al.
(författare)
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Methicillin-resistant Staphylococcus argenteus misidentified as methicillin-resistant Staphylococcus aureus emerging in western Sweden
- 2018
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Ingår i: Journal of Medical Microbiology. - : Microbiology Society. - 0022-2615 .- 1473-5644. ; 67:7, s. 968-971
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Tidskriftsartikel (refereegranskat)abstract
- Two strains included in a whole-genome sequencing project for methicillin-resistant Staphylococcus aureus (MRSA) were identified as non-Staphylococcus aureus when the sequences were analysed using the bioinformatics software ALEX (www.1928diagnostics.com, Gothenburg, Sweden). Sequencing of the sodA gene of these strains identified them as Staphylococcus argenteus. The collection of MRSA in western Sweden was checked for additional strains of this species. A total of 18 strains of S. argenteus isolated between 2011 and December 2017 were identified.
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| 5. |
- Tång Hallbäck, Erika, 1973
(författare)
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Molecular regulation of epithelial tube size
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In nature, epithelial tubes are vital structures in organ design and are required for transport of gases and liquids in organs, such as the vascular system, the vertebrate lung and the kidneys. The tubular epithelium is single layered, but is often reinforced by layers of muscular support. It constitutes an apical side facing the lumen and a basal side that contacts surrounding tissues. To ensure optimal flow, it is critical that the tubes are correctly sized and shaped. Epithelial tube growth depends on apical membrane enlargements, as well as sub-apical rearrangements, but the mechanisms involved in the regulation of size and shape of epithelial tubes are yet to be revealed. In this thesis the Drosophila respiratory (tracheal) system has been used as a model organ to identify essential genes and clarify the mechanisms involved in the making and shaping of tubes. Through genetic and molecular analyses, new biological concepts have been uncovered. The main tracheal tube, the dorsal trunk (DT), expands three-fold in diameter during a short interval followed by tube elongation. In this thesis we have dissected the roles of five genes in tube regulation, called kkv, knk rtv, dBest2 and DAAM. Analysis of kkv, knk and rtv led us to identify an unprecedented need for luminal matrix components in modeling tube shape. A chitinous luminal matrix is deposited in newly formed tubes and constitutes an expanding cord inside the tube that is required for uniform tube diameter growth. kkv is required for chitin synthesis while knk and rtv are needed for chitin filament assembly. If chitin is missing or fail to form an organized matrix, the expanding tubes develop severe local dilations and constrictions. The subsequent tube elongation requires dBest2 and DAAM. dBest2 encodes an apical chloride channel and is essential for lumen growth during elongation, suggesting that elongation is driven by an increased luminal osmotic pressure. DAAM has a function in actin organization. In the wild type trachea, actin filaments arrange as sub-apical rings perpendicular to tube length, thus allowing for lumen elongation, but not diametrical expansion, upon the increase in lumen pressure. In DAAM mutants, the actin rings are disorganized, thus lumen elongation is inhibited. The luminal chitin matrix has a second role at this stage by preventing excess tube elongation. A balance between combinatorial physical forces exerted by the lumen and sub-apical actin cytoskeleton determines final tube size.
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| 6. |
- Tång Hallbäck, Erika, 1973, et al.
(författare)
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Outbreak of OXA-48-producing Enterobacteriaceae in a neonatal intensive care unit in Western Sweden
- 2023
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Ingår i: European Journal of Clinical Microbiology and Infectious Diseases. - : Springer Science and Business Media LLC. - 1435-4373 .- 0934-9723. ; 42:5, s. 597-605
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Tidskriftsartikel (refereegranskat)abstract
- In 2015, an outbreak caused by OXA-48-producing Enterobacteriaceae affected a neonatal intensive care unit at a Swedish University Hospital. The aim was to explore the transmission of OXA-48-producing strains between infants and the transfer of resistance plasmids between strains during the outbreak. Twenty-four outbreak isolates from ten suspected cases were whole-genome sequenced. A complete assembly was created for the index isolate (Enterobacter cloacae) and used as a mapping reference to detect its plasmids in the remaining isolates (17 Klebsiella pneumoniae, 4 Klebsiella aerogenes, and 2 Escherichia coli). Strain typing was performed using core genome MLST and SNP analysis. As judged from sequencing and clinical epidemiological data, the outbreak involved nine cases (two developed sepsis) and four OXA-48-producing strains: E. cloacae ST1584 (index case), K. pneumoniae ST25 (eight cases), K. aerogenes ST93 (two cases), and E. coli ST453 (2 cases). Two plasmids from the index strain, pEclA2 and pEclA4, carrying blaOXA48 and blaCMY-4, respectively, were traced to all K. pneumoniae ST25 isolates. Klebsiella aerogenes ST93 and E. coli ST453 harboured either only pEclA2, or both pEclA2 and pEclA4. One suspected case harbouring OXA-162-producing K. pneumoniae ST37 could be excluded from the outbreak. Once initiated by an E. cloacae strain, the outbreak was caused by the dissemination of a K. pneumoniae ST25 strain and involved inter-species horizontal transfer of two resistance plasmids, one of which carried blaOXA-48. To our knowledge, this is the first description of an outbreak of OXA-48-producing Enterobacteriaceae in a neonatal setting in northern Europe.
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