Biology subjects

Fostervold, A.

Publications and source records attributed to Fostervold, A..

7 recordsLinked to original sources

bioRxiv2025

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

BACKGROUNDCiprofloxacin resistant Klebsiella pneumoniae is common or emerging in many geographies, and knowledge of local resistance rates is important for empirical therapy. Whilst there are known K. pneumoniae ciprofloxacin resistance determinants, there is a lack of systematic data on the effect of determinants, alone and in combination, and there are no publicly accessible tools for predicting resistance from whole genome sequence data. METHODSThe KlebNET-GSP AMR Genotype-Phenotype Group aggregated a matched genotype-phenotype dataset of n=12,167 K. pneumoniae species complex (KpSC) isolates from 27 countries between 2001-2021. We developed a rules-based classifier to predict ciprofloxacin resistance by categorizing the number of quinolone resistance determining regions mutations in gyrA and parC, the number of plasmid-mediated quinolone resistance genes, and the presence/absence of aac(6')-Ib-cr (which can acetylate ciprofloxacin). Predictive performance was assessed using the discovery dataset, for which we re-phenotyped discrepant isolates; and validated using externally contributed datasets (n=7,030 KpSC isolates). RESULTSThe rules-based classifier predicted R vs S/I with categorical agreement, sensitivity, and specificity >96%, and major/very major error rates <4%. Performance was similar across diverse KpSC sources (human, animal, other), species, and intra-species lineages. External validation of the classifier yielded overall 93.12% categorical agreement [95% confidence interval (CI), 92.50-93.74%], 8.65% major errors [95% CI, 7.34-9.97%], and 6.20% very major errors [95% CI, 5.51-6.90%]. We implemented the classifier in Kleborate, a command-line tool that is integrated into the Pathogenwatch web platform. Using this to assess the global distribution of ciprofloxacin resistance determinants in KpSC genomes available in Pathogenwatch (n=31,319, from 109 countries between years 2000-2023), we observed a significant positive association between national quinolone consumption rates and predicted ciprofloxacin resistance (R2=0.20, p=0.004). CONCLUSIONS Ciprofloxacin resistance phenotypes can be reasonably predicted from genotypes, which is sufficient for informing surveillance. However, unexplained resistance remains and accuracy is insufficient for clinical applications. We demonstrate the value of aggregating genotype-phenotype data to explore resistance mechanisms and develop predictors, but highlight complexities in combining phenotype data from different assays and standards.

genomics↗

bioRxiv2025

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome

Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) can colonise humans, animals, and various environments, and frequently cause nosocomial and community-acquired infections in humans. While plasmid-borne AMR genes are prevalent in clinical strains, the diversity, distribution, and association of plasmids encoding AMR and virulence across ecological niches remain poorly characterised. Understanding the traits governing successful plasmid transmission within and between ecological niches is critical for developing effective AMR prevention strategies. Here, we characterise the diversity and distribution of KpSC plasmids and identify potential niche associations of AMR, heavy metal resistance, virulence factors, and plasmid clusters. We analysed the plasmidome (i.e. total genetic content attributable to plasmids) of 578 whole-genome sequenced KpSC isolates collected in Norway between 2001-2020 from human (n=453), terrestrial animal (n=102), and marine (n=23) sources. Plasmids from complete hybrid assemblies were annotated and clustered to evaluate the plasmid diversity and content across niches. Additionally, the representativeness of this plasmid collection was determined by clustering with a global collection of 8656 circularised KpSC plasmids. In total, 1415 circularised plasmids were identified and grouped according to rearrangement distance using Pling, resulting in 130 clusters (containing >1 plasmid), of which 36% (n=47) contained plasmids from >1 niche. The plasmids exhibited significant diversity, as 37% (n=524) remained singletons after clustering. AMR and virulence genes existed across diverse clusters and singletons, but predominantly resided on 120-250 kbp conjugative or mobilisable plasmids harbouring various transposable elements. The human niche exhibited a significantly higher prevalence of plasmids with AMR genes compared to animal or marine niches (p<0.001), whereas the animal niche displayed a significantly higher prevalence of virulence-encoding plasmids compared to human or marine niches (p<0.001), which was largely due to an enrichment of iuc3 plasmids in pigs. The high diversity of the KpSC plasmids underscores the dynamic nature of plasmid evolution, driven by horizontal gene transfer, and selective pressures. The presence of variable clusters, marked by high genetic diversity, indicates a dynamic plasmidome capable of rapid adaptation to environmental pressures through the acquisition and rearrangement of accessory genes.

microbiology↗

bioRxiv2024

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed. Utilising 3,255 whole-genome sequenced isolates from human, animal and marine sources collected during 2001-2020 in Norway, we showed the KpSC populations in different niches were distinct but overlapping. Notably, human infection isolates showed greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives ([≤]22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. Infection prevention measures are essential to limit transmission within human clinical settings and reduce disease burden. However, as colonisation often precedes infection, preventing transmission that leads to colonisation, e.g. transmission between animals and humans in the community, and in the food chain, could also be beneficial.

microbiology↗

bioRxiv2024

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

Interpreting phenotypes of blaSHV alleles in Klebsiella pneumoniae genomes is complex. While all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal blaSHV alleles or additional plasmid-borne blaSHV alleles that have extended-spectrum {beta}-lactamase (ESBL) activity and/or {beta}-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/amino acid changes is not completely documented or understood. This has led to confusion in the literature and in antimicrobial resistance (AMR) gene databases (e.g., NCBIs Reference Gene Catalog and the {beta}-lactamase database (BLDB)) over the specific functionality of individual SHV protein variants. Therefore, identification of ESBL-producing strains from K. pneumoniae genome data is complicated. Here, we reviewed the experimental evidence for the expansion of SHV enzyme function associated with specific amino-acid substitutions. We then systematically assigned SHV alleles to functional classes (wildtype, ESBL, BLI-resistant) based on the presence of these mutations. This resulted in the re-classification of 37 SHV alleles compared with current assignments in NCBIs Reference Gene Catalog and/or BLDB (21 to wildtype, 12 to ESBL, 4 to BLI-resistant). Phylogenetic and comparative genomic analyses support that; i) SHV-1 (encoded by blaSHV-1) is the ancestral chromosomal variant; ii) ESBL and BLI-resistant variants have evolved multiple times through parallel substitution mutations; iii) ESBL variants are mostly mobilised to plasmids; iv) BLI-resistant variants mostly result from mutations in chromosomal blaSHV. We used matched genome-phenotype data from the KlebNET-GSP Genotype-Phenotype Group to identify 3,999 K. pneumoniae isolates carrying one or more blaSHV alleles but no other acquired {beta}-lactamases, with which we assessed genotype-phenotype relationships for blaSHV. This collection includes human, animal, and environmental isolates collected between 2001 to 2021 from 24 countries across six continents. Our analysis supports that mutations at Ambler sites 238 and 179 confer ESBL activity, while most omega-loop substitutions do not. Our data also provide direct support for wildtype assignment of 67 protein variants, including eight that were noted in public databases as ESBL. We reclassified these eight variants as wildtype, because they lack ESBL-associated mutations, and our phenotype data support susceptibility to 3GCs (SHV-27, SHV-38, SHV-40, SHV-41, SHV-42, SHV-65, SHV-164, SHV-187). The approach and results outlined here have been implemented in Kleborate v2.4.1 (a software tool for genotyping K. pneumoniae from genome assemblies), whereby known and novel blaSHV alleles are classified based on causative mutations. Kleborate v2.4.1 was also updated to include ten novel protein variants from the KlebNET-GSP dataset and all alleles in public databases as of November 2023. This study demonstrates the power of sharing AMR phenotypes alongside genome data to improve understanding of resistance mechanisms. Impact statementSince every K. pneumoniae genome has an intrinsic SHV {beta}-lactamase and may also carry additional mobile forms, the correct interpretation of blaSHV genes detected in genome data can be challenging and can lead to K. pneumoniae being misclassified as ESBL-producing. Here, we use matched K. pneumoniae genome and drug susceptibility data contributed from dozens of studies, together with systematic literature review of experimental evidence, to improve our understanding of blaSHV allele variation and mapping of genotype to phenotype. This study shows the value of coordinated data sharing, in this case via the KlebNET-GSP Genotype-Phenotype Group, to improve our understanding of the evolutionary history and functionality of blaSHV genes. The results are captured in an open-source AMR dictionary utilised by the Kleborate genotyping tool, that could easily be incorporated into or used to update other tools and AMR gene databases. This work is part of the wider efforts of the KlebNET-GSP group to develop and support a unified platform tailored for the analysis and interpretation of K. pneumoniae genomes by a wide range of stakeholders. Data summaryBlaSHV allele sequences and class assignments are distributed with Kleborate, v2.4.1, DOI:10.5281/zenodo.10469001. Table S1 provides a summary of blaSHV alleles, including primary accessions, class-modifying mutations, and supporting evidence for class assignments that differ from NCBIs Reference Gene Catalog or BLDB. Whole genome sequence data are publicly available as reads and/or assemblies, individual accessions are given in Table S2; corresponding genotypes and antibiotic susceptibility phenotypes and measurements are available in Tables S3 and S4, respectively.

genomics↗

bioRxiv2021

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-2015: Introduction and spread of ESBL facilitated by CG15 and CG307

SynopsisO_ST_ABSObjectiveC_ST_ABSWe have used the nationwide Norwegian surveillance program on resistant microbes in humans (NORM) to address longitudinal changes in the population structure K. pneumoniae isolates during 2001-15, encompassing the emergence and spread of ESBL-producing Enterobacterales (ESBL-E) in Norway. Material and methodsAmong blood (n= 6124) and urinary tract (n=5496) surveillance isolates from 2001-15, we used Illumina technology to whole genome sequence 201 ESBL-producing isolates from blood (n=130) and urine (n=71), and 667 non-ESBL isolates from blood. Complete genomes for four isolates were resolved with Oxford Nanopore sequencing. ResultsIn a highly diverse collection, Klebsiella variicola ssp. variicola caused a quarter of Klebsiella pneumoniae species complex bacteraemias. ESBL-production was limited to K. pneumoniae sensu stricto (98.5 %). A diverse ESBL population of 57 clonal groups (CGs) were dominated by multidrug resistant CG307 (17%), CG15 (12%), CG70 (6%), CG258 (5%) and CG45 (5%) carrying blaCTX-M-15. Yersiniabactin was significantly more common in ESBL-positive (37.8%) compared to non-ESBL K. pneumoniae sensu stricto isolates (12.7%), indicating convergence of virulence and resistance determinants Moreover, we found a significant lower prevalence of yersinabactin (3.0 %, 37.8 % and 17.3 %), IncFIB (58.7 %, 87.9 % and 79.4 %) and IncFII plasmid replicons (40.5 %, 82.8 % and 54.2%) in K. variicola ssp. variicola compared to ESBL- and non-ESBL K. pneumoniae sensu stricto, respectively. ConclusionThe increase in Norwegian KpSC ESBLs during 2010-15 was driven by blaCTX-M-15 carrying CG307 and CG15. K. variicola ssp. variicola was a frequent cause of invasive KpSC infection, but rarely carried ESBL.

microbiology↗

bioRxiv2018

Convergence of virulence and multidrug resistance in a single plasmid vector in multidrug-resistant Klebsiella pneumoniae ST15

SYNOPSISO_ST_ABSBackgroundC_ST_ABSMultidrug resistance (MDR) and hypervirulence (hv) are typically observed in separate Klebsiella pneumoniae populations. However, convergent strains with both properties have been documented and potentially pose a high risk to public health in the form of invasive infections with limited treatment options.\n\nObjectivesTo characterize the genetic determinants of virulence and antimicrobial resistance (AMR) in two ESBL-producing K. pneumoniae isolates belonging to the international MDR clone ST15.\n\nMethodsThe complete genome sequences of both isolates, including their plasmids, were resolved using Illumina and Oxford Nanopore sequencing.\n\nResultsBoth isolates carried large mosaic plasmids in which AMR and virulence loci have converged within the same vector. These closely related mosaic hv-MDR plasmids include sequences typical of the K. pneumoniae virulence plasmid 1 (KpVP-1; including aerobactin synthesis locus iuc) fused with sequences typical of IncFIIK conjugative AMR plasmids. One hv-MDR plasmid carried three MDR elements encoding the ESBL gene blaCTX-M-15 and eight other AMR genes (blaTEM, aac3-IIa, aph3-Ia, dfrA1, satA2, blaSHV, sul1, aadA1). The other carried remnants of these elements encoding blaTEM and aac3-IIa, and blaCTX-M-15 was located in a second plasmid in this isolate. The two isolates originated from patients hospitalized in Norway but have epidemiological and genomic links to Romania.\n\nConclusionsThe presence of both virulence and AMR determinants on a single vector enables simultaneous transfer in a single event and potentially rapid emergence of hv-MDR K. pneumoniae clones. This highlights the importance of monitoring for such convergence events with stringent genomic surveillance.

genomics↗

bioRxiv2018

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

Recent reports indicate the emergence of a new carbapenemase producing Klebsiella pneumoniae clone, ST307. Here we show that ST307 emerged in the mid-1990s (nearly 20 years prior to its first report), is already globally distributed and is intimately associated with a conserved plasmid harbouring the blaCTX-M-15 extended-spectrum beta-lactamase (ESBL) gene plus other antimicrobial resistance determinants. Our findings support the need for enhanced surveillance of this widespread ESBL clone in which carbapenem resistance is now emerging.

microbiology↗