Biology subjects

Schaufler, K.

Publications and source records attributed to Schaufler, K..

7 recordsLinked to original sources

bioRxiv2024

In-host evolution of classic to convergent Klebsiella pneumoniae sequence type 147 isolates and impact of associated capsular changes on different morphotypes

Klebsiella pneumoniae, an important opportunistic pathogen, has long been categorized into two distinct pathotypes: the often multidrug-resistant classic (cKp) and the highly virulent hypervirulent (hvKp). However, a recent global trend has witnessed the emergence of convergent strains, seamlessly combining antimicrobial resistance with hypervirulence. Our study delved into a series of K. pneumoniae isolates sourced from the same patient, all belonging to the international, high-risk clonal lineage of sequence type 147. As reported in a previous study, these isolates exhibited diverse morphotypes on blood agar, ranging from small white to normal-sized white, grey, or grey and dry (g/d) colonies. Through an interplay of omics and phenotypic experiments, we unraveled the intricate mechanisms governing these distinct colony morphologies and their implications on bacterial virulence and resilience. While the earlier isolates demonstrated modest levels of resistance and virulence, their later counterparts showed significantly heightened levels, attributed to the acquisition of additional plasmids. Bioinformatics analysis unveiled a chromosomal insertion of a hybrid plasmid in one isolate, marking an unprecedented in-host microevolution from the classic to the convergent pathotype. All morphotypes exhibited positive insertion sequences around or within the K loci, with the grey or g/d phenotypes arising from impaired K loci. Despite lower serum resistance, these morphotypes demonstrated superior adhesion to human epithelial cells. Interestingly, while capsule-deficient strains are conventionally associated with decreased virulence, our isolates displayed high mortality rates in the Galleria mellonella infection model. In conclusion, our findings not only provide unprecedented insights into in-host microevolution within a patient, transitioning from the classic to the convergent pathotype, but also contribute significantly to the understanding of the diverse morphotypes exhibited by K. pneumoniae.

microbiology↗

bioRxiv2024

Temperatures above 37°C increase virulence of a convergent Klebsiella pneumoniae sequence type 307 strain

Hypermucoviscosity in Klebsiella pneumoniae is often related to the overexpression of capsular polysaccharides, regulated by complex biosynthetic mechanisms in response to external cues. However, little is known about the processes involved in hypermucoviscosity in convergent K. pneumoniae, which combine extensive drug resistance with high bacterial virulence, under pathophysiological conditions. This study aimed to fill this gap by investigating the temperature dependence of hypermucoviscosity and overall virulence in a convergent K. pneumoniae strain isolated during a clonal outbreak belonging to the high-risk sequence type (ST)307. Hypermucoviscosity, biofilm formation, and mortality rates in Galleria mellonella larvae were examined at different temperatures (room temperature, 28{degrees}C, 37{degrees}C, 40{degrees}C and 42{degrees}C) and with various phenotypic experiments including electron microscopy. The underlying mechanisms of the phenotypic changes were explored via qPCR analysis to evaluate plasmid copy numbers, and transcriptomics. Our results indicate a temperature-dependent "switch" above 37{degrees}C to a hypermucoviscous phenotype, correlating with increased biofilm formation capacity and in vivo mortality, which might be due to a bacterial response to pathophysiological conditions, i.e., fever. In addition, we detected upregulation of a hybrid plasmid encoding both carbapenemase and the mucoid regulator rmpA genes. Surprisingly, rmpA did not exhibit temperature-dependent differential gene expression, suggesting other drivers. Apparent co-regulation of hypermucoviscosity and fimbrial expression was also identified. This study not only revealed the impact that increased temperatures above 37{degrees}C have on hypermucoviscosity and virulence in a convergent K. pneumoniae strain but contributes to the understanding of previously unrecognized dimension of K. pneumoniaes behavior, emphasizing its adaptability to changing environments. Abstract importanceUnderstanding the temperature-dependent dynamics of hypermucoviscosity in Klebsiella pneumoniae is crucial for unraveling the intricacies of its hypervirulence. This study investigates a convergent K. pneumoniae strain, ST307, revealing a temperature-dependent switch to hypermucoviscosity above 37 {degrees}C. The findings showcase a correlation between increased temperature, hypermucoviscosity, enhanced attachment, and heightened in vivo mortality. Notably, a hybrid plasmid encoding carbapenemase and mucoid regulator genes was upregulated at elevated temperatures. The study sheds light on previously unexplored aspects of K. pneumoniae behavior, emphasizing its adaptability in response to changing environments. The identified temperature-associated regulatory mechanisms offer insights into the pathogens response to fever, contributing to our broader understanding of bacterial adaptation. This research contributes to addressing the global challenge of hypervirulent, drug-resistant K. pneumoniae strains, providing valuable implications for future treatment strategies.

microbiology↗

bioRxiv2024

Klebsiella pneumoniae exhibiting a phenotypic hyper-splitting phenomenon including the formation of small colony variants

In this study, we characterized a Klebsiella pneumoniae strain in a patient with shrapnel hip injury, which resulted in multiple phenotypic changes, including the formation of a small colony variant (SCV) phenotype. Although already described since the 1960s, there is little knowledge about SCV phenotypes in Enterobacteriaceae. The formation of SCVs has been recognized as a bacterial strategy to evade host immune responses and compromise the efficacy of antimicrobial therapies, leading to persistent and recurrent courses of infections. In this case, 14 different, clonally identical resisto- and morpho-types were distinguished from the patients urine and tissue samples. Whole genome sequencing revealed the K. pneumoniae high-risk clonal lineage belonging to sequence type 147. Subculturing the SCV colonies consistently resulted in the reappearance of the initial SCV phenotype and three stable normal-sized phenotypes with distinct morphological characteristics. Additionally, an increase in resistance was observed over time in isolates that shared the same colony appearance. Our findings highlight the complexity of bacterial behavior by revealing a case of phenotypic "hyper-splitting" in a K. pneumoniae SCV and its potential clinical significance.

microbiology↗

bioRxiv2023

Multi-omics investigations uncover unique pathogenic markers in clinical Klebsiella pneumoniae that could be leveraged as novel antimicrobial targets

BackgroundKlebsiella pneumoniae (KP), often multidrug-resistant (MDR), is a significant public health concern and frequently associated with various diseases including urinary-tract infection. In addition, in recent years, an increasing number of studies reports on the emergence of convergent KP that combine MDR with hypervirulence leading to severely limited treatment options and thus calling for alternative approaches. MethodsIn this study, we compared high-risk clonal KP lineages with less pathogenic Klebsiella variicola (KV) and Klebsiella quasipneumoniae (KQ) strains on multiple-omics levels and performed integrative data analysis to identify unique markers that could be subsequently leveraged as novel targets in alternative treatment strategies. ResultsOur initial genomic analysis revealed 107 genes as part of the patho-core genome in eight clinical KP that were associated with different metabolic pathways. Subsequent transcriptome and proteome analyses in infection-mimicking media demonstrated similar regulatory patterns among KP vs. other Klebsiella strains, again with metabolic responses playing a pivotal role. In total, we identified 193 KP-specific, differentially expressed genes on transcriptomic and/or proteomic levels. When then comparing these regulated genes to over 6,000 publicly available Klebsiella genomes, we identified unique markers either in KP genomes or adaptively regulated on transcriptomics and/or proteomics levels. An example for the latter was a gene cluster for the cellobiose phosphotransferase system that has been previously described in the context of bacterial virulence and biofilm formation. ConclusionIn conclusion, our study not only highlights that KP strains demonstrate metabolic flexibility in response to particular environmental conditions, which is potentially important for their success as opportunistic pathogens, but identified unique KP-markers. Subsequent studies are needed to explore whether these markers might be prospectively used as novel anti-virulence targets, providing alternatives to traditional antibiotics.

microbiology↗

bioRxiv2023

Carbapenem- and cefiderocol-resistant Enterobacterales in surface waters in Kumasi, Ashanti Region, Ghana

This study investigated the presence of extended-spectrum {beta}-lactamase-producing Enterobacterales in selected surface waters in the Ashanti Region in Ghana. Subsequent genomic analysis revealed that one-fifth of the isolates were genotypically carbapenem-resistant. Phenotypic susceptibility testing not only confirmed their carbapenem resistance, but also uncovered two cefiderocol-resistant isolates.

microbiology↗

bioRxiv2023

Global diversity of enterococci and description of 18 novel species

Enterococci are commensal gut microbes of most land animals. They diversified over hundreds of millions of years adapting to evolving hosts and host diets. Of over 60 known enterococcal species, Enterococcus faecalis and E. faecium uniquely emerged in the antibiotic era among leading causes of multidrug resistant hospital-associated infection. The basis for the association of particular enterococcal species with a host is largely unknown. To begin deciphering enterococcal species traits that drive host association, and to assess the pool of Enterococcus-adapted genes from which known facile gene exchangers such as E. faecalis and E. faecium may draw, we collected 886 enterococcal strains from nearly 1,000 specimens representing widely diverse hosts, ecologies and geographies. This provided data on the global occurrence and host associations of known species, identifying 18 new species in the process expanding genus diversity by >25%. The novel species harbor diverse genes associated with toxins, detoxification, and resource acquisition. E. faecalis and E. faecium were isolated from a wide diversity of hosts highlighting their generalist properties, whereas most other species exhibited more restricted distributions indicative of specialized host associations. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades as well as genes associated with range expansion, such as B-vitamin biosynthesis and flagellar motility. Collectively, this work provides an unprecedentedly broad and deep view of the genus Enterococcus, potential threats to human health, and new insights into its evolution. SIGNIFICANCEEnterococci, host-associated microbes that are now leading drug-resistant hospital pathogens, arose as animals colonized land over 400 million years ago. To globally assess the diversity of enterococci now associated with land animals, we collected 886 enterococcal specimens from a wide range of geographies and ecologies, ranging from urban environments to remote areas generally inaccessible to humans. Species determination and genome analysis revealed host associations from generalists to specialists, and identified 18 new species, increasing the genus by over 25%. This added diversity provided greater resolution of the genus clade structure, identifying new features associated with species radiations. Moreover, the high rate of new species discovery shows that tremendous genetic diversity in Enterococcus remains to be discovered.

microbiology↗

bioRxiv2021

Anatomy of an Extensively Drug Resistant Klebsiella pneumoniae Outbreak in Tuscany, Italy

A protracted outbreak of New Delhi metallo-beta-lactamase (NDM)-producing carbapenem-resistant Klebsiella pneumoniae, started in Tuscany, Italy, in November 2018 and continued in 2020 and through 2021. To understand the regional emergence and transmission dynamics over time, we collected and sequenced the genomes of 117 extensively drug-resistant, NDM-producing K. pneumoniae isolates cultured over a 20-month period from 76 patients at several health care facilities in South-East Tuscany. All isolates belonged to high-risk clone ST-147 and were typically non-susceptible to all first line antibiotics. Albeit sporadic, resistances to colistin, tigecycline and fosfomycin were also observed as a result of repeated, independent mutations. Genomic analysis revealed that ST-147 isolates circulating in Tuscany were monophyletic, highly genetically related (including a network of 42 patients from the same hospital and sharing nearly identical isolates) and shared a recent ancestor with clinical isolates from the Middle East. While the blaNDM-1 gene was carried by an IncFIB-type plasmid, our investigations revealed that the ST-147 lineage from Italy also acquired a hybrid IncH-type plasmid carrying the 16S methyltransferase armA gene as well as key virulence biomarkers often found in hypervirulent isolates. This plasmid shared extensive homologies with mosaic plasmids circulating globally including from ST-11 and ST-307 convergent lineages. Phenotypically, the carriage of this hybrid plasmid resulted in increased siderophore production but did not confer virulence to the level of an archetypical, hypervirulent K. pneumoniae in a subcutaneous model of infection with immunocompetent CD1 mice. Our findings highlight the importance of performing genomic surveillance to identify emerging threats. Significance StatementCarbapenem-resistant Klebsiella pneumoniae belong to the "critical priority" tier of bacterial pathogens as identified by the World Health Organization. Emerging "high-risk" lineages are responsible for difficult-to-treat, hospital-acquired infections and outbreaks around the globe. By integrating genomic and epidemiological data for isolates collected over 20 months, this study revealed both the high, regional prevalence and the rapid spread, within a single hospital, of K. pneumoniae ST-147 in Italy. Besides resistance to nearly all antibiotics, we showed that this lineage carried a hybrid plasmid harboring a set of biomarker genes previously linked to hypervirulence. Convergence of multidrug resistance and hypervirulence is a major concern and these findings highlight the need for robust, global surveillance to monitor the emergence of high-risk K. pneumoniae.

microbiology↗