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174 results for “Klebsiella”
Characterization of cefiderocol resistant spontaneous mutant variants of Klebsiella pneumoniae producing NDM-5 with single mutation in cirA
<p>Cefiderocol (CFDC) is a siderophore-cephalosporin antibiotic designed to combat highly resistant Gram-negative bacterial infections. Its mechanism involves a strong affinity for iron and active transport into bacterial cells, providing an alternative against strains resistant to common antibiotics. However, the emergence of CFDC resistance in Klebsiella is a growing concern. Recent reports highlight increasing CFDC resistance in K. pneumoniae, particularly associated with mutations in the cirA gene, responsible for encoding a siderophore receptor. Co-localization of blaNDM-like gene and cirA mutations correlates with higher CFDC resistance. The study focuses on a carbapenem-resistant K. pneumoniae strain (Kp-1) with carbapenemases blaNDM-5 and blaOXA-181, recovered from a post-surgery patient. The strain exhibited resistance to all tested antibiotics but susceptibility to CFDC. Heteroresistant populations with the halo on inhibition of CFDC were observed. Genomic analysis identified a novel mutation (W123*) in the cirA gene associated with CFDC resistance. Additionally, increased blaNDM-5 expression in Kp-1 IHC (intra-halo colony) compared to Kp-1 was noted. The coexistence of blaNDM-like and cirA variants, along with high blaNDM-5 expression, explains the observed 21-fold increase in Minimum Inhibition Concentration (MIC) in Kp-1 IHC. The study contributes to understanding the molecular mechanisms driving the emergence of cefiderocol resistance, emphasizing the significance of coexisting mutations in cirA and blaNDM-like genes.</p>
Genomic Typing, Antimicrobial Resistance Gene, Virulence Factor and Plasmid Replicon Dataset for the Important Pathogenic Bacteria Klebsiella pneumoniae
<p>The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates usually called 'the clones of high risk' often drive the spread of resistance within particular species. </p> <p>Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and developing of spread prevention measures. However, the availability and uniformity of the data derived from the genomic sequences often represents a bottleneck for such investigations. </p> <p>In this dataset, we present the results of a genomic epidemiology analysis of 61,857 genomes of a dangerous bacterial pathogen <em>Klebsiella pneumoniae</em> obtained from NCBI Genbank database. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), capsular (KL) and oligosaccharide (OL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to clonal groups (CG). The presence of antimicrobial resistance and virulence genes, as well as plasmid replicons, within the genomes is also reported. </p> <p>These data will be useful for researchers in the field of <em>K. pneumoniae</em> genomic epidemiology, resistance analysis and prevention measure development.</p>
Compressed Database of Klebsiella pneumoniae for WhatsGNU
<p>WhatsGNU_Kp_Ortholog.zip: <em>Klebsiella pneumoniae</em> Version-04/28/2020 (compressed 46,072,343 proteins in 8752 genomes to 1,466,934 protein variants). Updated File to fix issue with download.</p>
mSWEEP/mGEMS Klebsiella database
<p>mSWEEP/mGEMS Klebsiella used in the article <a href="https://www.nature.com/articles/s41467-022-35178-5">Strong pathogen competition in neonatal gut colonisation</a> (published 01 Dec 2022).</p> <p><strong>Changelog</strong></p> <p>v1.1.1 (18 Dec 2023): Added a file linking the `id` field in Klebsiella_assemblies_info.tsv to the ENA/NCBI run accession.<br>v1.1.0 (18 Dec 2023): Added the assemblies.</p>
Genomic Analysis of Public Klebsiella Reference Strains
<p>A genomic resource of <em>Klebsiella </em>reference strains from ATCC, NCTC and BEI Resources MRSN Diversity Panel.</p>
Klebsiella sp003752615 BIGb0399
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Klebsiella sp003752615 BIGb0399, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Klebsiella terrigena BIGb0149
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Klebsiella terrigena BIGb0149, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Klebsiella sp004342285 BIGb0138
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Klebsiella sp004342285 BIGb0138, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Klebsiella terrigena BIGb0132
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Klebsiella terrigena BIGb0132, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Klebsiella terrigena JUb54
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Klebsiella terrigena JUb54, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Klebsiella terrigena BIGb0119
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Klebsiella terrigena BIGb0119, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Data from : Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B12-Producing Strain from Indonesian Tempeh
<p>Klebsiella pneumoniae strain IIEMP-3, isolated from Indonesian tempeh, is a vitamin B<sub>12</sub>-producing strain that exhibited a different genetic profile from pathogenic isolates. Here we report the draft genome sequence of strain IIEMP-3, which may provide insights on the nature of fermentation, nutrition, and immunological function of Indonesian tempeh.</p>
Figure 4 in Isolation and characterization of Klebsiella oxytoca from the rhizosphere of Lotus corniculatus and its biostimulating features
Figure 4. Enhancement of the root and shoot lengths of barley when inoculated with LCK121. *Indicates a significant effect (P value <0.05).
Figure 3 in Isolation and characterization of Klebsiella oxytoca from the rhizosphere of Lotus corniculatus and its biostimulating features
Figure 3. Enhancement of the root and shoot lengths of barley when inoculated with LCK121, A.LCK121-treated ones; B.control seedlings.
Figure 2 in Isolation and characterization of Klebsiella oxytoca from the rhizosphere of Lotus corniculatus and its biostimulating features
Figure 2. Evolutionary relationships of LCK121 and other related bacterial species as inferred using the neighbor-joining method.
Figure 5 in Isolation and characterization of Klebsiella oxytoca from the rhizosphere of Lotus corniculatus and its biostimulating features
Figure 5. Enhancement of the root and shoot dry weight of barley when inoculated with LCK121. *Indicates a significant effect (P value <0.05).
Short and Long Read Sequences from VIM-1 producing (Klebsiella pneumoniae test-dataset)
<p>Creation of a downsized version of the long and short reads data of VIM-1 producing <i>Klebsiella pneumoniae</i>. Samples were obtained from the Hospital Infanta Cristina (Badajoz, Spain) on October 11th, 2019. </p><p>- Long read data: Oxford Nanopore Technology (A1403KPN.fastq.gz).</p><p>- Short read data : Illumina (A1403KPN_R2_filtered.fastq.gz && A1403KPN_R2_filtered.fastq.gz)</p>
Emerging Resistance to Novel b-Lactam b-Lactamase Inhibitor Combinations in Klebsiella pneumoniae bearing KPC Variants
<p><em><span><span>Klebsiella pneumoniae</span></span></em><span><span> carbapenemase (KPC) variants, predominantly KPC-2 and KPC-3, are a significant global resistance mechanism in <em><span>K. pneumoniae</span></em>. KPC-2 and KPC-3 confer resistance to a broad range of β-lactams, including carbapenems, while remaining susceptible to ceftazidime-avibactam (CZA). Lately, new KPC variants have emerged and developed resistance to CZA, often through mutations, insertions, or deletions in key regions such as the Omega loop, the 237–243 loop, and the 266–275 loop. In the present work we aim to understand the role of these mutations in KPC in the emergence of cross-resistance to last-resort antibiotics like cefiderocol (FDC) and cefepime/zidebactam (FPZ). Fifteen clinical isolates of KPC-producing <em><span>Klebsiella</span></em> spp. were analyzed, representing 15 distinct KPC variants. CZA resistance was confirmed in 12 of the 15 KPC variants tested. Cross-resistance to FDC was observed in eight isolates, with five of these exhibiting spontaneous resistant subpopulations, including one originally categorized as FDC-susceptible. Six FDC-resistant strains carried mutations in the 266–275 loop. Cross-resistance to FPZ was observed in five KPC variants, particularly those with mutations in the 266–275 loop, although many omega loop and 237–243 loop mutants remained susceptible to FPZ. WGS of FDC-resistant subpopulations revealed additional mutations in genes such as <em><span>ompC</span></em>, <em><span>rpoC</span></em>, <em><span>dksA</span></em>, and <em><span>cirA</span></em>.<br>This study demonstrates that KPC variants show resistance to both CZA and FDC, with cross-resistance to FPZ observed to a lesser degree. The emergence of cross-resistance in strains that had not been exposed to these antibiotics raises concerns about the spread of resistance. The identification of mutations in <em><span>bla</span></em><sub>KPC</sub>, <em><span>cirA</span></em>, and other novel genes highlights the importance of understanding the molecular mechanisms driving resistance to develop effective therapeutic strategies. </span></span></p>
Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome
<p>In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.</p>
Raw Data for the article: Klebsiella pneumoniae Lipopolysaccharides Serotype O2afg Induce Poor Inflammatory Immune Responses Ex Vivo
<p>Currently, <em>Klebsiella pneumoniae</em> is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During <em>K. pneumoniae</em> infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role in immune evasion. The LPS O2a and LPS O2afg serotypes are prevalent in most multidrug resistant <em>K. pneumoniae</em> strains. Thus, we sought to understand if those two particular LPS serotypes were involved in a mechanism of immune evasion. We have extracted LPS (serotypes O1, O2a and O2afg) from <em>K. pneumoniae</em> strains and, using human monocytes ex vivo, we assessed the ability of those LPS antigens to induce the production of pro-inflammatory cytokines and chemokines. We observed that, when human monocytes are incubated with LPS serotypes O1, O2a or O2afg strains, O2afg and, to a lesser extent, O2a but not O1 failed to elicit the production of pro-inflammatory cytokines and chemokines, which suggests a role in immune evasion. Our preliminary data also shows that nuclear translocation of NF-κB, a process which regulates an immune response against infections, occurs in monocytes incubated with LPS O1 and, to a smaller extent, with LPS O2a, but not with the LPS serotype O2afg. Our results indicate that multidrug resistant <em>K. pneumoniae</em> expressing LPS O2afg serotypes avoid an initial inflammatory immune response and, consequently, are able to systematically spread inside the host unharmed, which results in the several pathologies associated with this bacterium.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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