Biology subjects

Guo, X.

Publications and source records attributed to Guo, X..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

Disentangling Mnemonic Metacognition from Confidence by Communication between the Precuneus and Hippocampus

Metacognition, the ability to introspectively monitor ones own performance, remains an area with poorly understood neural mechanisms, particularly regarding the intercommunication among various brain regions. Recent studies have identified the precuneus as a key region in mnemonic metacognitive tasks, while the hippocampus is recognized for its role in memory function. This study aimed to investigate the role of the precuneus and hippocampus in mnemonic metacognition by utilizing intracranial electrode recordings from patients with intractable epilepsy to analyze the correlational dynamics between these regions. Our findings revealed that high gamma activity serve as a key feature in both the precuneus and hippocampus for confidence judgment. Based on signal detection theory (SDT), we discovered that high gamma activity in the precuneus is significantly linked to type 2 sensitivity (meta-d), while hippocampal high gamma activity was primarily linked to type 1 sensitivity (d). Additionally, the correlation between high gamma activity in the hippocampus and precuneus was exclusively related to type 2 sensitivity (meta-d). Temporal analysis indicated that the hippocampus is initially engaged for the memory process, followed by its joint engagement together with the precuneus for confidence generation. These findings elucidate the distinct electrophysiological roles of the hippocampus and precuneus in mnemonic metacognition, providing deeper insights into the neural mechanisms underlying this cognitive process.

neuroscience↗

bioRxiv2024

The polyamine transporter ATP13A3 mediates DFMO-induced polyamine uptake in neuroblastoma

High-risk neuroblastomas, often associated with MYCN oncogene amplification, are addicted to polyamines, small polycations vital for cellular functioning. We have shown that neuroblastoma cells increase polyamine uptake when exposed to the polyamine biosynthesis inhibitor DFMO, currently in clinical trial, and that this mechanism limits the efficacy of the drug. While this finding resulted in the clinical development of polyamine transport inhibitors including AMXT 1501, presently under clinical investigation in combination with DFMO, the mechanisms and transporters involved in DFMO-induced polyamine uptake are unknown. Knockdown of ATP13A3, a member of the P5B-ATPase family, limited basal and DFMO-induced polyamine uptake, attenuated MYCN-amplified and non-MYCN-amplified neuroblastoma cell growth and potentiated the inhibitory effects of DFMO. Overexpression of ATP13A3 in neuroblastoma cells increased polyamine uptake, which was inhibited by AMXT 1501, highlighting ATP13A3 as a key target of the drug. The association between high ATP13A3 expression and poorer survival in neuroblastoma further supports a role of this transporter in neuroblastoma progression. Thus, this study identified ATP13A3 as a critical regulator of basal and DFMO-induced polyamine uptake and a novel therapeutic target for neuroblastoma. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/581161v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@11bef78org.highwire.dtl.DTLVardef@106c250org.highwire.dtl.DTLVardef@bf39b1org.highwire.dtl.DTLVardef@64d05f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Turnover of RNA-binding Proteins and MicroRNAs by intrinsically disordered region-directed ZSWIM8 ubiquitin ligase during brain development

Widely present in mammalian proteomes, intrinsically disordered regions (IDRs) in proteins play important biological functions by conferring structural flexibility and mediating biomolecular interactions. IDR-containing proteins, including many RNA-binding proteins (RBPs), are prone to misfolding and aggregation and must be constantly monitored. Here we show that the conserved ZSWIM8-type Cullin-RING ubiquitin ligase (CRLZSWIM8) is a master regulator of such proteins during brain development. ZSWIM8 selects its substrates via an IDR-dependent mechanism, and deletion of ZSWIM8 causes aberrant accumulation of numerous RBPs including AGO2 and ELAV1 in neonatal brains. Furthermore, AGO2 ubiquitination by ZSWIM8 is triggered by microRNA binding, leading to target-directed microRNA degradation (TDMD) of MiR7. Dysregulation of MiR7 in the absence of ZSWIM8 results in defects in oligodendrocyte maturation and functions. Together, our findings have demonstrated that, by utilizing variable target-recognition strategies, ZSWIM8 controls the abundance of conformationally flexible RBPs and miRNA metabolism that are essential for brain development. TeaserA conserved ubiquitin ligase controls the quality of disordered proteins to ensure brain development.

developmental biology↗

bioRxiv2024

Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota

ObjectiveN-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is still unclear. The purpose of this study is to investigate the effect of intestinal microbiota alteration on the pharmacokinetics of NBP and its related mechanisms. MethodsAfter treatment with antibiotics and probiotics, plasma NBP concentrations in SD rats were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The effect of intestinal microbiota changes on NBP pharmacokinetics was compared. Intestinal microbiota changes after NBP treatment were analyzed by 16S rRNA sequencing. Expressions of CYP3A1 mRNA and protein in the liver and small intestine tissues under different intestinal flora conditions were determined by qRT-PCR and Western Blot. KEGG analysis was used to analyze the effect of intestinal microbiota changes on metabolic pathways. ResultsCompared to the control group, the values of Cmax, AUC0-8, AUC0-{infty}, t1/2 in the antibiotic group increased by 56.1% (P<0.001), 56.4% (P<0.001), 53.2% (P<0.001), and 24.4% (P<0.05), respectively. In contrast, the CL and Tmax values decreased by 57.1% (P<0.001) and 28.6% (P<0.05), respectively. Treatment with antibiotics could reduce the richness and diversity of the intestinal microbiota. CYP3A1 mRNA and protein expressions in the small intestine of the antibiotic group were 61.2% and 66.1% of those of the control group, respectively. CYP3A1 mRNA and protein expressions in the liver were 44.6% and 63.9% of those in the control group, respectively. There was no significant change in the probiotic group. KEGG analysis showed that multiple metabolic pathways were significantly down-regulated in the antibiotic group. Among them, the pathways of drug metabolism, bile acid biosynthesis and decomposition, and fatty acid synthesis and decomposition were related to NBP biological metabolism. ConclusionAntibiotic treatment could affect the intestinal microbiota, decrease CYP3A1 mRNA and protein expressions and increase NBP exposure in vivo by inhibiting pathways related to NBP metabolism.

pharmacology and toxicology↗

bioRxiv2024

Contrast-enhanced photon-counting micro-CT of tumor xenograft models

Photon-counting micro computed tomography (micro-CT) offers new potential in preclinical imaging, particularly in distinguishing materials. It becomes especially helpful when combined with contrast agents, enabling the differentiation of tumors from surrounding tissues. There are mainly two types of contrast agents in the market for micro-CT: small molecule-based and nanoparticle-based. However, despite their widespread use in liver tumor studies, there is a notable gap in research on the application of these commercially available agents for photon-counting micro-CT in breast and ovarian tumors. Herein, we explored the effectiveness of these agents in differentiating tumor xenografts from various origins (AU565, MDA-MB-231, and SKOV-3) in nude mice, using photon-counting micro-CT. Specifically, ISOVUE-370 (a small molecule-based agent) and Exitrone Nano 12000 (a nanoparticle-based agent) were investigated in this context. To improve tumor visualization, we proposed a novel color visualization method for photon-counting micro-CT, which changes color tones to highlight contrast media distribution, offering a robust alternative to traditional material decomposition methods with less computational demand. Our in vivo experiments confirm its effectiveness, showing distinct enhancement characteristics for each contrast agent. Qualitative and quantitative analyses suggested that Exitrone Nano 12000 provides superior vasculature enhancement and better quantitative consistency across scans, while ISOVUE-370 gives more comprehensive tumor enhancement but with a significant variance between scans due to its short blood half-time. This variability leads to high sensitivity to timing and individual differences among mice. Further, a paired t-test on mean and standard deviation values within tumor volumes showed significant differences between the AU565 and SKOV-3 tumor models with the nanoparticle-based (p-values < 0.02), attributable to their distinct vascularity, as confirmed by immunohistochemistry. These findings underscore the utility of photon-counting micro-CT in non-invasively assessing the morphology and anatomy of different tumor xenografts, which is crucial for tumor characterization and longitudinal monitoring of tumor development and response to treatments.

bioengineering↗

bioRxiv2023

MERITS: a web-based integrated MycobacterialPE/PPE protein database

MotivationPE/PPE proteins, highly abundant in the Mycobacterium genome, play a vital role in virulence and immune modulation. Understanding their functions is key to comprehending the internal mechanisms of Mycobacterium. However, a lack of dedicated resources has limited research into PE/PPE proteins. ResultsAddressing this gap, we introduce MERITS, a comprehensive 3D structure database specifically designed for PE/PPE proteins. MERITS hosts 22,353 non-redundant PE/PPE proteins, encompassing details like physicochemical properties, subcellular localisation, post-translational modification sites, protein functions, and measures of antigenicity, toxicity, and allergenicity. MERITS also includes data on their secondary and tertiary structure, along with other relevant biological information. MERITS is designed to be user-friendly, offering interactive search and data browsing Features to aid researchers in exploring the potential functions of PE/PPE proteins. MERITS is expected to become a crucial resource in the field, aiding in developing new diagnostics and vaccines by elucidating the sequence-structure-functional relationships of PE/PPE proteins. Availability and implementationMERITS is freely accessible at http://merits.unimelb-biotools.cloud.edu.au/.

bioinformatics↗

bioRxiv2023

Climate change impacts dryland multifunctionality: A cascade of precipitation variability to species replacement in multitrophic microbiota

In the Anthropocene, the pervasive impacts of climate change on arid ecosystems are increasingly evident, resulting in significant alterations in both biodiversity and functionality. Although soil microbes are anticipated to be sensitive to changes in precipitation regimes, the mechanisms through which multifaceted precipitation changes impair the delivery of multiple functions by multitrophic microbiota in soils remain largely unexplored. In the drylands of Northwestern China, we examined the direct effects of historical precipitation regimes on the soil multifunctionality of biocrusts, a model system, and their indirect impacts mediated by microbial communities. Among abiotic predictors, precipitation variability, rather than mean annual precipitation, emerged as the primary driver of multifunctionality, leading to a convergence of less functionally beneficial species. By utilizing a biodiversity-ecosystem function relationship framework, our results underscore the crucial roles of - and {beta}-diversity of heterotrophic bacteria, fungi, and phototrophic cyanobacteria in maintaining soil functionality. However, the underlying mechanisms are distinct. We found that the local richness of heterotrophs and phylogenetic dissimilarity of photoautotrophs exert positive influences on multifunctionality, while species replacement, a component of {beta}-diversity, primarily enhances the variance in soil multifunctionality. Importantly, the findings illuminate the cascading effect of precipitation variability on dryland ecosystems, amplified by microbial diversity, potentially triggering a silent collapse of vulnerable arid habitats. Our study highlights the importance of considering indirect climate impacts via soil microbiota, contributing to a deeper understanding of the real-world consequences of climate change on drylands, and offering valuable insights for the management of biodiversity theory-inspired ecosystem restoration.

ecology↗

bioRxiv2023

Allocator is a graph neural network-based framework for mRNA subcellular localization prediction

MotivationThe asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computational tools for accurately identifying the subcellular localizations of mRNAs. However, considering multi-localization phenomena remains limited in existing approaches, with none considering the influence of RNAs secondary structure. ResultsIn this study, we propose Allocator, a multi-view parallel deep learning framework that seamlessly integrates the RNA sequence-level and structure-level information, enhancing the prediction of mRNA multi-localization. The Allocator models equip four efficient feature extractors, each designed to handle different inputs. Two are tailored for sequence-based inputs, incorporating multilayer perceptron and multi-head self-attention mechanisms. The other two are specialized in processing structure-based inputs, employing graph neural networks. Benchmarking results underscore Allocators superiority over state-of-the-art methods, showcasing its strength in revealing intricate localization associations. AvailabilityThe webserver of Allocator is available at http://Allocator.unimelb-biotools.cloud.edu.au; the source code and datasets are available at https://github.com/lifuyi774/Allocator

bioinformatics↗

bioRxiv2023

Single-cell 5' RNA sequencing of camelid peripheral B cells reveals cellular basis of heavy-chain antibody production

Camelids are capable of producing both conventional tetrameric antibodies (Abs) and dimeric heavy-chain antibodies (HCAbs). While B cells generating these two types of Abs exhibit distinct B-cell receptors (BCRs), it remains unclear whether these two B cell populations differ in their phenotypes and developmental processes. Here, we collected eight PBMC samples before and after immunization from four Bactrian camels and conducted single-cell 5 RNA sequencing. We characterized the functional subtypes and differentiation trajectories of circulating B cells in camels, including native B cells, memory B cells, intermediate B cells, atypical B cells, and plasma cells. Additionally, we reconstructed single-cell BCR sequences and revealed the IGHV and IGHC gene types. We found that B cells expressing variable genes of HACbs (VHH) were widely present in various functional subtypes and showed highly overlapping differentiation trajectories to B cells expressing variable genes of conventional Abs (VH). After immunization, the transcriptional changes in VHH+ and VH+ B cells were also largely consistent. Our study elucidates the cellular context of HCAb production in camels, and lays the foundation for the development of single B cell-based nanobody screening.

genomics↗

bioRxiv2023

Aalbo1200: global genetic differentiation and variability of the mosquito Aedes albopictus

The mosquito Aedes albopictus transmits human viruses including dengue and chikungunya and is an extremely successful invasive species expanding into new regions of the world. New tools are needed to complement existing tools to help monitor and control this species. Genomic resources are improving for this species including genome reference sequences, and whole genome sequencing data will help to catalog genetic diversity in this species and further enable genetic analysis. We collected populations of Ae. albopictus from throughout its distribution and generated whole genome sequencing data from population samples. These data will be used to address a number of basic and applied questions for this species. Here, we show genetic differentiation patterns among the tropical and temperate forms, as well as finer scale genetic clustering at the regional and population scale. These data and results will be a valuable resource for further study and tool development for this species.

evolutionary biology↗

bioRxiv2023

Peripheral gating of pain by glial endozepine

We report that diazepam binding inhibitor (DBI) is a glial messenger mediating satellite glia-sensory neuron crosstalk in the dorsal root ganglion (DRG). DBI is highly and specifically expressed in satellite glia cells (SGCs) of mice, rat and human, but not in sensory neurons or other DRG-resident cells. Knockdown of DBI results in a robust mechanical hypersensitivity without significant effects on other sensory modalities. In vivo overexpression of DBI in SGCs reduces sensitivity to mechanical stimulation and alleviates mechanical allodynia in neuropathic and inflammatory pain models. We further show that DBI acts as a partial agonist and positive allosteric modulator at the neuronal GABAA receptors, particularly strongly effecting those with a high-affinity benzodiazepine binding site. Such receptors are selectively expressed by a subpopulation of mechanosensitive DRG neurons and these are also more enwrapped with DBI-expressing glia, as compared to other DRG neurons, suggesting a mechanism for specific effect of DBI on mechanosensation. These findings identified a new, peripheral neuron-glia communication mechanism modulating pain signalling, which can be targeted therapeutically.

neuroscience↗

bioRxiv2023

Whole genome association testing in 333,100 individuals across three biobanks identifies rare non-coding single variant and genomic aggregate associations with height

The role of rare non-coding variation in complex human phenotypes is still largely unknown. To elucidate the impact of rare variants in regulatory elements, we performed a whole-genome sequencing association analysis for height using 333,100 individuals from three datasets: UK Biobank (N=200,003), TOPMed (N=87,652) and All of Us (N=45,445). We performed rare (<0.1% minor-allele-frequency) single-variant and aggregate testing of non-coding variants in regulatory regions based on proximal, intergenic and deep-intronic annotation. We observed 29 independent variants associated with height at P < 6 x 10-10 after conditioning on previously reported variants, with effect sizes ranging from -7cm to +4.7cm. We also identified and replicated non-coding aggregate-based associations proximal to HMGA1 containing variants associated with a 5cm taller height and of highly-conserved variants in MIR497HG on chromosome 17. We have developed a novel approach for identifying non-coding rare variants in regulatory regions with large effects from whole-genome sequencing data associated with complex traits.

genetics↗

bioRxiv2023

Accurate RNA velocity estimation based on multibatch network reveals complex lineage in batch scRNA-seq data

RNA Velocity, as an extension of trajectory inference, is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. Nevertheless, existing RNA velocity methods are limited by the batch effect because they cannot directly correct for batch effects in the input data, which comprises spliced and unspliced matrices in a proportional relationship. This limitation can lead to incorrect velocity graphs. This paper introduces VeloVGI, which addresses this issue innovatively in two key ways. Firstly, it employs an optimal transport (OT) and mutual nearest neighbor (MNN) approach to construct neighbors in batch data. This strategy overcomes the limitations of existing methods that are affected by the batch effect. Secondly, VeloVGI improves upon VeloVIs velocity estimation by incorporating the graph structure into the encoder for more effective feature extraction. The effectiveness of VeloVGI was demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb, as well as on several public datasets. The results showed that VeloVGI outperformed other methods in terms of metric performance. Significance StatementRNA Velocity is an effective method for understanding cell development using single-cell RNA sequencing (scRNA-seq) experiments. This paper introduces VeloVGI, which addresses this batch effect issue for existing RNA velocity methods. The effectiveness of VeloVGI was demonstrated in various scenarios, including the mouse spinal cord and olfactory bulb, as well as on several public datasets. The results showed that VeloVGI outperformed other methods in terms of metric performance.

bioinformatics↗

bioRxiv2023

coRIC map: a framework for the exploration of multifaceted subcellular RNA-binding proteins

The ability of RNA-binding proteins (RBPs) to form complexes with other biomolecules underpins a broad range of functions and remarkable structural properties. Understanding the precise spatiotemporal dynamics of RBPs and their interacting partners in the steady state and upon perturbation is key to deciphering these aspects. Here, we present the coRIC (compartmentalized RNA Interactome Capture) map, an experimental resource and analytical pipeline to study the subcellular dynamics of RBPs through multimodal dataset integration and machine learning. Using this approach, we have generated an atlas comprising 1,768 RBPs distributed in a broad panel of subcellular compartments and delineated their intermolecular and intercompartmental relationships. We have also defined the hierarchy of RBP-containing complexes at multiple scales across the cell, uncovering previously unknown functions of multiple RBPs. Furthermore, we have investigated the changes in RBP complex composition and subcellular distribution in response to C9ORF72 amyotrophic lateral sclerosis/frontotemporal dementia dipeptide repeats and DNA damage stress. The coRIC map provides a valuable new approach for defining the roles of RBPs in homeostasis and disease.

cell biology↗

bioRxiv2023

Dynamic Regulation of Innate Lymphoid Cell Development During Ontogeny

Innate lymphoid cells (ILCs) are crucial for maintaining tissue homeostasis. The dynamic composition of ILC subsets during ontogeny has been observed for over a decade, yet the underlying mechanisms remain incompletely understood. Here, we combined differentiation assay and scRNA-seq analysis to compare the fetal and adult ILC development, and assessed their contribution to the dynamic change of ILC subsets. We revealed the preference for LTi cell differentiation in fetal hematopoietic progenitors, contrasted with a non-LTi differentiation bias in adult stages. Our analyses elucidated that the two stages shared a conserved differentiation trajectory and regulatory programs but used different controlling logic. Through computational prediction and dose-response experiments, we proposed a model where a transition from fetal ROR{gamma}t-dominant states to adult Notch-GATA3-dominant states orchestrates these changes. This study suggests that ILC development can be modulated to accommodate the varying demands for specific ILC subsets within the body at different developmental stages. HighlightO_LIThe ratio of LTi cells to non-LTi ILCs decreases from fetal to adult stage C_LIO_LIModified fate determination of ILC progenitors contributes to this decrease of LTi cell ratio during ontogeny C_LIO_LIA conserved trajectory exists from early LPs to Innate Lymphoid Cell Precursors (ILCPs) during both fetal and adult ILC development C_LIO_LIEnhanced activity of Notch-GATA3 signaling in ILC precursors accounts for the transition of their differentiation from LTi cells in the fetal to non-LTi ILCs in adults. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/565141v2_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@11a031eorg.highwire.dtl.DTLVardef@c2d652org.highwire.dtl.DTLVardef@184cdfeorg.highwire.dtl.DTLVardef@1efe7ae_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

MetalPrognosis: a Biological Language Model-based Approach for Disease-Associated Mutations in Metal-Binding Site prediction

Protein-metal ion interactions play a central role in the onset of numerous diseases. When amino acid changes lead to missense mutations in metal-binding sites, the disrupted interaction with metal ions can compromise protein function, potentially causing severe human ailments. Identifying these disease-associated mutation sites within metal-binding regions is paramount for understanding protein function and fostering innovative drug development. While some computational methods aim to tackle this challenge, they often fall short in accuracy, commonly due to manual feature extraction and the absence of structural data. We introduce MetalPrognosis, an innovative, alignment-free solution that predicts disease-associated mutations within metal-binding sites of metalloproteins with heightened precision. Rather than relying on manual feature extraction, MetalPrognosis employs sliding window sequences as input, extracting deep semantic insights from pre-trained protein language models. These insights are then incorporated into a convolutional neural network, facilitating the derivation of intricate features. Comparative evaluations show MetalPrognosis outperforms leading methodologies like MCCNN and PolyPhen-2 across various metalloprotein test sets. Furthermore, an ablation study reiterates the effectiveness of our model architecture. To facilitate public use, we have made the datasets, source codes, and trained models for MetalPrognosis online available at http://metalprognosis.unimelb-biotools.cloud.edu.au/.

bioinformatics↗

bioRxiv2023

Lac-Phe mediates the anti-obesity effect of metformin

Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. The mechanisms that mediate metformins effects on energy balance remain incompletely defined. Here we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite Lac-Phe in mice as well as in two independent human cohorts. In cell culture, metformin drives Lac-Phe biosynthesis via inhibition of complex I, increased glycolytic flux, and intracellular lactate mass action. Other biguanides and structurally distinct inhibitors of oxidative phosphorylation also increase Lac-Phe levels in vitro. Genetic ablation of CNDP2, the principal biosynthetic enzyme for Lac-Phe, in mice renders animals resistant to metformins anorexigenic and anti-obesity effects. Mediation analyses also support a role for Lac-Phe in metformins effect on body mass index in humans. These data establish the CNDP2/Lac-Phe pathway as a critical mediator of the effects of metformin on energy balance.

physiology↗

bioRxiv2023

Co-existence of blaKPC-2 and blaVIM-2 in highly carbapenem-resistant Pseudomonas aeruginosa isolated in the ICU of a public hospital

In this study, highly carbapenem-resistant Pseudomonas aeruginosa (h-CRPA) 18102011 [the minimum inhibitory concentration (MIC) value of carbapenem antimicrobial imipenem (IP) for h-CRPA is 4,096 g/mL] was isolated from the bile of an intensive care unit (ICU) burn patient in China, and genomic sequencing revealed a complete genome. The genomes molecular characteristics were analyzed to assess the genetic environment of blaKPC-2 and blaVIM-2. Average nucleotide identity (ANI) comparisons were used for precise species-level identification, while serotyping, multi-locus sequence typing, and the identification of acquired resistance genes, and virulence genes were also carried out. The h-CRPA 18102011 strain carrying blaKPC-2 and blaVIM-2 was identified as strain ST2374 and the O4 serotype. Virulence genes (plcH, exoST) and resistance genes (aph(3)-IIb, aac(6)-Ib-cr, ant(2)-Ia, blaOXA-396, blaPAO, blaKPC-2, blaVIM-2, blaPER-1, sul1, catB7, qnrVC6, fosA) were both identified in the genome. In addition, the IncpRBL16 type mega-plasmid pP2011-1 carrying blaVIM-2 and the IncP6 type plasmid pP2011-2 carrying blaKPC-2 were identified in the strain. The genetic environment of blaVIM-2 and blaKPC-2 was specifically evaluated to assess their origins. blaVIM-2 was located in the region of In2075 (a novel type 1 integron) that was inserted into plasmid pP2011-1, this plasmid contained 3 novel recombination sites, as well as the typical recombination site 2 (umuC) observed for IncpRBL16 type plasmids. However, the core module Tn3-ISKpn27-blaKPC-{Delta}ISKpn6 was identified as the blaKPC-2 platform in plasmid pP2011-2. Conjugation experiments revealed that the plasmids pP2011-1 and pP2011-2 of the h-CRPA 18102011 strain could be transferred into Escherichia coli with a conjugation transfer efficiency of 10-6. The E. coli transconjugant carried blaKPC-2 and blaVIM-2 from the donor and the MIC value of IP to the E. coli transconjugant was 4,096 g/mL, which was the same as observed for the donor. Overall, this study revealed the molecular characteristics of a VIM-2 and KPC-2-co-producing strain that was typed as O4 and ST2374. The continuous monitoring of bacteria, such as the strain investigated here, that co-harbor different types of carbapenemase genes is critical for preventing the spread of these genes.

genomics↗