scholarly journals An unequivocal superbug: PDR Klebsiella pneumoniae with an arsenal of resistance and virulence factor genes

2021 ◽  
Vol 15 (03) ◽  
pp. 404-414
Author(s):  
Ahmad Sleiman ◽  
Bassel Awada ◽  
Michele Mocadie ◽  
Nour Sherri ◽  
Louis-Patrick Haraoui ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Virulence Factor ◽  
Molecular Mechanisms ◽  
Whole Genome Sequence ◽  
Drug Resistant ◽  
Type Iv ◽  
Antimicrobial Resistance Genes ◽  
Life Threatening ◽  
High Level ◽  
Virulence Factor Genes

Introduction: Infections caused by extensively-drug resistant (XDR) and pan-drug resistant (PDR) Klebsiella pneumoniae represent an emerging threat due to the high associated mortality. This study aimed to characterize two carbapenem resistant K. pneumoniae strains from the same patient, the first being PDR (referred to as IMP 1078b) and the second being XDR (referred to IMP 1078s) isolated from the same patient. Methodology: Antimicrobial susceptibility testing was done for the 2 K. pneumoniae isolates, followed by carbapenem/β-lactamase inhibitor combination assay, and fitness cost against cefepime and meropenem. Then, whole-genome sequence analysis was performed to decipher the molecular mechanisms behind the high level of resistance recorded in both isolates. Finally, qRT-PCR was done for β-lactam resistant genes. Results: This is the first report about a K. pneumoniae isolate harboring 47 antimicrobial resistance genes and having type IV pilli (Yersinia) and the fimbrial adherence determinant Stb (Salmonella) as virulence factors. Further analysis on both isolates are discussed within the article. Conclusion: The co-existence of a high number of antimicrobial resistant (AMR) genes and virulence factor genes may lead to a life threatening invasive and untreatable infection.

scholarly journals The Co-occurrence of NDM-5, MCR-1, and FosA3-Encoding Plasmids Contributed to the Generation of Extensively Drug-Resistant Klebsiella pneumoniae

2022 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhou ◽  
Wenxiu Ai ◽  
Yanhua Cao ◽  
Yinjuan Guo ◽  
Xiaocui Wu ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Efflux Pumps ◽  
Drug Resistant ◽  
E Coli ◽  
Extensively Drug Resistant ◽  
Antimicrobial Resistance Genes ◽  
Rnd Efflux Pumps ◽  
Comparative Genetic Analysis ◽  
High Level ◽  
Almost All

The rise and global dissemination of extensively drug-resistant (XDR) bacteria are often related to plasmid-borne mobile antimicrobial resistance genes. Notably, isolates having multiple plasmids are often highly resistant to almost all the antibiotics available. In this study, we characterized an extensively drug-resistant Klebsiella pneumoniae 1678, which exhibited high-level resistance to almost all the available antibiotics. Through whole-genome sequencing (WGS), more than 20 resistant elements and 5 resistant plasmids were observed. Notably, the tigecycline resistance of K. pneumoniae 1678 was not related to the plasmid-borne tetA gene but associated with the overexpression of AcrAB and OqxAB efflux pumps, according to the susceptibility results of tetA-transformant and the related mRNA quantification of RND efflux pumps. Except for tigecycline resistance, three plasmids, mediating resistance to colistin, Fosfomycin, and ceftazidime–avibactam, respectively, were focused. Detailed comparative genetic analysis showed that all these plasmids belonged to dominated epidemic plasmids, and harbored completed conjugation systems. Results of conjugation assay indicated that these three plasmids not only could transfer to E. coli J53 with high conjugation frequencies, respectively, but also could co-transfer to E. coli J53 effectively, which was additionally confirmed by the S1-PFGE plasmids profile. Moreover, multiple insertion sequences (IS) and transposons (Tn) were also found surrounding the vital resistant genes, which may form several novel mechanisms involved in the resistant determinants’ mobilization. Overall, we characterized and reported the uncommon co-existence and co-transferring of FosA3-, NDM-5, and MCR-1-encoding plasmids in a K. pneumoniae isolate, which may increase the risk of spread of these resistant phenotypes and needing great concern.

scholarly journals Review of therapeutic options for infections with carbapenem-resistant Klebsiella pneumoniae

2020 ◽  
Vol 10 (3) ◽  
pp. 115-124
Author(s):  
Rasmus G. Bandick ◽  
Soraya Mousavi ◽  
Stefan Bereswill ◽  
Markus M. Heimesaat
Keyword(s):  
Clinical Trials ◽  
Klebsiella Pneumoniae ◽  
Control Treatment ◽  
Drug Resistant ◽  
Treatment Regimens ◽  
Combined Application ◽  
Carbapenem Resistant ◽  
Antibiotic Compounds ◽  
Life Threatening

AbstractInfections with multi-drug resistant (MDR) bacteria including carbapenem-resistant Klebsiella pneumoniae are emerging worldwide but are difficult to treat with the currently available antibiotic compounds and therefore constitute serious threats to human health. This prompted us to perform a literature survey applying the MEDLINE database and Cochrane Register of Controlled Trials including clinical trials comparing different treatment regimens for infections caused by carbapenem-resistant K. pneumoniae. Our survey revealed that a combined application of antibiotic compounds such as meropenem plus vaborbactam, meropenem plus colistin and carbapenem plus carbapenem, resulted in significantly increased clinical cure and decreased mortality rates as compared to respective control treatment. However, further research on novel antibiotic compounds, but also on antibiotic-independent molecules providing synergistic or at least resistance-modifying properties needs to be undertaken in vitro as well as in large clinical trials to provide future options in the combat of emerging life-threatening infections caused by MDR bacteria.

scholarly journals High-Level Aminoglycoside Resistance in Human Clinical Klebsiella pneumoniae Complex Isolates and Characteristics of armA-Carrying IncHI5 Plasmids

2021 ◽  
Vol 12 ◽  
Author(s):  
Xueya Zhang ◽  
Qiaoling Li ◽  
Hailong Lin ◽  
Wangxiao Zhou ◽  
Changrui Qian ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Conjugative Plasmid ◽  
Comparative Genomic ◽  
Aminoglycoside Resistance ◽  
Life Threatening ◽  
Aminoglycoside Resistance Genes ◽  
High Level

Aminoglycosides are important options for treating life-threatening infections. However, high levels of aminoglycoside resistance (HLAR) among Klebsiella pneumoniae isolates have been observed to be increasing frequently. In this study, a total of 292 isolates of the K. pneumoniae complex from a teaching hospital in China were analyzed. Among these isolates, the percentage of HLAR strains was 13.7% (40/292), and 15 aminoglycoside resistance genes were identified among the HLAR strains, with rmtB being the most dominant resistance gene (70%, 28/40). We also described an armA-carrying Klebsiella variicola strain KP2757 that exhibited a high-level resistance to all aminoglycosides tested. Whole-genome sequencing of KP2757 demonstrated that the strain contained one chromosome and three plasmids, with all the aminoglycoside resistance genes (including two copies of armA and six AME genes) being located on a conjugative plasmid, p2757-346, belonging to type IncHI5. Comparative genomic analysis of eight IncHI5 plasmids showed that six of them carried two copies of the intact armA gene in the complete or truncated Tn1548 transposon. To the best of our knowledge, for the first time, we observed that two copies of armA together with six AME genes coexisted on the same plasmid in a strain of K. variicola with HLAR. Comparative genomic analysis of eight armA-carrying IncHI5 plasmids isolated from humans and sediment was performed, suggesting the potential for dissemination of these plasmids among bacteria from different sources. These results demonstrated the necessity of monitoring the prevalence of IncHI5 plasmids to restrict their worldwide dissemination.

scholarly journals High-Level Carbapenem Resistance among OXA-48-Producing Klebsiella pneumoniae with Functional OmpK36 Alterations: Maintenance of Ceftazidime/Avibactam Susceptibility

Antibiotics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1174
Author(s):  
Pilar Lumbreras-Iglesias ◽  
M. Rosario Rodicio ◽  
Pablo Valledor ◽  
Tomás Suárez-Zarracina ◽  
Javier Fernández
Keyword(s):  
Klebsiella Pneumoniae ◽  
Carbapenem Resistance ◽  
Inhibition Zone ◽  
Operating Characteristics ◽  
Outer Membrane Porin ◽  
Antimicrobial Resistance Genes ◽  
Disk Diffusion Assay ◽  
Performance Ability ◽  
High Level

The aim of this work was to analyze outer membrane porin-encoding genes (ompK35 and ompK36) in a collection of OXA-48 producing Klebsiella pneumoniae, to assess the effect of porin alterations on the susceptibility to ceftazidime/avibactam, and to describe a screening methodology for phenotypic detection of OXA-48-producing K. pneumoniae with disrupted porins. Antimicrobial susceptibility was tested by Microscan and Etest. The genomes of 81 OXA-48-producing K. pneumoniae were sequenced. MLST, detection of antimicrobial resistance genes, and analysis of ompK35 and ompK36 were performed in silico. Tridimensional structures of the OmpK36 variants were assessed. Receiver operating characteristics curves were built to visualize the performance ability of a disk diffusion assay using carbapenems and cefoxitin to detect OmpK36 functional alterations. A wide variety of OmpK36 alterations were detected in 17 OXA-48-producing K. pneumoniae isolates. All displayed a high-level meropenem resistance (MIC ≥ 8 mg/L), and some belonged to high-risk clones, such as ST15 and ST147. Alterations in ompK35 were also observed, but they did not correlate with high-level meropenem resistance. All isolates were susceptible to ceftazidime/avibactam and porin alterations did not affect the MICs of the latter combination. Cefoxitin together with ertapenem/meropenem low inhibition zone diameters (equal or lower than 16 mm) could strongly suggest alterations affecting OmpK36 in OXA-48-producing K. pneumoniae. OXA-48-producing K. pneumoniae with porin disruptions are a cause of concern; ceftazidime/avibactam showed good in vitro activity against them, so this combination could be positioned as the choice therapy to combat the infections caused by this difficult-to-treat isolates.

scholarly journals Comprehensive genomic analysis of Vibrio cholerae from three outbreaks in Uganda, 2014 - 2016

2019 ◽  
Author(s):  
Ivan Sserwadda ◽  
Dickson Aruhomukama ◽  
Gerald Mboowa
Keyword(s):  
Sequence Data ◽  
Response Regulator ◽  
Genomic Analysis ◽  
Enrichment Analysis ◽  
Type Iv Secretion ◽  
Whole Genome Sequence ◽  
Isomerase Activity ◽  
Type Iv ◽  
Antimicrobial Resistance Genes ◽  
Integrative And Conjugative Element

Abstract Objective: This study aimed at providing a comprehensive genomic analysis of whole-genome sequence data obtained from V. cholerae isolates from different outbreaks in Uganda using bioinformatics approaches. Results :The ten sequenced strains of V. cholerae were found to carry virulence-associated genes MakA, ctxA, ctxB, carA, carB, trpB, clpB, ace, toxR, zot, rtxA, ompW, ompR, gmhA, fur, hlyA, rstR, Type IV secretion system genes, T6SS genes vasA-L, vgrG-2, vgrG-3, vipA/mglA, and vipB/mglB; alsD; alsR; the flagella-mediated cytotoxin gene, makA; Type IV pilus genes tcpA-F, tcpH-J, tcpN, tcpP-T, and icmF/vasK; adherence genes acfA-D, IlpA, and quorum sensing system genes luxS and cqsA. Pathogenicity islands identified were VSP-1, VSP-2, VPI-1, and VPI-2. Antimicrobial resistance genes identified in the strains included strA and B, APH(3'')-I, APH(3'')-Ib, APH(6)-Id, APH(6)-Ic, murA, pare, dfrA1, floR, catB, and catB9. The strains also contained genes of the VC1786 integrative and conjugative element. SNP-based phylogenetic analysis revealed 218 shared SNPs in the strains, of these, 98 were missense. Gene enrichment analysis of the 98 SNPs revealed enrichment in genes that mediate transmembrane-signaling activity, peptidyl-prolyl cis-trans isomerase activity, and phosphorelay response regulator activity.

scholarly journals Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces

2017 ◽  
Author(s):  
Andre Mu ◽  
Jason C. Kwong ◽  
Nicole S. Isles ◽  
Anders Gonçalves da Silva ◽  
Mark B. Schultz ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Clinical Sample ◽  
Microbial Pathogens ◽  
Resistant Bacteria ◽  
Metagenomic Sequencing ◽  
Drug Resistant ◽  
Extensively Drug Resistant ◽  
Drug Resistant Bacteria ◽  
Culture Independent ◽  
High Level

AbstractWhole-genome sequencing of microbial pathogens is revolutionising modern approaches to outbreaks of infectious diseases and is reliant upon organism culture. Culture-independent methods have shown promise in identifying pathogens, but high level reconstruction of microbial genomes from microbiologically complex samples for more in-depth analyses remains a challenge. Here, using metagenomic sequencing of a human faecal sample and analysis by tetranucleotide frequency profiling projected onto emergent self-organising maps, we were able to reconstruct the underlying populations of two extensively-drug resistant pathogens, Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae and vancomycin-resistant Enterococcus faecium. From these genomes, we were able to ascertain molecular typing results, such as MLST, and identify highly discriminatory mutations in the metagenome to distinguish closely related strains. These proof-of-principle results demonstrate the utility of clinical sample metagenomics to recover sequences of important drug-resistant bacteria and application of the approach in outbreak investigations, independent of the need to culture the organisms.

scholarly journals Catastrophic Antiphospholipid Syndrome in Obstetric Practice

2012 ◽  
Vol 61 (3) ◽  
pp. 7-21 ◽  
Author(s):  
Alexander D Makatsariya ◽  
Viktoriya O Bitsadze ◽  
Dzhamilya Kh Khizroeva
Keyword(s):  
Antiphospholipid Syndrome ◽  
Molecular Mechanisms ◽  
Multiorgan Failure ◽  
Catastrophic Antiphospholipid Syndrome ◽  
Small Vessels ◽  
First Case ◽  
Threatening Condition ◽  
Life Threatening ◽  
Fatal Form ◽  
High Level

Catastrophic antiphospholipid syndrome (CAPS) is an uncommon, often fatal, form of the antiphospholipid syndrome that results in a widespread coagulopathy and affects predominantly small vessels supplying organs with the development of multiorgan failure against a background of high level of antiphospholipid antibodies. Thrombotic microvasculopathy is the basis of multiorgan failure and clinically manifests with CNS disturbances, adrenal failure, and the development of acute respiratory distress syndrome. CAPS is a life-threatening condition and requires urgent measures. Optimal treatment for CAPS is not developed yet. CAPS present a multidisciplinary problem. Authors demonstrate 17 cases of CAPS in patients which were managed from 2001 to 2012 years. Molecular mechanisms of pathogenesis and different obstetric and non-obstetric manifestations of CAPS are discussed in the article. There is the description of first case of management of pregnancy and labor of patient with CAPS in her history. The methods of CAPS prevention are described

scholarly journals Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11224
Author(s):  
Gopalan Krishnan Sivaraman ◽  
Visnuvinayagam Sivam ◽  
Balasubramanian Ganesh ◽  
Ravikrishnan Elangovan ◽  
Ardhra Vijayan ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Virulence Genes ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Drug Resistant ◽  
Methicillin Resistant ◽  
Antimicrobial Resistance Genes ◽  
Food Fish

Methicillin-resistant staphylococcus aureus (MRSA) sequence type 28 (ST 28) and spa type t021 is a CC30, prototype of ST-30, Community Associated-MRSA (CA-MRSA) (lukS-lukF +). It is a multi-drug resistant strain harbouring staphylococcal endotoxins, haemolysins, ureolysin, serine protease, and antimicrobial resistance genes. In this study, we report the draft genome sequence of this MRSA isolated from the most commonly used food fish, ribbon fish (Trichiurus lepturus). The total number of assembled paired-end high-quality reads was 7,731,542 with a total length of  2.8Mb of 2797 predicted genes. The unique ST28/ t021 CA- MRSA in fish is the first report from India, and in addition to antibiotic resistance is known to co-harbour virulence genes, haemolysins, aureolysins and endotoxins. Comprehensive comparative genomic analysis of CA-MRSA strain7 can help further understand their diversity, genetic structure, diversity and a high degree of virulence to aid in fisheries management.

scholarly journals Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae

2019 ◽  
Author(s):  
Enas Newire ◽  
Alp Aydin ◽  
Samina Juma ◽  
Virve I Enne ◽  
Adam P. Roberts
Keyword(s):  
Sequence Analysis ◽  
Klebsiella Pneumoniae ◽  
Drug Resistant ◽  
Rt Pcr ◽  
Chromosome Type ◽  
Bacterial Host ◽  
Type Iv ◽  
Transfer Genes ◽  
The Uk ◽  
The Relationship

AbstractDuring an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a novel CRISPR-Cas system (which we have designated Type IV-B) was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of other genomes available in GenBank revealed that this novel Type IV-B CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on the chromosome. Type IV-B is found exclusively on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Type IV-B has a single repeat-spacer array (CRISPR1) upstream of the cas loci with some spacers matching regions of conjugal transfer genes of IncFIIK/IncFIB(K) plasmids suggesting a role in plasmid incompatibility. Expression of the cas loci was confirmed in available clinical isolates by RT-PCR; indicating the system is active. To our knowledge, this is the first report describing a new subtype within Type IV CRISPR-Cas systems exclusively associated with IncHI1B/IncFIB plasmids.ImportanceHere, we report the identification of a novel subtype of Type IV CRISPR-Cas that is expressed and exclusively carried by IncHI1B/IncFIB plasmids in Enterobacteriaceae, demonstrating unique evolutionarily juxtaposed connections between CRISPR-Cas and mobile genetic elements (MGEs). Type IV-B encodes a variety of spacers showing homology to DNA from various sources, including plasmid specific spacers and is therefore thought to provide specific immunity against plasmids of other incompatible groups (IncFIIK/IncFIB(K)). The relationship between Type IV-B CRISPR-Cas and MGEs that surround and interrupt the system is likely to promote rearrangement and be responsible for the observed variability of this type. Finally, the Type IV-B CRISPR-Cas is likely to co-operate with other cas loci within the bacterial host genome during spacer acquisition.

scholarly journals Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates

2021 ◽  
Vol 9 (12) ◽  
pp. 2560
Author(s):  
Abdolrahman Khezri ◽  
Ekaterina Avershina ◽  
Rafi Ahmad
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Blood Culture ◽  
Klebsiella Pneumoniae ◽  
Virulence Factors ◽  
Whole Genome Sequence ◽  
Clinical Samples ◽  
Hybrid Assembly ◽  
Antimicrobial Resistance Genes ◽  
Quality Checks

Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.

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