Whole-Genome Analysis of KPC-Producing Klebsiella Pneumoniae Isolates From Hospital Acquired Post-Neurosurgical Meningitis

2021 ◽  
Author(s):  
Mingyue Sun ◽  
Weiqiang Xiao ◽  
Qingxia Xu
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bacterial Infections ◽  
Antimicrobial Agents ◽  
16S Rrna Gene Sequencing ◽  
Molecular Characteristics ◽  
Rrna Gene ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genomic Study ◽  
Neurosurgical Patients

Abstract Background: Nosocomial bacterial infections from carbapenem-resistant Klebsiella pneumoniae (CRKP) are associated with high mortality in neurosurgical patients. This study examined the post-neurosurgical meningitis outbreak caused by CRKP of patients with nervous system tumours，and analysed the molecular characteristics of the causative strain.Methods: Neurosurgical cancer patients with meningitis caused by CRKP between 2017–2019 were retrospectively analysed. Identification of strains and antimicrobial susceptibilities was conducted using BD Phoenix-100, 16S rRNA gene sequencing and broth microdilution. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to identify the subtypes of K. pneumoniae. The genotype correlation, resistance genes and plasmid of isolates were assessed by whole-genome sequencing (WGS).Results: Isolates were resistant to almost all of the tested antimicrobial agents except polymyxin and tigecycline. The PFGE and MLST revealed all isolates were the same strain - ST11–while WGS phylogenetic analysis indicated they were closely related. The isolates harboured blaKPC-2 and an IncFII-type plasmid; the blaKPC-2 gene had a similar genetic environment across isolates.Conclusions: The results of molecular analysis showed that ST11 and IncFII-type plasmid in CRKP have close correlations and indicate a long-term retrospective genomic study throughout the hospital for KPC-producing K. pneumoniae is necessary.

scholarly journals Efficacious antibacterial potency of novel bacteriophages against ESBL-producing Klebsiella pneumoniae isolated from burn wound infections

2021 ◽  
Author(s):  
Ladan Rahimzadeh Torabi ◽  
Nafiseh Sadat Naghavi ◽  
Monir Doudi ◽  
Ramesh Monajemi
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bacterial Infections ◽  
Burst Size ◽  
16S Rrna Gene Sequencing ◽  
Morphological Characterization ◽  
Host Cells ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Bacteriophage Therapy ◽  
Burn Wound

Background and Objectives: Prevalence of extended spectrum β-lactamase (ESBL) leads to the development of antibi- otic resistance and mortality in burn patients. One of the alternative strategies for controlling ESBL bacterial infections is clinical trials of bacteriophage therapy. The aim of this study was to isolate and characterize specific bacteriophages against ESBL-producing Klebsiella pneumoniae in patients with burn ulcers. Materials and Methods: Clinical samples were isolated from the hospitalized patient in burn medical centers, Iran. Bio- chemical screenings and 16S rRNA gene sequencing were determined. The phages were isolated from municipal sewerage treatment plants, Isfahan, Iran. TEM and FESEM, adsorption velocity, growth curve, host range, and the viability of the phage particles as well as proteomics and enzyme digestion patterns were examined. Results: The results showed that Klebsiella pneumoniae Iaufa_lad2 (GenBank accession number: MW836954) was con- firmed as an ESBL-producing strain using combined disk method. This bacterium showed significant sensitivity to three phages including PɸBw-Kp1, PɸBw-Kp2, and PɸBw-Kp3. Morphological characterization demonstrated that the phage PɸBw-Kp3 to the Siphoviridae family (lambda-like phages) and both phages PɸBw-Kp1 and ɸBw-Kp2 to the Podoviridae family (T1-like phages). The isolated bacteriophages had a large burst size, thermal and pH viability and efficient adsorption rate to the host cells. Conclusion: In present study, the efficacy of bacteriophages against ESBL pathogenic bacterium promises a remarkable achievement for phage therapy. It seems that, these isolated bacteriophages, in the form of phage cocktails, had a strong an- tibacterial impacts and a broad-spectrum strategy against ESBL-producing Klebsiella pneumoniae isolated from burn ulcers.

scholarly journals Isolation and Characterization of Novel Phages Targeting Pathogenic Klebsiella pneumoniae

2021 ◽  
Vol 11 ◽  
Author(s):  
Na Li ◽  
Yigang Zeng ◽  
Rong Bao ◽  
Tongyu Zhu ◽  
Demeng Tan ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Bacterial Infections ◽  
Antimicrobial Agents ◽  
Multidrug Resistant ◽  
S1 Nuclease ◽  
Isolation And Characterization ◽  
Comprehensive Knowledge ◽  
Future Challenges ◽  
Lactamase Gene

Klebsiella pneumoniae is a dominant cause of community-acquired and nosocomial infections, specifically among immunocompromised individuals. The increasing occurrence of multidrug-resistant (MDR) isolates has significantly impacted the effectiveness of antimicrobial agents. As antibiotic resistance is becoming increasingly prevalent worldwide, the use of bacteriophages to treat pathogenic bacterial infections has recently gained attention. Elucidating the details of phage-bacteria interactions will provide insights into phage biology and the better development of phage therapy. In this study, a total of 22 K. pneumoniae isolates were assessed for their genetic and phenotypic relatedness by multi-locus sequence typing (MLST), endonuclease S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and in vitro antibiotic susceptibility testing. In addition, the beta-lactamase gene (blaKPC) was characterized to determine the spread and outbreak of K. pneumoniae carbapenemase (KPC)-producing enterobacterial pathogens. Using these ST11 carbapenem-resistant K. pneumoniae isolates, three phages (NL_ZS_1, NL_ZS_2, and NL_ZS_3) from the family of Podoviridae were isolated and characterized to evaluate the application of lytic phages against the MDR K. pneumoniae isolates. In vitro inhibition assays with three phages and K. pneumoniae strain ZS15 demonstrated the strong lytic potential of the phages, however, followed by the rapid growth of phage-resistant and phage-sensitive mutants, suggesting several anti-phage mechanisms had developed in the host populations. Together, this data adds more comprehensive knowledge to known phage biology and further emphasizes their complexity and future challenges to overcome prior to using phages for controlling this important MDR bacterium.

scholarly journals Whole-Genome Sequencing ofAggregatibacterSpecies Isolated from Human Clinical Specimens and Description ofAggregatibacter kilianiisp. nov.

2018 ◽  
Vol 56 (7) ◽  
Author(s):  
May Murra ◽  
Lisbeth Lützen ◽  
Aynur Barut ◽  
Reinhard Zbinden ◽  
Marianne Lund ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Clinical Specimens ◽  
Phylogenetic Cluster ◽  
Invasive Infections ◽  
Rrna Gene Sequencing

ABSTRACTAggregatibacterspecies are commensal bacteria of human mucosal surfaces that are sometimes involved in serious invasive infections. During the investigation of strains cultured from various clinical specimens, we encountered a coherent group of 10 isolates that could not be allocated to any validly named species by phenotype, mass spectrometry, or partial 16S rRNA gene sequencing. Whole-genome sequencing revealed a phylogenetic cluster related to but separate fromAggregatibacter aphrophilus. The meanin silicoDNA hybridization value for strains of the new cluster versusA. aphrophiluswas 56% (range, 53.7 to 58.0%), whereas the average nucleotide identity was 94.4% (range, 93.9 to 94.8%). The new cluster exhibited aggregative properties typical of the genusAggregatibacter. Key phenotypic tests for discrimination of the new cluster from validly namedAggregatibacterspecies are alanine-phenylalanine-proline arylamidase,N-acetylglucosamine, and β-galactosidase. The nameAggregatibacter kilianiiis proposed, with PN_528 (CCUG 70536Tor DSM 105094T) as the type strain.

Comparison of VITEK 2, MALDI-TOF MS, 16S rRNA gene sequencing, and whole-genome sequencing for identification of Roseomonas mucosa

2019 ◽  
Vol 134 ◽  
pp. 103576 ◽  
Author(s):  
Wolfram W. Rudolph ◽  
Florian Gunzer ◽  
Melanie Trauth ◽  
Boyke Bunk ◽  
Richard Bigge ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Whole Genome ◽  
Vitek 2 ◽  
Rrna Gene Sequencing ◽  
Roseomonas Mucosa ◽  
Tof Ms

scholarly journals Aeromonas veronii and Plesiomonas shigelloides (Gammaproteobacteria) isolated from Glossogobius aureus (Gobiidae) in Lake Sampaloc, Laguna, Philippines

2020 ◽  
Vol 14 (1) ◽  
Keyword(s):  
Bacterial Infections ◽  
Management Practices ◽  
16S Rrna Gene Sequencing ◽  
Gut Bacteria ◽  
Inland Waters ◽  
Rrna Gene ◽  
Farmed Fish ◽  
Biochemical Tests ◽  
Plesiomonas Shigelloides ◽  
Aeromonas Veronii

Bacterial infections are high-risk factors in fisheries, with reports of high mortality among diseased fish stocks posing a threat to both capture and aquaculture fisheries in inland waters. Diseases-causing bacteria in fishes may lead to decreased yield and economic loss to fishers, whose livelihood primarily depends on landed catch. Lake fisheries are most affected by such disruptive changes because of limitations in water turnover aggravated by wastewater inputs. In this study, we isolated and characterized gut bacteria from landed catch of the gobiid Glossogobius aureus from Lake Sampaloc, a small but commercially important aquaculture area in Luzon. Isolated axenic gut bacteria were identified through Gram stain reaction, microscopy, API biochemical tests, and 16s rRNA gene sequencing. From these, we identified two species with known fish pathogenicity, namely Aeromonas veronii and Plesiomonas shigelloides which are known to thrive in disrupted and nutrient-rich habitats and cause visible damage to fish health. Interestingly, our samples have shown no such visible signs of the disease. It is therefore important for future researches to determine what conservation and management practices in small inland waters like lakes will limit potential environmental stressors that may trigger susceptibility of both capture and farmed fish species to infection. Ultimately, rehabilitation of inland water aquaculture areas such as Lake Sampaloc is essential not only to fish conservation but also to public health and local food security.

scholarly journals Phenotypic, Genotypic, and Antimicrobial Characteristics of Streptococcus halichoeri Isolates from Humans, Proposal To Rename Streptococcus halichoeri as Streptococcus halichoeri subsp. halichoeri, and Description of Streptococcus halichoeri subsp. hominis subsp. nov., a Bacterium Associated with Human Clinical Infections

2016 ◽  
Vol 54 (3) ◽  
pp. 739-744 ◽  
Author(s):  
P. L. Shewmaker ◽  
A. M. Whitney ◽  
B. W. Humrighouse
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Whole Genome Analysis ◽  
Content Type

Phenotypic, genotypic, and antimicrobial characteristics of six phenotypically distinct human clinical isolates that most closely resembled the type strain ofStreptococcus halichoeriisolated from a seal are presented. Sequencing of the 16S rRNA,rpoB,sodA, andrecNgenes; comparative whole-genome analysis; conventional biochemical and Rapid ID 32 Strep identification methods; and antimicrobial susceptibility testing were performed on the human isolates, the type strain ofS.halichoeri, and type strains of closely related species. The six human clinical isolates were biochemically indistinguishable from each other and showed 100% 16S rRNA,rpoB,sodA, andrecNgene sequence similarity. Comparative 16S rRNA gene sequencing analysis revealed 98.6% similarity toS. halichoeriCCUG 48324T, 97.9% similarity toS. canisATCC 43496T, and 97.8% similarity toS. ictaluriATCC BAA-1300T. A 3,530-bp fragment of therpoBgene was 98.8% similar to theS. halichoeritype strain, 84.6% to theS. canistype strain, and 83.8% to theS.ictaluritype strain. TheS. halichoeritype strain and the human clinical isolates were susceptible to the antimicrobials tested based on CLSI guidelines forStreptococcusspecies viridans group with the exception of tetracycline and erythromycin. The human isolates were phenotypically distinct from the type strain isolated from a seal; comparative whole-genome sequence analysis confirmed that the human isolates wereS. halichoeri. On the basis of these results, a novel subspecies,Streptococcushalichoerisubsp.hominis, is proposed for the human isolates andStreptococcus halichoerisubsp.halichoeriis proposed for the gray seal isolates. The type strain of the novel subspecies is SS1844T= CCUG 67100T= LMG 28801T.

Detection and Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST340/CG258 Producing CTX-M-15 in a Companion Animal

2020 ◽  
Vol 26 (6) ◽  
pp. 611-615
Author(s):  
Juan Valencia-Bacca ◽  
Meire M. Silva ◽  
Louise Cerdeira ◽  
Fernanda Esposito ◽  
Brenda Cardoso ◽  
...  
Keyword(s):  
High Risk ◽  
Klebsiella Pneumoniae ◽  
Genome Analysis ◽  
Companion Animal ◽  
Whole Genome ◽  
Whole Genome Analysis

scholarly journals Massilia Cellulosiltytica Sp. Nov., A Novel Cellulose-degrading Bacterium Isolated from Rhizosphere Soil of Rice (Oryza Sativa L.) and whole Genome Analysis

2021 ◽  
Author(s):  
Chuanjiao Du ◽  
Chenxu Li ◽  
Peng Cao ◽  
Tingting Li ◽  
Dandan Du ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Analysis ◽  
Rhizosphere Soil ◽  
Oryza Sativa L ◽  
Rrna Gene ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
North East ◽  
Degrading Bacterium

Abstract A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1T (98.46 %) and Massilia putida 6NM-7T (98.41 %). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11T formed a stable cluster with M. phosphatilytica 12-OD1T and M. putida 6NM-7T. The major fatty acids of the strain were C16:0, C17:0-cyclo and C16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11T and M. phosphatilytica 12-OD1T and M. putida 6NM-7T were 45.4% and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11T was 66.2 %. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to had the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain NEAU-DD11T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11T (= CCTCC AB 2019141T = DSM 109721T).

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