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

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.

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

10.21203/rs.3.rs-993958/v1 ◽

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.

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Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection

Biomedicines ◽

10.3390/biomedicines9040342 ◽

2021 ◽

Vol 9 (4) ◽

pp. 342

Author(s):

Ahmed R. Sofy ◽

Noha K. El-Dougdoug ◽

Ehab E. Refaey ◽

Rehab A. Dawoud ◽

Ahmed A. Hmed

Keyword(s):

Klebsiella Pneumoniae ◽

Burst Size ◽

Phylogenetic Analyses ◽

Foodborne Pathogen ◽

Gc Content ◽

Full Genome Sequence ◽

Multiple Drug ◽

Lytic Phage ◽

Trna Genes ◽

Bacteriophage Therapy

Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.

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Phylogenetic tree analysis based on the 16S sequence alignment for Klebsiella spp. isolated from different sources

Iraqi Journal of Science ◽

10.24996/ijs.2019.60.9.8 ◽

2019 ◽

pp. 1957-1966

Author(s):

Mustafa Basil Abdul Qader ◽

Marwa Hameed AlKhafaji

Keyword(s):

16S Rrna ◽

Klebsiella Pneumoniae ◽

16S Rrna Gene ◽

Enteric Bacteria ◽

Apium Graveolens ◽

Clinical Samples ◽

Identification System ◽

Rrna Gene ◽

Vitek 2 ◽

Klebsiella Spp

16S ribosomal RNA (16S rRNA) gene sequences used to study bacterial phylogeny and taxonomy have been by far the most common housekeeping genetic marker utilized for identification and ancestor determination. This study aimed to investigate, for the first time, the relationship between Klebsiella spp. isolated from clinical and environmental samples in Iraq. Fifty Klebsiella spp. isolates were isolated from clinical and environmental sources. Twenty-five isolates were collected from a fresh vegetable (Apium graveolens) and 25 from clinical samples (sputum, wound swab, urine). Enteric bacteria were isolated on selective and differential media and identified by an automatic identification system, vitek-2. The total DNA was extracted and PCR amplified for selected isolates. The 16S rRNA gene was amplified by using the universal primer 27F (5'- AGAGTTTGATCCTGGCTCAG- 3') and 1492R (5'- GGTTACCTTGTTACGACTT- 3â€™). The 16SrRNA gene sequence was analysed among some local isolates, and the results were compared with the standard data of similar registered strains in NCBI. The most common species of Klebsiella was Klebsiella pneumoniae pneumoniae (Kpp), followed by Klebsiella pneumoniae ozaenae (Kpo) and Klebsiella oxytoca (Ko). The results of the identification of species and sub species by using the biochemical test (vitek-2) were more precise than those obtained by the use of the universal primer.Phylogenetic tree strategies have clearly indicated a relatively close similarity amongst all analysed Klebsiella isolates and revealed the intra-species genetic distance between the individual isolates of the Klebsiella spp. In conclusion, our results revealed the main advantage of using universal primers for the identification of Klebsiella spp. and their root from nature.

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

10.26757/pjsb2020a14009 ◽

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.

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Identification of a Novel Brevibacillus laterosporus Strain With Insecticidal Activity Against Aedes albopictus Larvae

Frontiers in Microbiology ◽

10.3389/fmicb.2021.624014 ◽

2021 ◽

Vol 12 ◽

Author(s):

Giulia Barbieri ◽

Carolina Ferrari ◽

Stefania Mamberti ◽

Paolo Gabrieli ◽

Michele Castelli ◽

...

Keyword(s):

Aedes Albopictus ◽

Mosquito Control ◽

Control Strategies ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Morphological Characterization ◽

Soil Samples ◽

Rrna Gene ◽

Breeding Sites ◽

Brevibacillus Laterosporus

Bacterial species able to produce proteins that are toxic against insects have been discovered at the beginning of the last century. However, up to date only two of them have been used as pesticides in mosquito control strategies targeting larval breeding sites: Bacillus thuringensis var. israelensis and Lysinibacillus sphaericus. Aiming to expand the arsenal of biopesticides, bacterial cultures from 44 soil samples were assayed for their ability to kill larvae of Aedes albopictus. A method to select, grow and test the larvicidal capability of spore-forming bacteria from each soil sample was developed. This allowed identifying 13 soil samples containing strains capable of killing Ae. albopictus larvae. Among the active isolates, one strain with high toxicity was identified as Brevibacillus laterosporus by 16S rRNA gene sequencing and by morphological characterization using transmission electron microscopy. The new isolate showed a larvicidal activity significantly higher than the B. laterosporus LMG 15441 reference strain. Its genome was phylogenomically characterized and compared to the available Brevibacillus genomes. Thus, the new isolate can be considered as a candidate adjuvant to biopesticides formulations that would help preventing the insurgence of resistance.

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SPDB: a specialized database and web-based analysis platform for swine pathogens

Database ◽

10.1093/database/baaa063 ◽

2020 ◽

Vol 2020 ◽

Author(s):

Xiaoru Wang ◽

Zongbao Liu ◽

Xiaoying Li ◽

Danwei Li ◽

Jiayu Cai ◽

...

Keyword(s):

Related Species ◽

16S Rrna Gene Sequencing ◽

Clinical Samples ◽

Rrna Gene ◽

Swine Pathogen ◽

Negative Impacts ◽

Rrna Gene Sequencing ◽

Swine Disease ◽

Swine Diseases ◽

Analysis Platform

Abstract The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/

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Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63189-0 ◽

2005 ◽

Vol 55 (1) ◽

pp. 433-436 ◽

Cited By ~ 25

Author(s):

Hideki Yamamura ◽

Masayuki Hayakawa ◽

Youji Nakagawa ◽

Tomohiko Tamura ◽

Tetsuro Kohno ◽

...

Keyword(s):

Activated Sludge ◽

Reference Strain ◽

16S Rrna Gene Sequencing ◽

Morphological Characterization ◽

Rrna Gene ◽

Biochemical Tests ◽

Sequencing Studies ◽

Rrna Gene Sequencing ◽

Physiological And Biochemical

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98·1–98·3 % similarity), Nocardia brasiliensis (97·9–98·0 %) and Nocardia tenerifensis (97·8–97·9 %). However, the results of DNA–DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

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Azospirillum melinis sp. nov., a group of diazotrophs isolated from tropical molasses grass

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64025-0 ◽

2006 ◽

Vol 56 (6) ◽

pp. 1263-1271 ◽

Cited By ~ 63

Author(s):

Guixiang Peng ◽

Huarong Wang ◽

Guoxia Zhang ◽

Wei Hou ◽

Yang Liu ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Pcr Amplification ◽

16S Rrna Gene Sequencing ◽

Morphological Characterization ◽

Phenotypic Characterization ◽

Rrna Gene ◽

Bacterial Strains ◽

Azospirillum Lipoferum ◽

Protein Patterns

Fifteen bacterial strains isolated from molasses grass (Melinis minutiflora Beauv.) were identified as nitrogen-fixers by using the acetylene-reduction assay and PCR amplification of nifH gene fragments. These strains were classified as a unique group by insertion sequence-PCR fingerprinting, SDS-PAGE protein patterns, DNA–DNA hybridization, 16S rRNA gene sequencing and morphological characterization. Phylogenetic analysis of the 16S rRNA gene indicated that these diazotrophic strains belonged to the genus Azospirillum and were closely related to Azospirillum lipoferum (with 97.5 % similarity). In all the analyses, including in addition phenotypic characterization using Biolog MicroPlates and comparison of cellular fatty acids, this novel group was found to be different from the most closely related species, Azospirillum lipoferum. Based on these data, a novel species, Azospirillum melinis sp. nov., is proposed for these endophytic diazotrophs of M. minutiflora, with TMCY 0552T (=CCBAU 5106001T=LMG 23364T=CGMCC 1.5340T) as the type strain.

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Aerococcus suis sp. nov., isolated from clinical specimens from swine

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64537-0 ◽

2007 ◽

Vol 57 (6) ◽

pp. 1291-1294 ◽

Cited By ~ 21

Author(s):

A. I. Vela ◽

N. García ◽

M. V. Latre ◽

A. Casamayor ◽

C. Sánchez-Porro ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Molecular Genetic ◽

16S Rrna Gene Sequencing ◽

Clinical Samples ◽

Rrna Gene ◽

Biochemical Tests ◽

Sequencing Studies ◽

Micro Organisms

Biochemical and molecular genetic studies were performed for five isolates of unknown Gram-positive, catalase-negative, cocci-shaped micro-organisms obtained from clinical samples from pigs. The micro-organisms were tentatively identified as Aerococcus species on the basis of the results from cellular morphological and biochemical tests. 16S rRNA gene sequencing studies confirmed the provisional identification of the isolates as members of the genus Aerococcus, but the micro-organism did not correspond to any recognized species of this genus. The nearest phylogenetic relatives of these unknown cocci isolated from pigs were Aerococcus viridans (95.9 % 16S rRNA gene sequence similarity) and Aerococcus urinaeequi (95.8 %). The unknown bacterium, however, was distinguishable from these two species and from other animal aerococci by using biochemical tests. On the basis of both phenotypic and phylogenetic findings, the isolates represent a novel species of the genus Aerococcus, for which the name Aerococcus suis sp. nov. is proposed. The type strain is 1821/02T (=CECT 7139T=CCUG 52530T).

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Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64378-0 ◽

2006 ◽

Vol 56 (11) ◽

pp. 2671-2676 ◽

Cited By ~ 24

Author(s):

Ana I. Vela ◽

María C. Gutiérrez ◽

Enevold Falsen ◽

Eduardo Rollán ◽

Isabel Simarro ◽

...

Keyword(s):

Sequence Similarity ◽

Molecular Genetic ◽

16S Rrna Gene Sequencing ◽

Clinical Samples ◽

Rrna Gene ◽

The Novel ◽

Biochemical Tests ◽

Sequencing Studies ◽

Rrna Gene Sequencing ◽

Callithrix Geoffroyi

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as a Pseudomonas species on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescens intrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species of Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novel Pseudomonas isolates are classified as Pseudomonas simiae sp. nov. The type strain of P. simiae is OLiT (=CCUG 50988T=CECT 7078T).

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