The impact of horizontal gene transfer on targeting the internal transcribed spacer region (ITS) to identify <i>Acinetobacter junii</i>
 strains

Maslunka, Christopher; Gürtler, Volker; Seviour, Robert J.

doi:10.1111/jam.12800

Cited by 5 publications

(3 citation statements)

References 17 publications

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“…For example, two typical strains PAO1 and PAO7 of P. aeruginosa (NCBI representative genome database) demonstrate less than 94% nucleotide identity, while E. coli and Shigella sonnei both belong to Enterobateriaceae and their representative genomes share more than 98% nucleotide identity. Therefore, the widely used method to identify bacteria with conserved genes may not be a good choice ( Maslunka et al, 2015 ; Liu et al, 2021 ). We developed an innovative algorithm and designed a workflow to figure out the best DNA tag for each species for diagnostic application based on 1791 microbe genomes from 232 species ( Figure 2A ).…”

Section: Resultsmentioning

confidence: 99%

Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial

Wang

Liang

Jiang

et al. 2022

eLife

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Background:Severe pneumonia is one of the common acute diseases caused by pathogenic bacteria infection, especially by pathogenic bacteria, leading to sepsis with a high morbidity and mortality rate. However, the existing bacteria cultivation method cannot satisfy current clinical needs requiring rapid identification of bacteria strain for antibiotic selection. Therefore, developing a sensitive liquid biopsy system demonstrates the enormous value of detecting pathogenic bacterium species in pneumonia patients.Methods:In this study, we developed a tool named Species-Specific Bacterial Detector (SSBD, pronounce as "speed") for detecting selected bacterium. Newly designed diagnostic tools combining specific DNA-tag screened by our algorithm and CRISPR/Cas12a, which were first tested in the lab to confirm the accuracy, followed by validating its specificity and sensitivity via applying on bronchoalveolar lavage fluid (BALF) from pneumonia patients. In the validation I stage, we compared the SSBD results with traditional cultivation results. In the validation II stage, a randomized and controlled clinical trial was completed at the ICU of Nanjing Drum Tower Hospital to evaluate the benefit SSBD brought to the treatment.Results:In the validation stage I, 77 BALF samples were tested, and SSBD could identify designated organisms in 4 hours with almost 100% sensitivity and over 87% specific rate. In validation stage II, the SSBD results were obtained in 4 hours, leading to better APACHE II scores (p=0.0035, ANOVA test). Based on the results acquired by SSBD, cultivation results could deviate from the real pathogenic situation with polymicrobial infections. In addition, nosocomial infections were found widely in ICU, which should deserve more attention.Funding:National Natural Science Foundation of China. The National Key Scientific Instrument and Equipment Development Project. Project number: 81927808.Clinical trial:This study was registered at ClinicalTrilas.gov (NCT04178382).

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Section: Resultsmentioning

confidence: 99%

Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial

Wang

Liang

Jiang

et al. 2022

eLife

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“…Unlike viruses or animals, bacteria were quite similar between close-related species but sometimes quite different among different strains of one species due to fast evolution and horizontal gene transfer [13][14][15]. Therefore, the widely-used method to identify bacteria with conserved genes may not be a good choice [16,17]. We developed an innovative algorithm and designed a workflow to figure out the best DNA tag for each species for diagnostic application based on 1791 microbe genomes from 232 species (Fig 2A).…”

Section: The Identification Of Species-specific Dna Fragmentsmentioning

confidence: 99%

Species-specific bacterial detector for fast pathogen diagnosis of severe pneumonia patients in the intensive care unit

Wang

Liang

Jiang

et al. 2022

Preprint

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Rapid diagnosis of pathogens is the cornerstone of appropriate therapy and is also a great challenge to be overcome. Although NGS and some other PCR-based pathogen detection methods were applied to improve the speed and accuracy of clinical diagnosis, it was still a long way from the clinical needs of rapid and accurate diagnostic therapy in the intensive care unit (ICU). In this study, we aimed at developing a new rapid diagnostic tool, Species-Specific Bacterial Detector (SSBD), to evaluate the existence and quantification of 10 most usual pathogenic bacteria in ICU in 4 hours. Briefly, the species-specific genome fragments of each bacterium were identified by our algorithm using 1791 microbe genomes from 232 species and then used to combine with CRISPR/Cas12 to establish diagnosis tools. Based on the tests of 77 samples, SSBD demonstrated 100% sensitivity and 87% specificity compared with conventional culture test (CCT). Later on, an interventional random-grouped study was applied to evaluate the clinical benefits of SSBD. Briefly, SSBD demonstrated more accurate and faster diagnosis results and led to earlier antibiotics adjustment than CCT. Based on the results acquired by SSBD, cultivation results could deviate from the real pathogenic situation with polymicrobial infections. In addition, nosocomial infections were found widely in ICU, which should deserve more attention.

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“…Acinetobacter sp. is a group of bacteria that are naturally widely distributed [ 15 ], and they can be isolated from surface water [ 16 ], sewage pipes [ 17 ], soil, plants and animals [ 18 ]. With the advent of sequencing technology, a large number of members of Acinetobacter have been identified, and their systematic taxonomic status has been gradually developed [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Biodegradation of Oil by a Newly Isolated Strain Acinetobacter junii WCO-9 and Its Comparative Pan-Genome Analysis

et al. 2023

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Waste oil pollution and the treatment of oily waste present a challenge, and the exploitation of microbial resources is a safe and efficient method to resolve these problems. Lipase-producing microorganisms can directly degrade waste oil and promote the degradation of oily waste and, therefore, have very significant research and application value. The isolation of efficient oil-degrading strains is of great practical significance in research into microbial remediation in oil-contaminated environments and for the enrichment of the microbial lipase resource library. In this study, Acinetobacter junii WCO-9, an efficient oil-degrading bacterium, was isolated from an oil-contaminated soil using olive oil as the sole carbon source, and its enzyme activity of ρ-nitrophenyl decanoate (ρ-NPD) decomposition was 3000 U/L. The WCO-9 strain could degrade a variety of edible oils, and its degradation capability was significantly better than that of the control strain, A junii ATCC 17908. Comparative pan-genome and lipid degradation pathway analyses indicated that A. junii isolated from the same environment shared a similar set of core genes and that the species accumulated more specific genes that facilitated resistance to environmental stresses under different environmental conditions. WCO-9 has accumulated a complete set of oil metabolism genes under a long-term oil-contamination environment, and the compact arrangement of abundant lipase and lipase chaperones has further strengthened the ability of the strain to survive in such environments. This is the main reason why WCO-9 is able to degrade oil significantly more effectively than ATCC 17908. In addition, WCO-9 possesses a specific lipase that is not found in homologous strains. In summary, A. junii WCO-9, with a complete triglyceride degradation pathway and the specific lipase gene, has great potential in environmental remediation and lipase for industry.

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The impact of horizontal gene transfer on targeting the internal transcribed spacer region (ITS) to identify Acinetobacter junii strains

Cited by 5 publications

References 17 publications

Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial

Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial

Species-specific bacterial detector for fast pathogen diagnosis of severe pneumonia patients in the intensive care unit

Biodegradation of Oil by a Newly Isolated Strain Acinetobacter junii WCO-9 and Its Comparative Pan-Genome Analysis

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