Outer membrane vesicles from X-ray-irradiated Pseudomonas aeruginosa alleviate lung injury caused by P. aeruginosa infection-mediated sepsis.

Pseudomonas aeruginosa infection causes pneumonia and sepsis. Previous research found that X-ray radiation can induce P. aeruginosa to release outer membrane vesicles (OMVs) of relatively consistent sizes. This study found that OMVs derived from X-ray-irradiated P. aeruginosa can significantly inhibit lung leakage, inflammatory cell infiltrating into lung, and the production of pro-inflammatory cytokines, IL-1ß and TNFα caused by P. aeruginosa infection under preventive and therapeutic administration conditions. Under the same conditions, OMVs also significantly alleviated pathological characteristics of lung injury, including pulmonary edema, pulmonary hemorrhage, and alveolar wall thickening. OMVs also significantly reduced bacterial burdens in peritoneal cavity, accompanied by a reduction in the number of viable bacteria capable of forming bacterial colonies. Pretreating macrophages and neutrophils with OMVs enhances their bactericidal ability. When bacteria were cocultured with treated cells, the number of viable bacteria capable of forming bacterial colonies was significantly reduced. OMVs themselves have not been shown to cause any lung injury or affect bacterial viability. Therefore, OMVs derived from X-ray-irradiated P. aeruginosa may not only be applied in prevention and treatment of diseases associated with P. aeruginosa infection, but also served as an excellent vaccine development platform.

Disseminated Mycobacterium colombiense infection mimicking malignancy: A case report.

Mycobacterium colombiense, an infrequently reported non-tuberculous mycobacterium, is characterized by its slow-growing nature and capacity to simulate malignancies in clinical presentation. This report details a case of disseminated M. colombiense infection initially misidentified as cancer due to atypical symptoms, negative etiological tests, and imaging suggestive of a neoplastic disease. However, comprehensive diagnostic investigations, including a bone marrow biopsy and flow cytometry analysis, excluded malignancy as the diagnosis. The patient subsequently developed palpable masses, from which a definitive diagnosis was made using metagenomic Next-Generation Sequencing (mNGS) and culture of aspirate. A regimen of clarithromycin, ethambutol, rifampin, and amikacin was administered, leading to substantial improvement and resumption of activities at the eight-month follow-up. This case highlights the diagnostic challenges posed by the nonspecific clinical presentation of disseminated M. colombiense infection and the importance of rigorous investigation to avoid grave misdiagnosis and treatment delays.

Degradation of Ciprofloxacin in Water by Magnetic-Graphene-Oxide-Activated Peroxymonosulfate.

Antibiotics are extensively applied in the pharmaceutical industry, while posing a tremendous hazard to the ecosystem and human health. In this study, the degradation performance of ciprofloxacin (CIP), one of the typical contaminants of antibiotics, in an oxidation system of peroxymonosulfate (PMS) activated by magnetic graphene oxide (MGO) was investigated. The effects of the MGO dosage, PMS concentration and pH on the degradation of CIP were evaluated, and under the optimal treatment conditions, the CIP degradation rate was up to 96.5% with a TOC removal rate of 63.4%. A kinetic model of pseudo-secondary adsorption indicated that it involves an adsorption process with progressively intensified chemical reactions. Furthermore, the MGO exhibited excellent recyclability and stability, maintaining strong catalytic activity after three regenerative cycles, with a CIP removal rate of 87.0%. EPR and LC-MS experiments suggested that •OH and SO4-• generated in the MGO/PMS system served as the main reactants contributing to the decomposition of the CIP, whereby the CIP molecule was effectively destroyed to produce other organic intermediates. Results of this study indicate that organic pollutants in the aqueous environment can be effectively removed in the MGO/PMS system, in which MGO has excellent catalytic activity and stabilization for being recycled to avoid secondary pollution, with definite research value and application prospects in the field of water treatment.

Proposal for Acinetobacter higginsii sp. nov. to accommodate organisms of human clinical origin previously classified as Acinetobacter genomic species 16.

In 1989, Bouvet and Jeanjean delineated five proteolytic genomic species (GS) of Acinetobacter, each with two to four human isolates. Three were later validly named, whereas the remaining two (GS15 and GS16) have been awaiting nomenclatural clarification. Here we present the results of the genus-wide taxonomic study of 13 human strains classified as GS16 (n=10) or GS15 (n=3). Based on core genome phylogenetic analysis, the strains formed two respective but closely related phylogroups within the Acinetobacter haemolytic clade. The intraspecies genomic average nucleotide identity based on blast (ANIb) values for GS16 and GS15 reached ≥94.9 % and ≥98.7, respectively, whereas ANIb values between them were 92.5-93.5% and those between them and the known species were ≤91.5 %. GS16 and GS15 could be differentiated from the other Acinetobacter species by their ability to lyse gelatin and sheep blood and to assimilate d,l-lactate, along with their inability to acidify d-glucose and assimilate glutarate. In contrast, GS16 and GS15 were indistinguishable from one another by metabolic/physiological features or whole-cell MALDI-TOF mass spectra. All the GS15/GS16 genomes contained genes encoding a class D ß-lactamase, Acinetobacter-derived cephalosporinase and aminoglycoside 6'-N-acetyltransferase. Searching NCBI databases revealed genome sequences of three additional isolates of GS16, but none of GS15. We conclude that our data support GS16 as representing a novel species, but leave the question of the taxonomic status of GS15 open, given its close relatedness to GS16 and the small number of available strains. We propose the name Acinetobacter higginsii sp. nov. for GS16, with the type strain NIPH 1872T (CCM 9243T=CIP 70.18T=ATCC 17988T).

Precise Species Identification for Acinetobacter: a Genome-Based Study with Description of Two Novel Acinetobacter Species.

The genus Acinetobacter comprises species with ecological significance and opportunistic pathogens and has a complicated taxonomy. Precise species identification is a foundation for understanding bacteria. In this study, we found and characterized two novel Acinetobacter species, namely, Acinetobacter tianfuensis sp. nov. and Acinetobacter rongchengensis sp. nov., based on phenotype examinations and genome analyses of the two strains WCHAc060012T and WCHAc060115T. The two strains had ≤89.69% (mean, 79.28% or 79.72%) average nucleotide identity (ANI) and ≤36.4% (mean, 20.89% or 22.19%) in silico DNA-DNA hybridization (isDDH) values compared with each other and all known Acinetobacter species. Both species can be differentiated from all hitherto known Acinetobacter species by a combination of phenotypic characteristics. We found that Acinetobacter pullorum B301T and Acinetobacter portensis AC 877T are actually the same species with 98.59% ANI and 90.4% isDDH values. We then applied the updated taxonomy to curate 3,956 Acinetobacter genomes in GenBank and found that 6% of Acinetobacter genomes (n = 234) are required to be corrected or updated. We identified 56 novel tentative Acinetobacter species, extending the number of Acinetobacter species to 144, including 68 with species names and 76 unnamed taxa. We also found that ANI and the average amino acid identity (AAI) values among type or reference strains of all Acinetobacter species and taxa are ≥76.97% and ≥66.5%, respectively, which are higher than the proposed cutoffs to define the genus boundary. This study highlights the complex taxonomy of Acinetobacter as a single genus and the paramount importance of precise species identification. The newly identified unnamed taxa warrant further studies. IMPORTANCE Acinetobacter species are widely distributed in nature and are of important ecological significance and clinical relevance. In this study, first, we significantly update the taxonomy of Acinetobacter by reporting two novel Acinetobacter species, namely, Acinetobacter tianfuensis and Acinetobacter rongchengensis, and by identifying Acinetobacter portensis as a synonym of Acinetobacter pullorum. Second, we curated Acinetobacter genome sequences deposited in GenBank (n = 3,956) using the updated taxonomy by correcting species assignations for 6% (n = 234) genomes and by assigning 94 (2.4%) to 56 previously unknown tentative species (taxa). Therefore, after curation, we further update the genus Acinetobacter to comprise 144 species, including 68 with species names and 76 unnamed taxa. Third, we addressed the question of whether such a large number of species should be divided in different genera and found that Acinetobacter is indeed a single genus. Our study significantly advanced the taxonomy of Acinetobacter, an important genus with science and health implications.

KPC-12 with a L169M substitution in the Ω loop has reduced carbapenemase activity.

KPC-12 is a variant of KPC-2 with a L169M substitution in the Ω loop, but its resistance spectrum was not reported. blaKPC-12 was cloned, and KPC-12 exhibited significantly decreased activities against imipenem, meropenem, aztreonam, and piperacillin-tazobactam with ≥4-fold lower MICs than KPC-2. However, unlike the L169P substitution in KPC-35, activities against ceftazidime and ceftazidime-avibactam of KPC-12 were unaltered. This highlights that different substitutions at the same position of carbapenemases may have varied impact on the activity.

Characterization of Acinetobacter chengduensis sp. nov., isolated from hospital sewage and capable of acquisition of carbapenem resistance genes.

Two strains of the genus Acinetobacter, WCHAc060005T and WCHAc060007, were isolated from hospital sewage in China. The two strains showed different patterns of resistance to clinically important antibiotics and their taxonomic positions were investigated. Cells are Gram-negative, obligate aerobic, non-motile, catalase-positive and oxidase-negative coccobacilli. A preliminary analysis based on the 16S rRNA gene sequences indicated that the two strains had the highest similarity to Acinetobacter cumulans WCHAc060092T (99.02%). Whole-genome sequencing of the two strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and in silico DNA-DNA hybridization values between the two new genomes were 99.77% and 98.7% respectively, whereas those between the two genomes and the known Acinetobacter species were <88.93% and <34.0%, respectively. A total of 7 different genes were found in the two genome sequences which encode resistance to five classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, and quinolones. In addition, the combination of their ability to assimilate gentisate, but not l-glutamate and d,l-lactate could distinguish the two strains from all known Acinetobacter species. Based on these combined data, we concluded that the two strains represent a novel species of the genus Acinetobacter, for which the name Acinetobacter chengduensis sp. nov. is proposed. The type strain is WCHAc060005T (CCTCC AB 2019139=GDMCC 1.1622=JCM 33509).

Pseudomonas defluvii sp. nov., isolated from hospital sewage.

A novel Gram-negative, obligate aerobic, mobile, rod-shaped and non-spore-forming bacterial strain, WCHP16T, was isolated from the wastewater treatment plant at West China Hospital in Chengdu, PR China. It was characterized using a polyphasic approach. Analysis of its 16S rRNA gene sequence showed that strain WCHP16T belonged to the genus Pseudomonas with the highest similarity to Pseudomonas qingdaonensis JJ3T (99.34 %), Pseudomonas shirazica VM14T (99.0 %), Pseudomonas plecoglossicida NBRC 103162T (99.0 %) and Pseudomonas asiatica RYU5T (99.0 %). Phylogenomic analysis based on 107 core gene sequences demonstrated that WCHP16T was a member of the Pseudomonas putida group but was distant from all closely related species. Whole-genome comparisons, using average nucleotide identity based on blast (ANIb) and in silico DNA-DNA hybridization (isDDH), confirmed low genome relatedness to all the known Pseudomonas species (below the recommended thresholds of 95 % [ANIb] and 70 % [isDDH] for species delineation). Phenotypic characterization tests showed that the utilization of phenylacetic acid and capric acid, but not d-arabitol, and inability to produce fluorescent (King B medium) in combination could distinguish this strain from other related species of the genus Pseudomonas. Therefore, based on genetic and phenotypic evidence, it is clear that strain WCHP16T represents a novel species, for which the name Pseudomonas defluvii sp. nov. is proposed. The type strain is WCHP16T (GDMCC1.1215T=CCTCC AB 2017103T=KCTC 52991T).

Pseudomonas huaxiensis sp. nov., isolated from hospital sewage.

A novel Gram-negative, obligate aerobic, rod-shaped, motile by one or two polar flagella, non-spore-forming bacterial strain, WCHPs060044T, was isolated from the wastewater treatment plant at West China Hospital in Chengdu, PR China. Analysis of its 16S rRNA gene sequence showed that strain WCHPs060044T belonged to the genus Pseudomonas with the highest similarity to Pseudomonas alkylphenolica KL28T (99.73 %), Pseudomonas donghuensis HYST (99.52 %) and Pseudomonas wadenswilerensis CCOS 846T (99.38 %). Phylogenomic analysis based on 107 core gene sequences demonstrated that WCHPs060044T was a member of the Pseudomonas putida group but was distant from all closely related species. Whole-genome comparisons, using average nucleotide identity based on blast (ANIb) and in silico DNA-DNA hybridization (isDDH), confirmed low genome relatedness to its close phylogenetic neighbours [below the recommended thresholds of 95 % (ANIb) and 70 % (isDDH) for species delineation]. Phenotypic characterization tests showed that the utilization of l-arginine, l-fucose, d-galacturonic, d-glucuronic acid, inositol and sorbitol in combination could distinguish this strain from other related species of the genus Pseudomonas. Therefore, based on genetic and phenotypic evidence, strain WCHPs060044T represents a novel species, for which the name Pseudomonas huaxiensis sp. nov. is proposed. The type strain is WCHPs060044T (GDMCC 1.1396T=JCM 32907T=CCTCC AB 2018120T=CNCTC 7663T).

Acinetobacter cumulans sp. nov., isolated from hospital sewage and capable of acquisition of multiple antibiotic resistance genes.

We studied the taxonomic position of six phenetically related strains of the genus Acinetobacter, which were recovered from hospital sewage in China and showed different patterns of resistance to clinically important antibiotics. Whole-genome sequencing of these strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and digital DNA-DNA hybridization values between the six new genomes were 97.25-98.67% and 79.2-89.3%, respectively, whereas those between them and the genomes of the known species were ≤78.57% and ≤28.5%, respectively. The distinctness of the strains at the species level was also supported by the results of the cluster analysis of the whole-cell protein fingerprints generated by MALDI-TOF MS. Moreover, the strains displayed a catabolically unique profile and could be differentiated from the phylogenetically closest species at least by their inability to grow on d,l-lactate. A total of 18 different genes were found in the six genome sequences which encode resistance to seven classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, or aminoglycosides. These genes occurred in five different combinations, with three to 10 different genes per strain. We conclude that the six strains represent a novel Acinetobacter species, for which we propose the name Acinetobacter cumulans sp. nov. to reflect its ability to acquire and cumulate diverse resistance determinants. The type strain is WCHAc060092T (ANC 5797T=CCTCC AB 2018119T=GDMCC 1.1380T=KCTC 62576T).

Acinetobacter chinensis, a novel Acinetobacter species, carrying blaNDM-1, recovered from hospital sewage.

Two strains of the genus Acinetobacter, named WCHAc010005 and WCHAc010052, were isolated from hospital sewage at West China Hospital in Chengdu, China. The two strains were found to be resistant to carbapenems due to the presence of carbapenemase gene blaNDM-1. Based on the comparative analysis of the rpoB sequence, the two strains formed a strongly supported and internally coherent cluster (intracluster identity of 98.7%), which was clearly separated from all known Acinetobacter species (≤ 83.4%). The two strains also formed a tight and distinct cluster based on the genuswide comparison of whole-cell mass fingerprints generated by MALDI-TOF mass spectrometry. In addition, the combination of their ability to assimilate malonate but not benzoate, and the inability to grow at 37°C could distinguish the two strains from all known Acinetobacter species. The two strains were subjected to whole genome sequencing using both short-read Illumina HiSeq2500 platform and the longread MinION sequencer. The average nucleotide identity and in silico DNA-DNA hybridization value between the genomes of WCHAc010005 and WCHAc010052 was 96.69% and 74.3% respectively, whereas those between the two genomes and the known Acinetobacter species were < 80% and < 30%, respectively. Therefore, the two strains represent a novel species of the genus Acinetobacter, for which the name Acinetobacter chinensis sp. nov. is proposed, and the type strain is WCHAc- 010005T (= GDMCC 1.1232T = KCTC 61813T).

Pseudomonas sichuanensis sp. nov., isolated from hospital sewage.

A bacterial strain, designated WCHPs060039T, was isolated from hospital sewage in China. The strain was Gram-stain-negative, obligate aerobic, flagellum-motile and positive for oxidase and catalase. A preliminary analysis of the 16S rRNA gene sequences indicated that strain WCHPs060039T belonged to the genus Pseudomonasand was closely related to members of the Pseudomonas putida group, with the highest similarities to Pseudomonas entomophila L48T (99.5 %), Pseudomonas mosselii CIP 105259T (99.52 %), Pseudomonas taiwanensis BCRC 17751T (99.45 %) and Pseudomonas plecoglossicida NBRC 103162T (99.31 %). Whole genome sequencing of the strain was performed. Phylogenetic analysis based on a set of core gene sequences revealed that the strain was distinct from its closest Pseudomonas species. Average nucleotide identity based on blast and in silico DNA-DNA hybridizationrevealed low genome relatedness to its closest Pseudomonas species (below the recommended thresholds of 95 and 70 %, respectively, for species delineation). The major fatty acids of the strain were 16:0, 17:0 cyclo, summed feature 3 (16:1ω7c/16:1ω6c and 16:1ω6c/16:1ω7c) and summed feature 8 (18:1ω7c). The ability to utilize inositol, sorbitol and d-glucuronic acid could differentiate strain WCHPs060039T from the closely related Pseudomonas species. It is therefore evident that strain WCHPs060039T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sichuanensis sp. nov. is proposed. The type strain is WCHPs060039T (GDMCC 1.1424T=CNCTC 7662T).

Acinetobacter sichuanensis sp. nov., recovered from hospital sewage in China.

A novel Acinetobacter strain, WCHAc060041T, was recovered from hospital sewage at West China Hospital in Chengdu, Sichuan Province, China. The strain was Gram-negative coccobacillus, non-spore-forming, non-motile and strictly aerobic. The genomic DNA G+C content was 37.02 mol%. The 16S rRNA and rpoB gene sequences of the strain were ≤98.2 and≤89.5 % identical to the type strains of all known Acinetobacter species, respectively. The strain formed a distinct branch based on the genus-wide comparison of whole-cell mass fingerprints generated by matrix-assisted laser desorption/ionization-time-of flight mass spectrometry. Strain WCHAc060041T was subjected to whole genome sequencing. The average nucleotide identity based on blast (ANIb) and in silico DNA-DNA hybridization (isDDH) values between strain WCHAc060041T and type strains of other Acinetobacter species were ≤82.7 and ≤26.9 %, respectively. Strain WCHAc060041T could be distinguished from all known Acinetobacter species by its ability to assimilate gentisate and levulinate, but not to citrate (Simmons'). Genotypic and phenotypic characteristics from this study indicate that strain WCHAc060041T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter sichuanensis sp. nov. is proposed. The type strain is WCHAc060041T (=CCTCC AB 2018118T=GDMCC 1.1383T=KCTC 62575T).

Acinetobacter wuhouensis sp. nov., isolated from hospital sewage.

We recovered eight strains of the genus Acinetobacter from hospital sewage at West China Hospital in Chengdu, China. Based on the comparative analysis of the rpoB sequence, these strains formed a strongly supported and internally coherent cluster (intra-cluster identity of ≥98.0 %), which was clearly separated from all known Acinetobacter species (≤91.1 %). The eight strains also formed a tight and distinct cluster based on the genus-wide comparison of whole-cell mass fingerprints generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In addition, the combination of their ability to assimilate 2,3-butanediol and phenylacetate, but not 4-hydroxybenzoate, and the inability to grow at 37 °C could distinguish these eight strains from all known Acinetobacter species. Whole-genomic sequencing has been performed for two selected strains, WCHA60T and WCHA62. There were 96.65 % average nucleotide identity (ANI) and 72 % in silico DNA-DNA hybridization (isDDH) values between WCHA60T and WCHA62, suggesting that the two strains indeed belonged to the same species. In contrast, the ANI and isDDH values between the two strains and the known Acinetobacter species were <83 and <30 %, respectively; both of which were far below the cut-off to define a bacterial species. Therefore, the eight strains should be considered to represent a novel species of the genus Acinetobacter, for which the name Acinetobacterwuhouensis sp. nov. is proposed. The type strain is WCHA60T (=CCTCC AB 2016204T=GDMCC 1.1100T=KCTC 52505T).