36 results on '"Zhenzhou Huang"'
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2. Genome-wide expanding of genetic evolution and potential pathogenicity in Vibrio alginolyticus
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Zhenzhou Huang, Yanjun Li, Keyi Yu, Lizhi Ma, Bo Pang, Qin Qin, Jie Li, Duochun Wang, He Gao, and Biao Kan
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Vibrio alginolyticus ,whole genome sequencing ,population structure ,virulence-related factors ,antibiotic resistance genes ,Infectious and parasitic diseases ,RC109-216 ,Microbiology ,QR1-502 - Abstract
ABSTRACTVibrio alginolyticus, an emergent species of Vibrio genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still unclear. Here, we performed a multi-dimensional comparative genomic analysis to explore the population phylogeny, virulence-related genes and potential drug resistance genes of 184 V. alginolyticus isolates. Although genetic diversity is complex, we analysed the population structure using three sub-datasets, including the subdivision for three lineages into sublineages and the distribution of strains in the marine ecological niche. Accessory genes, most of which reclassified V. alginolyticus genomes as different but with relatively close affinities, were nonuniformly distributed among these isolates. We demonstrated that the spread of some post-evolutionary isolates (mainly L3 strains isolated from Chinese territorial seas) was likely to be closely related to human activities, whereas other more ancestral strains (strains in the L1 and L2) tended to be locally endemic and formed clonal complex groups. In terms of pathogenicity, the potential virulence factors were mainly associated with toxin, adherence, motility, chemotaxis, and the type III secretion system (T3SS). We also found five types of antibacterial drug resistance genes. The prevalence of β-lactam resistance genes was 100%, which indicated that there may be a potential risk of natural resistance to β-lactam drugs. Our study reveals insights into genomic characteristics, evolution and potential virulence-associated gene profiles of V. alginolyticus.
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- 2024
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3. Genomic insights into the evolution, pathogenicity, and extensively drug-resistance of emerging pathogens Kluyvera and Phytobacter
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Zhenzhou Huang, Guozhong Zhang, Zhibei Zheng, Xiuqin Lou, Feifei Cao, Lingyi Zeng, Duochun Wang, Keyi Yu, and Jun Li
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Kluyvera ,Phytobacter ,evolution ,pathogenicity ,drug-resistance ,Microbiology ,QR1-502 - Abstract
IntroductionKluyvera is a Gram-negative, flagellated, motile bacillus within the Enterobacteriaceae. The case reports of clinical infections shed light on the importance of this organism as an emerging opportunistic pathogen. The genus Phytobacter, which often be misidentified with Kluyvera, is also an important clinically relevant member of the Enterobacteriaceae. However, the identification of Kluyvera and Phytobacter is problematic, and their phylogenetic relationship remains unclear.MethodsHere, 81 strains of Kluyvera and 16 strains of Phytobacter were collected. A series of comparative genomics approaches were applied to the phylogenetic relationship reconstruction, virulence related genes profiles description, and antibiotic resistance genes prediction.ResultsUsing average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH), we offered reliable species designations of 97 strains, in which 40 (41.24%) strains were incorrectly labeled. A new Phytobacter genomospecies-1 were defined. Phytobacter and Kluyvera show great genome plasticity and inclusiveness, which may be related to their diverse ecological niches. An intergenomic distances threshold of 0.15875 was used for taxonomy reassignments at the phylogenomic-group level. Further principal coordinates analysis (PCoA) revealed 11 core genes of Kluyvera (pelX, mdtL, bglC, pcak-1, uhpB, ddpA-2, pdxY, oppD-1, cptA, yidZ, csbX) that could be served as potential identification targets. Meanwhile, the Phytobacter specific virulence genes clbS, csgA-C, fliS, hsiB1_vipA and hsiC1_vipB, were found to differentiate from Kluyvera. We concluded that the evolution rate of Kluyvera was 5.25E-6, approximately three times higher than that of Phytobacter. Additionally, the co-existence of ESBLs and carbapenem resistance genes were present in approximately 40% strains, suggesting the potential development of extensively drug-resistant or even fully drug-resistant strains.DiscussionThis work provided a better understanding of the differences between closely related species Kluyvera and Phytobacter. Their genomes exhibited great genome plasticity and inclusiveness. They not only possess a potential pathogenicity threat, but also a risk of multi-drug resistance. The emerging pathogens Kluyvera and Phytobacter warrant close attention.
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- 2024
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4. Prevalence and molecular characteristics of Shewanella infection in diarrhea patients in Beijing, China 2017–2019
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Ying Kang, Keyi Yu, Zhenzhou Huang, Bo Pang, Shengtian Liu, Tao Peng, Ying Li, and Duochun Wang
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Shewanella ,prevalence ,molecular characteristics ,diarrhea ,antibiotic susceptibility ,Microbiology ,QR1-502 - Abstract
IntroductionShewanella is an important opportunistic pathogen distributed in marine environments that has caused an increasing number of clinical infections. However, there are few reports on the distribution and characteristics of Shewanella in the diarrheal pathogen spectrum. In this study, we have systematically described the prevalence of Shewanella infections in diarrhea patients in Beijing, China 2017–2019, and genome characteristics and antimicrobial susceptibility of Shewanella isolates.MethodsStool samples were collected from diarrhea patients in a surveillance project from 2017 to 2019. Shewanella strains were isolated, and identified using VITEKR 2 COMPACT and MALDI-TOF MS. Average nucleotide identity (ANI) analysis, multi-locus sequence typing (MLST), phylogenetic analysis, virulence-associated genes and antimicrobial resistance genes analysis were used for genome characteristics description. The antibiotic susceptibility test was performed with microbroth dilution method.Results1104 fecal samples were collected, and the Shewanella detection rate was 2.36% (26/1104). The main manifestations of infection caused by Shewanella spp. were diarrhea (100%, 26/26), abdominal pain (65.38%, 17/26), and vomiting (38.46%, 10/26). The 26 isolates were classified into 3 species (S. algae (n = 18), S. indica (n = 5), and S. chilikensis (n = 3)) and 22 sequence types. Core genome single nucleotide polymorphism-based evolutionary tree identified three clone groups corresponding to three infection events in the same months in 2017 and 2019. The putative virulence-associated gene pool consisted of 56 potential virulence genes, including 19 virulence gene factors. The resistance rates of the 26 isolates to 17 antibiotics from high to low were as follows: polymyxin E (76.92%), cefotaxime (57.69%), ampicillin (50%), ampicillin-sulbactam (34.62%), nalidixic acid (15.38%), ciprofloxacin (11.54%), selectrin (3.846%,1/26), and tetracycline (3.846%, 1/26). The rate of multidrug resistance was 38.46% (10/26).DiscussionMonitoring for Shewanella spp. should be added to the routine surveillance of infectious diarrhea during the epidemic season.
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- 2024
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5. Stenotrophomonas maltophilia complex: insights into evolutionary relationships, global distribution and pathogenicity
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Kun Li, Keyi Yu, Zhenzhou Huang, Xiao Liu, Li Mei, Xiaodong Ren, Xuemei Bai, He Gao, Zhiwen Sun, Xiaoning Liu, and Duochun Wang
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Stenotrophomonas maltophilia complex ,evolution ,global distribution ,pathogenicity ,swimming motility ,biofilm ,Microbiology ,QR1-502 - Abstract
IntroductionStenotrophomonas maltophilia complex (Smc) comprises opportunistic Gram-negative bacilli responsible for various nosocomial infections. Limited data exists concerning its evolutionary lineage, global prevalence and pathogenicity.MethodsWe conducted an extensive genomic analysis on 734 Smc genomes, of which 90 were newly sequenced and isolated from different patients. The species composition and evolutionary relationships of Smc were examined using core protein sequence analysis. Pathogenicity evaluation was used by assays for swimming motility, biofilm formation and identification of virulence factors. The broth microdilution method was used to evaluate the drug resistance spectrum of clinical isolates.ResultsPhylogenetic analyses delineated 24 species-level clades, dominated by S. maltophilia (42.8%), S. sepilia (13.6%) and S. geniculata (9.9%). Geographically, strains were primarily distributed in Europe (34.2%), Asia (33.7%) and North America (24.0%), with intricate global distribution patterns. Meanwhile, 154 virulence-associated genes and 46 antimicrobial resistance genes within Smc were identified. These genes encoded span various functions, including motility, adherence, toxin, RND antibiotic efflux pumps, beta-lactamases and aminoglycoside-modifying enzymes. Moreover, significant variations were indicated in swimming motility and biofilm-forming capability across the different species, with S. sepilia exhibiting superior levels of both traits. Additionally, no statistically significant discrepancy was detected among Smc species to other antibiotics, despite the fact that all S. geniculata isolates were resistant to Ceftazidime and much higher than other species.ConclusionOur findings indicate the need to pay increased attention to other mainstream species of Smc besides S. maltophilia in order to better manage Smc-related infections and tailor effective treatment strategies.
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- 2024
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6. Vibrio metschnikovii as an emergent pathogen: analyses of phylogeny and O-antigen and identification of possible virulence characteristics
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Zhenzhou Huang, Keyi Yu, Ruiting Lan, J. Glenn Morris, Yue Xiao, Julian Ye, Leyi Zhang, Longze Luo, He Gao, Xuemei Bai, and Duochun Wang
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Phylogeny ,O-antigen biosynthesis gene clusters ,pathogenicity ,genomics ,Vibrio metschnikovii ,Infectious and parasitic diseases ,RC109-216 ,Microbiology ,QR1-502 - Abstract
Vibrio metschnikovii is an emergent pathogen that causes human infections which may be fatal. However, the phylogenetic characteristics and pathogenicity determinants of V. metschnikovii are poorly understood. Here, the whole-genome features of 103 V. metschnikovii strains isolated from different sources are described. On phylogenetic analysis V. metschnikovii populations could be divided into two major lineages, defined as lineage 1 (L1) and 2 (L2), of which L1 was more likely to be associated with human activity. Meanwhile, we defined 29 V. metschnikovii O-genotypes (VMOg, named VMOg1–VMOg29) by analysis of the O-antigen biosynthesis gene clusters (O-AGCs). Most VMOgs (VMOg1 to VMOg28) were assembled by the Wzx/Wzy pathway, while only VMOg29 used the ABC transporter pathway. Based on the sequence variation of the wzx and wzt genes, an in silico O-genotyping system for V. metschnikovii was developed. Furthermore, nineteen virulence-associated factors involving 161 genes were identified within the V. metschnikovii genomes, including genes encoding motility, adherence, toxins, and secretion systems. In particular, V. metschnikovii was found to promote a high level of cytotoxicity through the synergistic action of the lateral flagella and T6SS. The lateral flagellar-associated flhA gene played an important role in the adhesion and colonization of V. metschnikovii during the early stages of infection. Overall, this study provides an enhanced understanding of the genomic evolution, O-AGCs diversity, and potential pathogenic features of V. metschnikovii.
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- 2023
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7. Shewanella infection in humans: Epidemiology, clinical features and pathogenicity
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Keyi Yu, Zhenzhou Huang, Yue Xiao, and Duochun Wang
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Shewanella spp. ,Shewanella infection ,epidemiology ,clinical features ,pathogenicity ,virulence ,Infectious and parasitic diseases ,RC109-216 - Abstract
The genus Shewanella consists of Gram-negative proteobacteria that are ubiquitously distributed in environment. As the members of this genus have rapidly increased within the past decade, several species have become emerging pathogens worldwide, attracting the attention of the medical community. These species are also associated with severe community- and hospital-acquired infections. Patients infected with Shewanella spp. had experiences of occupational or recreational exposure; meanwhile, the process of infection is complex and the pathogenicity is influenced by a variety of factors. Here, an exhaustive internet-based literature search was carried out in PUBMED using terms “Achromobacter putrefaciens,” “Pseudomonas putrefaciens,” “Alteromonas putrefaciens” and “Shewanella” to search literatures published between 1978 and June 2022. We provided a comprehensive review on the epidemiology, clinical features and pathogenicity of Shewanella, which will contribute a better understanding of its clinical aetiology, and facilitate the timely diagnosis and effective treatment of Shewanella infection for clinicians and public health professionals.
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- 2022
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8. Influencing factors on the preservation of lytic bacteriophage VP3
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Yue Xiao, Pin Huang, Zhenzhou Huang, Keyi Yu, Yang Song, Ning Guo, Hang Dai, Mengnan Jiang, Yi Xu, Duochun Wang, and Qiang Wei
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Influencing factors ,Preservation ,Lytic bacteriophage ,Cryoprotectant ,Infectious and parasitic diseases ,RC109-216 ,Public aspects of medicine ,RA1-1270 - Abstract
Long-term and stable preservation of bacteriophages is of crucial importance. Although many efforts have been made in the past decades to explore the influence of external factors on bacteriophage preservation, there is still little understanding, and a systematic description is lacking. In this study, we explored the influence of different factors on the preservation of lytic bacteriophage VP3, one of the typing bacteriophages of Vibrio cholerae O1 biotype El Tor, and attempted to optimize its preservation. We examined external factors, including temperature, solution, and cryoprotectant, in stable cooling/freezing conditions or alternate cooling/freezing and thawing. We found that whether in Luria-Bertani (LB) medium or SM buffer, in terms of 20-week stable cooling or freezing, −20 °C was the most damaging while 4 °C, −80 °C, and −196 °C were protective. Thirteen cycles of alternate cooling/freezing and thawing caused a loss in the survival rates of bacteriophages. The addition of cryoprotectant, glycerol (30%, w/v) or dimethyl sulfoxide (DMSO, 10%, w/v) significantly improved the survival rates of bacteriophages preserved at −20 °C. However, at 4 °C, −80 °C, and −196 °C, the cryoprotectant effect was only slightly positive or even harmful. In summary, for bacteriophage VP3, the best preservation method is to directly preserve the bacteriophage stocks in LB medium at −80 °C or −196 °C instead of storing them in SM buffer or adding cryoprotectant. Our results provided insights into the external influencing factors on bacteriophage VP3 during preservation at low temperature and can be applied to the optimization of bacteriophage preservation in the future.
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- 2022
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9. Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup
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Keyi Yu, Zhenzhou Huang, Ruiting Lan, J. Glenn Morris, Yue Xiao, Songzhe Fu, He Gao, Xuemei Bai, Kun Li, and Duochun Wang
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Kluyvera ,drug resistance ,ESBLs ,blaCTX-Ms ,Biology (General) ,QH301-705.5 - Abstract
A rising incidence of clinical infections has been caused by Kluyvera, a significant opportunistic pathogen. Meanwhile, Kluyvera acts as an important reservoir of blaCTX-Ms, which are the dominant genes of class A extended-spectrum β-lactamases (ESBLs). In this work, 60 strains of Kluyvera were subjected to phylogenetic relationship reconstruction, antimicrobial susceptibility testing, and antibiotic resistance genes prediction. All mature blaCTX-Ms were gathered to perform subgroup reclassification. The findings demonstrate that Kluyvera has a large gene pool with significant genetic flexibility. Notably, 25% of strains showed simultaneous detection of ESBLs and carbapenem resistance genes. The genotypes of fourteen novel blaCTX-Ms were identified. A new subgroup classification approach for blaCTX-Ms was defined by using 20 amino acid site variants, which could split blaCTX-Ms into 10 subgroups. The results of the subgroup division were consistent with the phylogenetic clustering. More significantly, we proposed a novel blaCTX-M subgroup, KLUS, that is chromosomally encoded in K. sichuanensis and the new species put forward in this study, showing amino acid differences from the currently known sequences. Cloning and transformation tests demonstrated that the recipient bacteria had a robust phenotype of cefotaxime resistance. Closely related Kluyvera species had blaCTX-Ms in the same subgroup. Our research lays the groundwork for a deeper comprehension of Kluyvera and emphasizes how important a blaCTX-M reservoir it is. We provide an update on blaCTX-M subgroups reclassification from the aspects of phylogenetic relationship, amino acid differences, and the new subgroup KLUS, which needs to be strengthen monitored due to its strong resistance phenotype to cefotaxime.
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- 2023
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10. Effects and related mechanisms of Huang's SiYu pills on Leydig cell function in kidney-yin deficiency rat models
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Aomen Wei, Doudou Huang, Shanyao Wei, Zhihui Li, Meijuan Chen, and Zhenzhou Huang
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Huang's SiYu pills ,Kidney-yin deficiency ,Leydig cells ,Male infertility ,Medical technology ,R855-855.5 - Abstract
The prescription “Huang's SiYu Pill” (HSYP) was founded by professor Huang Haibo, a famous traditional Chinese medicine in Inner Mongolia, based on long-term clinical experience. In this study we observed the effects of HYSP on sperm quality, hormone level and the expression level of reproductive related genes and proteins in testicular stromal cells of rats with kidney-yin deficiency to explore the therapeutic mechanism of HSYP in the treatment of infertility with kidney-yin deficiency, Liuwei Dihuang Pill group (LDP) and Tamoxifen Citrate Tablets combined with Pancreatic Kallidinogenase Enteric Coated Tablets were used to be the positive control drug. After 25 days of medicine administration, the animals were anesthetized and killed, the serum and testicular tissues were retained for further experiments. The ELISA results showed that HSYP had a better effect on increasing serum FSH level than the conventional Chinese medicine or western medicine, while there was no remarkable difference in the regulation of serum LH in each administration group. The results of RT-qPCR showed that the transcription levels of Cyp11a1, Hsd3b1, Lhcgr and Star genes in the medium and high dose groups of HSYP were significantly upregulated compared with the model group of kidney-yin deficiency, while the expression of Nr5a1 gene was not significantly affected. The results of HE and immunohistochemistry showed that HSYP significantly improved the development level of testicular stromal cells and promoted the expression levels of CYP11A1 and HSD11B1 in testicular stromal cells, compared with the model group of kidney-yin deficiency. Together, our results showed that Huang's SiYu Pills can significantly improve the development and function of Leydig cells in SD rats with kidney-yin deficiency model, which provided a good research basis for deep research on relevant pharmacological mechanisms of the medicine.
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- 2022
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11. The Potential of Cylindromatosis (CYLD) as a Therapeutic Target in Oxidative Stress-Associated Pathologies: A Comprehensive Evaluation
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Zhenzhou Huang and Yanjie Tan
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oxidative stress ,CYLD ,disease ,deubiquitination ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Oxidative stress (OS) arises as a consequence of an imbalance between the formation of reactive oxygen species (ROS) and the capacity of antioxidant defense mechanisms to neutralize them. Excessive ROS production can lead to the damage of critical biomolecules, such as lipids, proteins, and DNA, ultimately contributing to the onset and progression of a multitude of diseases, including atherosclerosis, chronic obstructive pulmonary disease, Alzheimer’s disease, and cancer. Cylindromatosis (CYLD), initially identified as a gene linked to familial cylindromatosis, has a well-established and increasingly well-characterized function in tumor inhibition and anti-inflammatory processes. Nevertheless, burgeoning evidence suggests that CYLD, as a conserved deubiquitination enzyme, also plays a pivotal role in various key signaling pathways and is implicated in the pathogenesis of numerous diseases driven by oxidative stress. In this review, we systematically examine the current research on the function and pathogenesis of CYLD in diseases instigated by oxidative stress. Therapeutic interventions targeting CYLD may hold significant promise for the treatment and management of oxidative stress-induced human diseases.
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- 2023
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12. Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of Genus Brevundimonas and Description of Brevundimonas pishanensis sp. nov.
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Zhenzhou Huang, Keyi Yu, Yue Xiao, Yonglu Wang, Di Xiao, and Duochun Wang
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Brevundimonas ,comparative genomics ,new species proposed ,pathogenicity ,slow growth ,Microbiology ,QR1-502 - Abstract
ABSTRACT The genus Brevundimonas consists of Gram-negative bacteria widely distributed in environment and can cause human infections. However, the genomic characteristics and pathogenicity of Brevundimonas remain poorly studied. Here, the whole-genome features of 24 Brevundimonas type strains were described. Brevundimonas spp. had relatively small genomes (3.13 ± 0.29 Mb) within the family Caulobacteraceae but high G+C contents (67.01 ± 2.19 mol%). Two-dimensional hierarchical clustering divided those genomes into 5 major clades, in which clades II and V contained nine and five species, respectively. Interestingly, phylogenetic analysis showed a one-to-one match between core and accessory genomes, which suggested coevolution of species within the genus Brevundimonas. The unique genes were annotated to biological functions like catalytic activity, signaling and cellular processes, multisubstance metabolism, etc. The majority of Brevundimonas spp. harbored virulence-associated genes icl, tufA, kdsA, htpB, and acpXL, which encoded isocitrate lyase, elongation factor, 2-dehydro-3-deoxyphosphooctonate aldolase, heat shock protein, and acyl carrier protein, respectively. In addition, genomic islands (GIs) and phages/prophages were identified within the Brevundimonas genus. Importantly, a novel Brevundimonas species was identified from the feces of a patient (suffering from diarrhea) by the analyses of biochemical characteristics, phylogenetic tree of 16S rRNA gene, multilocus sequence analysis (MLSA) sequences, and genomic data. The name Brevundimonas pishanensis sp. nov. was proposed, with type strain CHPC 1.3453 (= GDMCC 1.2503T = KCTC 82824T). Brevundimonas spp. also showed obvious slow growth compared with that of Escherichia coli. Our study reveals insights into genomic characteristics and potential virulence-associated genes of Brevundimonas spp., and provides a basis for further intensive study of the pathogenicity of Brevundimonas. IMPORTANCE Brevundimonas spp., a group of bacteria from the family Caulobacteraceae, is associated with nosocomial infections, deserve widespread attention. Our study elucidated genes potentially associated with the pathogenicity of the Brevundimonas genus. We also described some new characteristics of Brevundimonas spp., such as small chromosome size, high G+C content, and slow-growth phenotypes, which made the Brevundimonas genus a good model organism for in-depth studies of growth rate traits. Apart from the comparative analysis of the genomic features of the Brevundimonas genus, we also reported a novel Brevundimonas species, Brevundimonas pishanensis, from the feces of a patient with diarrhea. Our study promotes the understanding of the pathogenicity characteristics of Brevundimonas species bacteria.
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- 2022
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13. Corrigendum: Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi
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Yang Song, Xinmin Xu, Zhenzhou Huang, Yue Xiao, Keyi Yu, Mengnan Jiang, Shangqi Yin, Mei Zheng, Huan Meng, Ying Han, Yajie Wang, Duochun Wang, and Qiang Wei
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genomic characteristics ,plasmid-mediated pathogenicity ,rifamycin resistance ,Rhodococcus equi ,pan-genome ,Microbiology ,QR1-502 - Published
- 2022
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14. Screening of Staphylococcus aureus for Disinfection Evaluation and Transcriptome Analysis of High Tolerance to Chlorine-Containing Disinfectants
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Yixiao Li, Yang Song, Zhenzhou Huang, Li Mei, Mengnan Jiang, Duochun Wang, and Qiang Wei
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standard strain ,Staphylococcus aureus ,MIC ,tolerance to chlorine-containing disinfectants ,DEGs ,Biology (General) ,QH301-705.5 - Abstract
The nonstandard use of disinfectants can lead to the disinfectant resistance of bacteria and even increase antibiotic resistance. However, compared with the study of antibiotic resistance, studies of bacterial resistance to disinfectants are relatively few in number. In this study, we explored the standard strain screening procedure for the evaluation of disinfection efficacy. Staphylococcus aureus strains with different sources and substrates were selected from the National Pathogen Resource Center of China and screened the standard strains that could evaluate the long-term bacteriostatic effect of the chlorine-containing disinfectants through the determination of the physical properties, genome-based safety evaluation, and disinfection test evaluation. In this process, one S. aureus strain was more resistant to the long-term bacteriostasis of chlorine-containing disinfectants than the other strains. This strain and the standard strain ATCC 6538 were cultured in the medium containing a low concentration of chlorine-containing disinfectant synchronously. Then, comparative transcriptome analysis was carried out to investigate the potential mechanism of a high tolerance to chlorine-containing disinfectants. The pathway of significant differential expression is related to the oxocarboxylic acid metabolic mechanism, amino acid metabolic mechanism, and pyrimidine mechanism, which may be the molecular mechanism of S. aureus evolution to adapt to chlorine-containing disinfectants. Our study established a technical process for screening and evaluating standard strains for disinfection, which also provided a reference for studying the bacterial evolution mechanism toward chlorine tolerance.
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- 2023
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15. Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi
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Yang Song, Xinmin Xu, Zhenzhou Huang, Yue Xiao, Keyi Yu, Mengnan Jiang, Shangqi Yin, Mei Zheng, Huan Meng, Ying Han, Yajie Wang, Duochun Wang, and Qiang Wei
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genomic characteristics ,plasmid-mediated pathogenicity ,rifamycin resistance ,Rhodococcus equi ,pan-genome ,Microbiology ,QR1-502 - Abstract
Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.
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- 2022
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16. Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O’Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015
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Hang Dai, Binghuai Lu, Zhenpeng Li, Zhenzhou Huang, Hongyan Cai, Keyi Yu, and Duochun Wang
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Proteus ,Multilocus sequence analysis ,Taxonomy ,Identification ,Microbiology ,QR1-502 - Abstract
Abstract Background Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus. Results Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date. Conclusions This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.
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- 2020
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17. Distribution and Molecular Characteristics of Vibrio Species Isolated from Aquatic Environments in China, 2020
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Yue Xiao, Zhenzhou Huang, Keyi Yu, Maoshu Wang, He Gao, Xuemei Bai, Mengnan Jiang, and Duochun Wang
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distribution ,molecular characteristics ,Vibrio species ,aquatic environment ,China ,Biology (General) ,QH301-705.5 - Abstract
To understand the characteristics of Vibrio isolates in aquatic environments in China and their public health significance, this study investigated water samples in six cities in China in 2020. A total of 88 sampling locations were included and Vibrio isolates were identified in 81 of them. A total of 143 Vibrio isolates belonging to 16 species were selected for characterization. The population structure of Vibrio species showed great differences among the six cities, indicating regional specificity. The presence of virulence genes was examined for the isolates (n = 78) of five pathogenic Vibrio species. All isolates except one (n = 77) contained at least one virulence gene and isolates belonging to the same species showed very similar virulence gene profiles. Then, 26 isolates from 12 species were examined by multilocus sequence typing and were assigned to 25 STs, of which 24 STs were new. Also, the presence of antibiotic-resistant genes was investigated for all 143 isolates and only three isolates were found to contain genes from aminoglycosides, phenicols, beta-lactams or the tetracycline family. Our results provide valuable insights into the Vibrio community in Chinese aquatic environments and can be applied as guidance for the environmental surveillance of the risk of Vibrio isolates.
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- 2022
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18. Development and Evaluation of Duplex MIRA-qPCR Assay for Simultaneous Detection of Staphylococcus aureus and non-aureus Staphylococci
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Jiulian Lai, Zhenzhou Huang, Yue Xiao, Keyi Yu, Xuemei Bai, He Gao, Hang Dai, Xiaoning Liu, and Duochun Wang
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Staphylococcus aureus ,non-aureus Staphylococci ,MIRA ,duplex quantitative PCR ,conventional PCR ,detection ,Biology (General) ,QH301-705.5 - Abstract
Staphylococcus spp., especially Staphylococcus aureus (S. aureus), is an important pathogen in hospital-acquired infection and food poisoning. Here, we developed a multienzyme isothermal rapid amplification combined with duplex quantitative PCR (duplex MIRA-qPCR) method, which can simultaneously detect the S. aureus species-specific conserved gene FMN-bgsfp and the Staphylococcus genus-specific conserved gene tuf. This assay enabled the amplification of DNA within 20 min at a constant temperature of 39 °C. Specificity analysis indicated that all nine common Staphylococcus species were positive and non-Staphylococcus spp. were negative for tuf gene, whereas S. aureus was positive, non-aureus Staphylococci species and non-Staphylococcus spp. were negative for FMN-bgsfp gene, suggesting that duplex MIRA-qPCR exhibited high specificity. Meanwhile, the sensitivity was tested and the limit of detection (LoD) was 3 × 102 CFU/mL. The coefficient variation values ranged from 0.13% to 2.09%, indicating that the assay had good repeatability. Furthermore, all the nine common Staphylococcus species (including S. aureus) could be detected from four kinds of simulated samples and the LoD of S. aureus was 8.56 × 103 CFU/mL. In conclusion, the duplex MIRA-qPCR has advantages of stronger specificity, lower detection threshold, shorter detection time, and simpler operation, which is an effective tool to detect S. aureus and non-aureus Staphylococci spp. infections rapidly.
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- 2022
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19. Establishment and Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Detection of Shewanella Genus
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Keyi Yu, Zhenzhou Huang, Ying Li, Qingbo Fu, Lirong Lin, Shiyao Wu, Hang Dai, Hongyan Cai, Yue Xiao, Ruiting Lan, and Duochun Wang
- Subjects
MALDI-TOF mass spectrometry ,detection ,Shewanella ,multilocus sequence analysis ,establishment and application ,Microbiology ,QR1-502 - Abstract
Shewanella species are widely distributed in the aquatic environment and aquatic organisms. They are opportunistic human pathogens with increasing clinical infections reported in recent years. However, there is a lack of a rapid and accurate method to identify Shewanella species. We evaluated here matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of Shewanella. A peptide mass reference spectra (PMRS) database was constructed for the type strains of 36 Shewanella species. The main spectrum projection (MSP) cluster dendrogram showed that the type strains of Shewanella species can be effectively distinguished according to the different MS fingerprinting. The PMRS database was validated using 125 Shewanella test strains isolated from various sources and periods; 92.8% (n = 116) of the strains were correctly identified at the species level, compared with the results of multilocus sequence analysis (MLSA), which was previously shown to be a method for identifying Shewanella at the species level. The misidentified strains (n = 9) by MALDI-TOF MS involved five species of two groups, i.e., Shewanella algae–Shewanella chilikensis–Shewanella indica and Shewanella seohaensis–Shewanella xiamenensis. We then identified and defined species-specific biomarker peaks of the 36 species using the type strains and validated these selected biomarkers using 125 test strains. Our study demonstrated that MALDI-TOF MS was a reliable and powerful tool for the rapid identification of Shewanella strains at the species level.
- Published
- 2021
- Full Text
- View/download PDF
20. Molecular characterization and antibiotic resistance of Acinetobacter baumannii in cerebrospinal fluid and blood.
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Xiaohong Shi, Hong Wang, Xin Wang, Huaiqi Jing, Ran Duan, Shuai Qin, Dongyue Lv, Yufeng Fan, Zhenzhou Huang, Kyle Stirling, Lei Zhang, and Jiazheng Wang
- Subjects
Medicine ,Science - Abstract
The increasing prevalence of carbapenem-resistant Acinetobacter baumannii (CRAB) caused nosocomial infections generate significant comorbidity and can cause death among patients. Current treatment options are limited. These infections pose great difficulties for infection control and clinical treatment. To identify the antimicrobial resistance, carbapenemases and genetic relatedness of Acinetobacter baumannii isolates from cerebrospinal fluid (CSF) and blood, a total of 50 nonrepetitive CSF isolates and 44 blood isolates were collected. The resistance phenotypes were determined, and polymerase chain reaction (PCR) was performed to examine the mechanisms of carbapenem resistance. Finally, multilocus sequence typing (MLST) was conducted to determine the genetic relatedness of these isolates. It was observed that 88 of the 94 collected isolates were resistant to imipenem or meropenem. Among them, the blaOXA-23 gene was the most prevalent carbapenemase gene, with an observed detection rate of 91.5% (86/94), followed by the blaOXA-24 gene with a 2.1% detection rate (2/94). Among all carbapenem-resistant Acinetobacter baumannii (CRAB) observations, isolates with the blaOXA-23 gene were resistant to both imipenem and meropenem. Interestingly, isolates positive for the blaOXA-24 gene but negative for the blaOXA-23 gene showed an imipenem-sensitive but meropenem-resistant phenotype. The MLST analysis identified 21 different sequence types (STs), with ST195, ST540 and ST208 most frequently detected (25.5%, 12.8% and 11.7%, respectively). 80 of the 94 isolates (85.1%) were clustered into CC92 which showed a carbapenem resistance phenotype (except AB13). Five novel STs were detected, and most of them belong to CRAB. In conclusion, these findings provide additional observations and epidemiological data of CSF and blood A. baumannii strains, which may improve future infection-control measures and aid in potential clinical treatments in hospitals and other clinical settings.
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- 2021
- Full Text
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21. Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis
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Zhenzhou Huang, Keyi Yu, Yujie Fang, Hang Dai, Hongyan Cai, Zhenpeng Li, Biao Kan, Qiang Wei, and Duochun Wang
- Subjects
Vibrio fujianensis ,comparative genomics ,transcriptomics ,environmental adaptability ,cross-agglutination reaction ,salt tolerance ,Biology (General) ,QH301-705.5 - Abstract
The genus Vibrio is ubiquitous in marine environments and uses numerous evolutionary characteristics and survival strategies in order to occupy its niche. Here, a newly identified species, Vibrio fujianensis, was deeply explored to reveal a unique environmental adaptability. V. fujianensis type strain FJ201301T shared 817 core genes with the Vibrio species in the population genomic analysis, but possessed unique genes of its own. In addition, V. fujianensis FJ201301T was predicated to carry 106 virulence-related factors, several of which were mostly found in other pathogenic Vibrio species. Moreover, a comparative transcriptome analysis between the low-salt (1% NaCl) and high-salt (8% NaCl) condition was conducted to identify the genes involved in salt tolerance. A total of 913 unigenes were found to be differentially expressed. In a high-salt condition, 577 genes were significantly upregulated, whereas 336 unigenes were significantly downregulated. Notably, differentially expressed genes have a significant association with ribosome structural component and ribosome metabolism, which may play a role in salt tolerance. Transcriptional changes in ribosome genes indicate that V. fujianensis may have gained a predominant advantage in order to adapt to the changing environment. In conclusion, to survive in adversity, V. fujianensis has enhanced its environmental adaptability and developed various strategies to fill its niche.
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- 2020
- Full Text
- View/download PDF
22. Nonsense-mediated mRNA decay promote C2C12 cell proliferation by targeting PIK3R5
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Zhenzhou Huang, Yishu Peng, Yuhui Wei, and Yanjie Tan
- Subjects
Physiology ,Cell Biology ,Biochemistry - Abstract
Nonsense mediated mRNA decay (NMD) is a highly conserved RNA quality control system, which can specifically clear abnormal mRNA and play an important role in tumorigenesis. Myoblast proliferation plays an important role in the repair of skeletal muscle injury and the development of myosarcoma, and is controlled by a variety of transcription factors and signals. The molecular mechanism by which NMD regulates the proliferation of myoblast cells is not completely clear. In this study, we found that the NMD activity of skeletal muscle is high in 1-week-old mice but decreases gradually with age, corresponding to a weakening capacity for muscle growth and regeneration. Here, we provide evidence that NMD plays an important role in myoblast proliferation and apoptosis. In addition, we found that PIK3R5 is an NMD substrate gene which can inhibit AKT activity and C2C12 cell proliferation. Therefore, NMD can target PIK3R5 to enhance AKT activity, which in turn promotes C2C12 cell proliferation. This study provides new insights into NMD regulatory mechanisms in muscular development and into potential novel therapeutic strategies for muscle atrophy.
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- 2022
23. Genomic analysis reveals high intra-species diversity of
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Zhenzhou, Huang, Keyi, Yu, Songzhe, Fu, Yue, Xiao, Qiang, Wei, and Duochun, Wang
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China ,Shewanella ,Genomic Islands ,Virulence ,Prophages ,Adaptation, Biological ,Genetic Variation ,Genomics ,Microbial Sensitivity Tests ,Anti-Bacterial Agents ,Species Specificity ,Drug Resistance, Bacterial ,Humans ,CRISPR-Cas Systems ,Genome, Bacterial ,Phylogeny - Published
- 2022
24. Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi
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Yang Song, Xinmin Xu, Zhenzhou Huang, Yue Xiao, Keyi Yu, Mengnan Jiang, Shangqi Yin, Mei Zheng, Huan Meng, Ying Han, Yajie Wang, Duochun Wang, and Qiang Wei
- Subjects
plasmid-mediated pathogenicity ,Rhodococcus equi ,rifamycin resistance ,pan-genome ,genomic characteristics ,Microbiology ,QR1-502 - Abstract
Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.
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- 2022
25. Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of
- Author
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Yang, Song, Xinmin, Xu, Zhenzhou, Huang, Yue, Xiao, Keyi, Yu, Mengnan, Jiang, Shangqi, Yin, Mei, Zheng, Huan, Meng, Ying, Han, Yajie, Wang, Duochun, Wang, and Qiang, Wei
- Subjects
Virulence ,Rhodococcus equi ,Humans ,Rifamycins ,Phylogeny ,Plasmids - Published
- 2021
26. Establishment and Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Detection of
- Author
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Keyi, Yu, Zhenzhou, Huang, Ying, Li, Qingbo, Fu, Lirong, Lin, Shiyao, Wu, Hang, Dai, Hongyan, Cai, Yue, Xiao, Ruiting, Lan, and Duochun, Wang
- Subjects
inorganic chemicals ,Shewanella ,multilocus sequence analysis ,establishment and application ,MALDI-TOF mass spectrometry ,detection ,bacteria ,equipment and supplies ,Microbiology ,Original Research - Abstract
Shewanella species are widely distributed in the aquatic environment and aquatic organisms. They are opportunistic human pathogens with increasing clinical infections reported in recent years. However, there is a lack of a rapid and accurate method to identify Shewanella species. We evaluated here matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of Shewanella. A peptide mass reference spectra (PMRS) database was constructed for the type strains of 36 Shewanella species. The main spectrum projection (MSP) cluster dendrogram showed that the type strains of Shewanella species can be effectively distinguished according to the different MS fingerprinting. The PMRS database was validated using 125 Shewanella test strains isolated from various sources and periods; 92.8% (n = 116) of the strains were correctly identified at the species level, compared with the results of multilocus sequence analysis (MLSA), which was previously shown to be a method for identifying Shewanella at the species level. The misidentified strains (n = 9) by MALDI-TOF MS involved five species of two groups, i.e., Shewanella algae–Shewanella chilikensis–Shewanella indica and Shewanella seohaensis–Shewanella xiamenensis. We then identified and defined species-specific biomarker peaks of the 36 species using the type strains and validated these selected biomarkers using 125 test strains. Our study demonstrated that MALDI-TOF MS was a reliable and powerful tool for the rapid identification of Shewanella strains at the species level.
- Published
- 2020
27. Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O’Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015
- Author
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Duochun Wang, Binghuai Lu, Hang Dai, Keyi Yu, Zhenzhou Huang, Hongyan Cai, and Zhenpeng Li
- Subjects
Microbiology (medical) ,Identification ,Sequence analysis ,lcsh:QR1-502 ,Biology ,Microbiology ,Genome ,lcsh:Microbiology ,03 medical and health sciences ,Bacterial Proteins ,Mycology ,Humans ,Phylogeny ,Taxonomy ,030304 developmental biology ,Genetics ,Cross Infection ,0303 health sciences ,Genes, Essential ,Phylogenetic tree ,030306 microbiology ,Proteus ,biology.organism_classification ,Bacterial Typing Techniques ,Housekeeping gene ,Genetic marker ,Multilocus sequence analysis ,bacteria ,Taxonomy (biology) ,Multilocus Sequence Typing ,Research Article - Abstract
Background Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus. Results Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date. Conclusions This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.
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- 2020
28. A multilocus sequence analysis for the taxonomic update and identification of the genus Proteus
- Author
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Duochun Wang, Hang Dai, Zhenzhou Huang, Keyi Yu, Hongyan Cai, Binghuai Lu, and Zhenpeng Li
- Subjects
Sequence analysis ,Evolutionary biology ,Identification (biology) ,Genus Proteus ,Biology - Abstract
Background: The members of the genus Proteus are commonly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species are remain unelucidated. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within genus of Proteus. Results: Of all 223 Proteus strains collected in current study, phylogenetic tree of concatenated five HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided into eleven clusters, which representative of their counterpart species. Meanwhile, phylogenetic trees of the five individual HKGs were also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intra-species distance of HKGs concatenation, all inter-species indicated more significant different distances than those of intra-species, which revealed these HKGs concatenation can be used as gene marker to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA and each of eleven clusters were congruent with eleven different Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus, and found that P. mirabilis is the most species of Proteus. However, the top second is P. terrae, but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, three species, P. terrae, P. cibarius and Proteus genospecies 5 should be regarded as the heterotypic synonyms.Conclusions: Our data suggested the MLSA was a powerful method for the discrimination and classification of the Proteus at species level. The MLSA scheme provides a rapid, economical and precise identification of Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in clinical diagnosis and treatment of Proteus infection.
- Published
- 2020
29. Molecular Characterization and Antibiotic Resistance of Acinetobacter baumannii in Cerebrospinal Fluid and Blood
- Author
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Shuai Qin, Huaiqi Jing, Ran Duan, Xin Wang, Xiaohong Shi, B. Kyle Stirling, Yufeng Fan, Jiazheng Wang, Lei Zhang, Dongyue Lv, Hong Wang, and Zhenzhou Huang
- Subjects
0301 basic medicine ,Acinetobacter baumannii ,Imipenem ,Physiology ,Antibiotics ,Crabs ,Artificial Gene Amplification and Extension ,Pathology and Laboratory Medicine ,Nervous System ,Polymerase Chain Reaction ,law.invention ,law ,Drug Resistance, Multiple, Bacterial ,Medicine and Health Sciences ,polycyclic compounds ,Polymerase chain reaction ,Cerebrospinal Fluid ,Multidisciplinary ,Acinetobacter ,Antimicrobials ,Drugs ,Eukaryota ,Anti-Bacterial Agents ,Body Fluids ,Bacterial Pathogens ,Crustaceans ,Blood ,Medical Microbiology ,Medicine ,Anatomy ,Pathogens ,medicine.drug ,Acinetobacter Infections ,Research Article ,Arthropoda ,medicine.drug_class ,Science ,030106 microbiology ,Microbial Sensitivity Tests ,Biology ,Research and Analysis Methods ,Meropenem ,Microbiology ,beta-Lactamases ,03 medical and health sciences ,Antibiotic resistance ,Bacterial Proteins ,Microbial Control ,medicine ,Humans ,Animals ,Molecular Biology Techniques ,Gene ,Microbial Pathogens ,Molecular Biology ,Pharmacology ,Bacteria ,Organisms ,Biology and Life Sciences ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,bacterial infections and mycoses ,Invertebrates ,030104 developmental biology ,Carbapenems ,Antibiotic Resistance ,Multilocus sequence typing ,Antimicrobial Resistance ,Zoology - Abstract
BackgroundThe increasing rates of carbapenem-resistant Acinetobacter baumannii (CRAB) caused nosocomial infections generate significant comorbidity and sometime cause death among patients. Current treatment options are limited. These infections pose great difficulties for infection control and clinical treatment. This study identifies the antimicrobial resistance, carbapenemases and genetic relatedness of A. baumannii isolates from cerebrospinal fluid (CSF) and blood in a hospital in Shandong, China. Methods A total of 50 nonrepetitive CSF A. baumannii isolates and 44 blood isolates were collected. The resistance phenotypes were determined according to the Clinical and Laboratory Standards Institute guidelines. We performed Polymerase Chain Reaction (PCR) experiments to detect the carbapenem resistance mechanism. Finally, we conducted Multilocus Sequence Typing (MLST) to depict the genetic relatedness of these isolates. Results We observed that eighty-eight of the 94 isolates collected were resistant to imipenem or meropenem. Among them, the bla OXA-23 gene was the most prevalent carbapenemase gene with a 91.5% (86/94) detection rate, followed by the bla OXA-24 gene that showed a 2.1% (2/94) detection rate isolates. Among all CRAB observations in this study, isolates with the bla OXA-23 gene were resistant to both imipenem and meropenem. However, isolates positive for the bla OXA-24 gene but negative for the bla OXA-23 gene showed an imipenem-sensitive but meropenem-resistant phenotype. The outcome of multilocus sequence typing analysis showed 21 different STs were distinguished, of which ST195 (25.5%), ST540 (12.8%) and ST208 (11.7%) were most frequently observed. Eighty of the 94 isolates (85.1%) were clustered into CC92, and all CC92 isolates showed a carbapenem resistance phenotype (except AB13). Five novel STs were detected, and most of them were CRAB, some of which belonged to CC92. Conclusion A high level of carbapenem resistance was detected in this study. The CC92 and bla OXA-23 gene were predominant. Five novel STs were detected, and these new STs require further investigation to understand the nature of and to prevent outbreaks caused by A. baumannii . Our study provides additional observations and epidemiological data of CSF and blood A. baumannii strains, which may improve future infection control measures and aid in potential clinical treatment in hospitals and other clinical settings.
- Published
- 2020
30. Additional file 1 of Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O’Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015
- Author
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Dai, Hang, Binghuai Lu, Zhenpeng Li, Zhenzhou Huang, Hongyan Cai, Keyi Yu, and Duochun Wang
- Abstract
Additional file 1: Figure S1. Intra- and inter-species distances of eleven species infer by five individual genes. In each boxplot, from bottom to top: minimum, median and maximum. Table S1. Intra- and inter-species genetic distance median values and ranges of concatenated 5-gene and five individual genes.
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- 2020
- Full Text
- View/download PDF
31. Proteus alimentorum sp. nov., isolated from pork and lobster in Ma’anshan city, China
- Author
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Hang Dai, Yujie Fang, Duochun Wang, Biao Kan, Zhenzhou Huang, and Yonglu Wang
- Subjects
DNA, Bacterial ,0301 basic medicine ,China ,Swine ,Proteus vulgaris ,Microbiology ,03 medical and health sciences ,RNA, Ribosomal, 16S ,Animals ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Base Composition ,biology ,Phylogenetic tree ,Strain (biology) ,Fatty Acids ,Nucleic Acid Hybridization ,Sequence Analysis, DNA ,General Medicine ,Proteus ,biology.organism_classification ,16S ribosomal RNA ,rpoB ,Proteus mirabilis ,Bacterial Typing Techniques ,Nephropidae ,Red Meat ,030104 developmental biology ,Seafood ,Bacteria - Abstract
Two strains of Gram-stain-negative, facultatively anaerobic short-rod bacteria were recovered from two different food samples in Ma’anshan city, Anhui province, China in 2008. The bacteria were characterized in a polyphasic taxonomic study that included phenotypic, phylogenetic and genotypic methodologies. Phylogenetic analysis of the 16S rRNA gene demonstrated that the two strains belonged to the genus Proteus and were most similar to Proteus vulgaris ATCC 29905T with a score of 99.7 %. Phylogenetic analysis of the rpoB gene placed the two strains into a cluster with a distinctly interspecies phylogenetic branch that was clearly separated from six type strains of the genus Proteus , with the most closely related species being Proteus mirabilis ATCC 29906T. In silico genomic comparisons, including in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) analysis showed that the representative strain, 08MAS0041T, and all six Proteus species share less than 70 % isDDH and have a 95 % ANI cutoff level, supporting the designation of the two strains as a novel species of the genus Proteus . The predominant cellular fatty acids of strain 08MAS0041T were C16 : 0 (24.8 %), C16 : 1ω7c/16 : 1ω6c (16.5 %), C18 : 1ω6c/C18 : 1 ω7c (14.5 %), C17 : 0 cyclo (12.6 %) and C16 : 1iso I/C14 : 0 3-OH (10.6 %). The analysis of biochemical, phylogenetic and genomic data confirmed that the two strains were clearly different from all recognized species of the genus Proteus and represent a novel Proteus species, for which the name Proteus alimentorum sp. nov. is proposed. The type strain is 08MAS0041T (=DSM 104685T=CGMCC 1.15939T).
- Published
- 2018
32. Distribution and characteristics of SGI1/PGI2 genomic island from Proteus strains in China
- Author
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Binghuai Lu, Duochun Wang, Tao Xiao, Zhenpeng Li, Hang Dai, Hongyan Cai, Biao Kan, and Zhenzhou Huang
- Subjects
0301 basic medicine ,Microbiology (medical) ,China ,Genomic Islands ,Klebsiella pneumoniae ,030106 microbiology ,Integron ,Microbiology ,Integrons ,03 medical and health sciences ,Salmonella ,Genomic island ,Drug Resistance, Multiple, Bacterial ,Genetics ,Humans ,Molecular Biology ,Proteus mirabilis ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Phylogenetic tree ,biology ,biology.organism_classification ,Multiple drug resistance ,Proteus ,030104 developmental biology ,Infectious Diseases ,Gene cassette ,GenBank ,biology.protein ,Plasmids - Abstract
The emergence of multidrug-resistant Salmonella genomic island 1 (SGI1) and Proteus genomic island (PGI) bearing P. mirabilis present a serious threat to public health. In this study, we screened 288 Proteus isolates recovered from seven provinces in China. Fourteen strains (4.9%) all belonged to P. mirabilis were positive for SGI1/PGI2, including twelve from clinical samples (5.3%) and two from food (3.3%). A Blastn search against GenBank and phylogenetic analyses identified eight different SGI1 variants and one PGI2 variant from the fourteen SGI1/PGI2 variants. All SGI1 variants shared a common backbone and harbored different resistance gene(s), except the sul1 gene at its multidrug-resistant (MDR) region. Among the variants, three novel SGI1 variants, designated as SGI1-PmCA11, SGI1-PmCA14 and SGI1-PmCA46, contained different gene cassettes, which were similar to sequences in plasmids or class 1 integrons of Klebsiella pneumoniae, P. mirabilis, Escherichia coli and Salmonella. Moreover, one novel PGI2, designated as PGI2-PmCA72, had an identical gene cassette to the first class 1 integron from PGI2 (GenBank accession no. MG201402.1) in P. mirabilis, but varied due to missing, replaced, inserted and inverted gene clusters. The four novel SGI1/PGI2 variants contained the cmlA5, dfrA14, blaOXA-10, aadA15, blaOXA-1, catB3 and dfrA16 resistance genes, which have never been reported in SGI1/PGI2 variants. Phenotypically, all fourteen SGI1/PGI2-containing strains showed multidrug resistance. All except four strains were resistant to the first, or the second and/or-third generation cephalosporins. Considering the increasing number and the emergence of new SGI1/PGI2 variants, further surveillance is needed to prevent the spreading of the MDR genomic islands among Proteus isolates from human and food.
- Published
- 2018
33. Proteus columbae sp. nov., isolated from a pigeon in Ma'anshan, China
- Author
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Yujie Fang, Tao Xiao, Biao Kan, Zhenzhou Huang, Yonglu Wang, Hang Dai, and Duochun Wang
- Subjects
0301 basic medicine ,DNA, Bacterial ,China ,030106 microbiology ,Proteus vulgaris ,Microbiology ,03 medical and health sciences ,Monophyly ,RNA, Ribosomal, 16S ,Animals ,Columbidae ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Base Composition ,biology ,Phylogenetic tree ,Strain (chemistry) ,Fatty Acids ,Nucleic Acid Hybridization ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,16S ribosomal RNA ,rpoB ,Proteus ,Proteus penneri ,Bacterial Typing Techniques ,Genes, Bacterial - Abstract
A Gram-negative, facultatively anaerobic bacillus, strain 08MAS2615T, was isolated from the flesh of a pigeon specimen collected in Ma’anshan, Anhui province, China. Phylogenetic analysis of 16S rRNA gene sequences confirmed that strain 08MAS2615T belonged to the genus Proteus , and formed an independent branch which was clearly separated from the other six known species of Proteus . Strain 08MAS2615T was more closely related to Proteus vulgaris ATCC 29905T and Proteus penneri NCTC 12737T than other Proteus species. Similar independent phylogenetic results were obtained using rpoB gene sequence analysis, whereas strain 08MAS2615T clustered near the species of Proteus cibarius JS9T and Proteus terrae N5/687T. Furthermore, the genome-wide core-single nucleotide polymorphism-based phylogenetic tree confirmed that strain 08MAS2615T formed a monophyletic and robust clade. Based on whole-genome sequences, the range of in silico DNA–DNA hybridization and average nucleotide identity between strain 08MAS2615T and the six Proteus species were 25.5–48.8 % and 82.8–92.9 %, respectively, less than the proposed cutoff level for species delineation, i.e. 70 and 95 %. In addition, the major cellular fatty acid profile of strain 08MAS2615T was C14 : 0 (12.4 %), C16 : 0 (23.8 %), C17 : 0cyclo (14.4 %), summed feature 2 (C16 : 1iso I/C14 : 0 3-OH) (11.0 %), summed feature 3 (C16 : 1ω7c/16 : 1ω6c) (18.5 %) and summed feature 8 (C18 : 1ω6c) (18.6 %). On the basis of these results, strain 08MAS2615T represents a novel species of the genus Proteus , for which the name Proteus columbae sp. nov. is proposed with strain 08MAS2615T (=DSM 104686T=CGMCC 1.15982T) designated as the species type strain.
- Published
- 2018
34. A Novel Herbal Formula Induces Cell Cycle Arrest and Apoptosis in Association With Suppressing the PI3K/AKT Pathway in Human Lung Cancer A549 Cells
- Author
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Meijuan Chen, Haian Fu, Mingyan Wang, Yuping Tang, Kejun Chen, Jing Zhou, Fei Xiong, Miao Jiang, Zhen Zhan, Lihong Ye, Jin-Ao Duan, Xu Zhang, Lian Yin, and Zhenzhou Huang
- Subjects
Lung Neoplasms ,Herbal Medicine ,Mice, Nude ,Antineoplastic Agents ,Apoptosis ,Treatment of lung cancer ,Traditional Chinese medicine ,Pharmacology ,Mice ,Nude mouse ,Carcinoma, Non-Small-Cell Lung ,Cell Line, Tumor ,Animals ,Humans ,Medicine ,Adverse effect ,Lung cancer ,PI3K/AKT/mTOR pathway ,Cell Proliferation ,Phosphoinositide-3 Kinase Inhibitors ,Mice, Inbred BALB C ,biology ,business.industry ,Cancer ,Cell Cycle Checkpoints ,Cell cycle ,medicine.disease ,biology.organism_classification ,Xenograft Model Antitumor Assays ,Gene Expression Regulation, Neoplastic ,Complementary and alternative medicine ,Oncology ,Cancer research ,Female ,Plant Preparations ,Cisplatin ,business ,Proto-Oncogene Proteins c-akt - Abstract
Aim of the study. In recent years, the incidence of lung cancer, as well as the mortality rate from this disease, has increased. Moreover, because of acquired drug resistance and adverse side effects, the effectiveness of current therapeutics used for the treatment of lung cancer has decreased significantly. Chinese medicine has been shown to have significant antitumor effects and is increasingly being used for the treatment of cancer. However, as the mechanisms of action for many Chinese medicines are undefined, the application of Chinese medicine for the treatment of cancer is limited. The formula tested has been used clinically by the China National Traditional Chinese Medicine Master, Professor Zhonging Zhou for treatment of cancer. In this article, we examine the efficacy of Ke formula in the treatment of non–small cell lung cancer and elucidate its mechanism of action. Methods. A Balb/c nude mouse xenograft model using A549 cells was previously established. The mice were randomly divided into normal, mock, Ke, cisplatin (DDP), and co-formulated (Ke + DDP) groups. After 15 days of drug administration, the animals were sacrificed, body weight and tumor volume were recorded, and the tumor-inhibiting rate was calculated. A cancer pathway finder polymerase chain reaction array was used to monitor the expression of 88 genes in tumor tissue samples. The potential antiproliferation mechanism was also investigated by Western blot analysis. Results. Ke formula minimized chemotherapy-related weight loss in tumor-bearing mice without exhibiting distinct toxicity. Ke formula also inhibited tumor growth, which was associated with the downregulation of genes in the PI3K/AKT, MAPK, and WNT/β-catenin pathways. The results from Western blot analyses further indicated that Ke blocked the cell cycle progression at the G1/S phase and induced apoptosis mainly via the PI3K/AKT pathway. Conclusion. Ke formula inhibits tumor growth in an A549 xenograft mouse model with no obvious side effects. Moreover, Ke exhibits synergistic antitumor effects when combined with DDP. The mechanism of action of Ke is to induce cell cycle arrest and apoptosis by suppressing the PI3K/AKT pathway. Further research will be required to determine the mechanism of action behind the synergistic effect of Ke and DDP.
- Published
- 2013
35. Ophiopogonin B-induced autophagy in non-small cell lung cancer cells via inhibition of the PI3K/Akt signaling pathway
- Author
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Kejun Chen, Jing Zhou, Xu Zhang, Yuping Tang, Miao Jiang, Jin-Αo Duan, Fengrong Jiang, Fei Xiong, Yuhong Du, Meijuan Chen, Lian Yin, Min Qui, Zhen Zhan, Lihong Ye, Jianping Chen, Zhenzhou Huang, Hai-Αn Fu, and Mingyan Wang
- Subjects
Cancer Research ,autophagy ,Cytoplasm ,Lung Neoplasms ,Cell ,Biology ,Phosphatidylinositol 3-Kinases ,Carcinoma, Non-Small-Cell Lung ,Cell Line, Tumor ,medicine ,Spirostans ,Humans ,Protein kinase B ,PI3K/AKT/mTOR pathway ,natural medicines ,non-small cell lung cancer ,Cell Proliferation ,Cell growth ,Plant Extracts ,Autophagy ,General Medicine ,Articles ,Cell Cycle Checkpoints ,Cell cycle ,Saponins ,Ophiopogonin B ,Cell biology ,medicine.anatomical_structure ,Oncology ,Apoptosis ,Vacuoles ,Signal transduction ,PI3K/Akt/mTOR ,Microtubule-Associated Proteins ,Proto-Oncogene Proteins c-akt ,Signal Transduction - Abstract
Ophiopogonin B (OP-B) is a bioactive component of Radix Ophiopogon Japonicus, which is often used in Chinese traditional medicine to treat pulmonary disease. However, whether or not OP-B has any potential antitumor activity has not been reported. Here, we show that the non-small cell lung cancer (NSCLC) cell lines NCI-H157 and NCI-H460 treated with OP-B grow more slowly and accumulate vacuoles in their cytoplasm compared to untreated control cells. Flow cytometric analysis showed that the cells were arrested in G0/G1 phase. Nuclear morphology, Annexin-V/PI staining, and expression of cleaved caspase-3 all confirm that OP-B does not induce apoptosis. Instead, based on results from both transmission electron microscopy (TEM) and the expression of microtubule-associated protein 1 light chain 3-II (LC3-II), we determined that OP-B treatment induced autophagy in both cell lines. Next, we examined the PI3K/Akt/mTOR signaling pathway and found that OP-B inhibited phosphorylation of Akt (Ser473, Thr308) in NCI-H157 cells and also inhibited several key components of the pathway in NCI-H460 cells, such as p-Akt(Ser473, Thr308), p-p70S6K (Thr389). Additionally, insulin-mediated activation of the PI3K/Akt/mTOR pathway provides evidence that activation of this pathway may correlate with induction of autophagy in H460 cells. Therefore, OP-B is a prospective inhibitor of PI3K/Akt and may be used as an alternative compound to treat NSCLC.
- Published
- 2012
36. JIN Formula Inhibits Tumorigenesis Pathways in Human Lung Carcinoma Cells and Tumor Growth in Athymic Nude Mice
- Author
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Yuhui Zhou, Ming Jiang, Xu Zhang, Zhen Zhan, Zhenzhou Huang, Jinao Duan, Jian Ma, Luyu Zheng, Fei Xiong, Miao Jiang, and Yuping Tang
- Subjects
Lung ,business.industry ,Phlegm ,Cancer ,Blood stasis ,Traditional Chinese medicine ,Treatment of lung cancer ,respiratory system ,medicine.disease ,medicine.disease_cause ,respiratory tract diseases ,medicine.anatomical_structure ,Immunology ,medicine ,Cancer research ,medicine.symptom ,Lung cancer ,business ,Carcinogenesis - Abstract
Lung cancer as the most common cancer in the world represents a major public health problem (1). Worldwide it has the highest rate of cancer mortality, exceeding the mortality rates of colorectal, breast and prostate cancers combined (2). Despite major advances in the treatment and management of lung cancer, most patients with lung cancer eventually die of this disease. Because conventional therapies have failed to make a major impact on survival, newer approaches are necessary in the battle against lung cancer. The poor lung cancer survival figures argue powerfully for new approaches to control this disease through chemoprevention, which has been defined as the use of agents that could reverse, suppress or completely halt tumor development. Developing novel mechanism-based chemopreventive approaches for lung cancer which humans can accept has become an important goal. Many traditional Chinese medicine (TCM) formulas have been used in cancer therapy. JIN formula, an ancient herbal formula from classical book JIN KUI YAO LUE (Golden Chamber) for the treatment of lung cancer, which is composed of Ophiopogon japonicus 30g, Prepared Rhizoma Pinelliae15g, Ginseng radix 30g, Glycyrrhiza radix 12g, Peach Kernel 15g, Unprepared Coix lachryma jobi seed 30g, Chinese waxgourd seed 30g, and Phragmititis Caulis 30g. TCM theory regarded that lung cancer is related with both deficiency of Qi and Yin, or Qi insufficiency of the Spleen and Lung, as well as pathological changes of Qi stagnation, blood stasis, and accumulation of phlegm and toxin. Whereas, JIN formula could replenish both Qi and Yin, strengthen the Spleen and Lung, clear lung, resolve phlegm, activate blood circulation and remove stasis.
- Published
- 2012
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