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Hao F, Liu X, Zhou B, Tian Z, Zhou L, Zong H, Qi J, He J, Zhang Y, Zeng P, Li Q, Wang K, Xia K, Guo X, Li L, Shao W, Zhang B, Li S, Yang H, Hui L, Chen W, Peng L, Liu F, Rong ZQ, Peng Y, Zhu W, McCallum JA, Li Z, Xu X, Yang H, Macknight RC, Wang W, Cai J. Chromosome-level genomes of three key Allium crops and their trait evolution. Nat Genet 2023; 55:1976-1986. [PMID: 37932434 DOI: 10.1038/s41588-023-01546-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/20/2023] [Indexed: 11/08/2023]
Abstract
Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.
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Affiliation(s)
- Fei Hao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xue Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Lina Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jiyan Qi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Juan He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yongting Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Peng Zeng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Qiong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Kai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Keke Xia
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
- BGI Research, Wuhan, China
| | - Li Li
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Wenwen Shao
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | | | - Shengkang Li
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Haifeng Yang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Linchong Hui
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Wei Chen
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Lixin Peng
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Feipeng Liu
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, China
| | - Zi-Qiang Rong
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenbo Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - John A McCallum
- The New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Hui Yang
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | | | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
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Barbu IC, Gheorghe-Barbu I, Grigore GA, Vrancianu CO, Chifiriuc MC. Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors. Int J Mol Sci 2023; 24:7892. [PMID: 37175597 PMCID: PMC10178704 DOI: 10.3390/ijms24097892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.
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Affiliation(s)
- Ilda Czobor Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Georgiana Alexandra Grigore
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050044 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
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CRISPR in Modulating Antibiotic Resistance of ESKAPE Pathogens. Mol Biotechnol 2023; 65:1-16. [PMID: 35939207 DOI: 10.1007/s12033-022-00543-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 07/13/2022] [Indexed: 01/11/2023]
Abstract
The ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) isolates both from the clinical settings and food products are demonstrated to gain resistance to multiple antimicrobials. Therefore, the ESKAPE pathogens pose a serious threat to public health, which warrants specific attention to developing alternative novel therapeutics. The clustered regularly interspaced short palindromic repeats associated (CRISPR-Cas) system is one of the novel methods for managing antibiotic-resistant strains. Specific Cas nucleases can be programmed against bacterial genomic sequences to decrease bacterial resistance to antibiotics. Moreover, a few CRISPR-Cas nucleases have the ability to the sequence-specific killing of bacterial strains. However, some pathogens acquire antibiotic resistance due to the presence of the CRISPR-Cas system. In brief, there is a wide range of functional diversity of CRISPR-Cas systems in bacterial pathogens. Hence, to be an effective and safe infection treatment strategy, a comprehensive understanding of the role of CRISPR-Cas systems in modulating antibiotic resistance in ESKAPE pathogens is essential. The present review summarizes all the mechanisms by which CRISPR confers and prevents antibiotic resistance in ESKAPE. The review also emphasizes the relationship between CRISPR-Cas systems, biofilm formation, and antibiotic resistance in ESKAPE.
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Afeke I, Adu-Amankwaah J, Nyarko M, Bushi A, Ablordey AS, Duah PA, I Wowui P, Orish VN. Acinetobacter baumannii-induced infective endocarditis: new insights into pathophysiology and antibiotic resistance mechanisms. Future Microbiol 2022; 17:1335-1344. [DOI: 10.2217/fmb-2021-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Infective endocarditis (IE), characterized by inflammation of the endocardial surface of the heart and its valves, results from infections caused by Staphylococcus, Streptococcus and Acinetobacter species and less commonly fungi. Acinetobacter-induced IE is a relatively rare condition with significant morbidity and mortality worldwide. Notably, its mortality rate is greater than that of endocarditis induced by Haemophilus species, Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens and Kingella kingae. Although it is rare, Acinetobacter-induced IE caused by A. baumannii might bring unique therapeutic challenges such as increased antibiotic resistance. Therefore, it is vital to understand perfectly the possible pathophysiologic and antibiotic resistance mechanisms adopted by A. baumannii during IE. This review discusses the probable underlying pathomechanisms involved in A. baumannii-induced IE and highlights the potential antibiotic resistance mechanisms, suggesting therapeutic targets for A. baumannii-induced IE.
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Affiliation(s)
- Innocent Afeke
- Department of Medical Laboratory Sciences, School of Allied Health Sciences, University of Health & Allied Sciences, PM 31, Ho, Volta Region, Ghana
| | - Joseph Adu-Amankwaah
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
- Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Mary Nyarko
- Department of Nursing & Midwifery, Pentecost University, Sowutuom, Ghana
| | - Aisha Bushi
- Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Anthony S Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Priscilla A Duah
- Department of Pharmacy, Nanjing Technology University, Nanjing, Jiangsu, China
| | - Prosperl I Wowui
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
- Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Verner N Orish
- Department of Microbiology & Immunology, School of Medicine, University of Health & Allied Sciences, Ho, Ghana
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Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890. PLoS One 2022; 17:e0264374. [PMID: 35263355 PMCID: PMC8906637 DOI: 10.1371/journal.pone.0264374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/09/2022] [Indexed: 11/24/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic gram-negative bacteria typically attributed to hospital-associated infection. It could also become multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) during a short period. Although A. baumannii has been documented extensively, complete knowledge on the antibiotic-resistant mechanisms and virulence factors responsible for pathogenesis has not been entirely elucidated. This study investigated the drug resistance pattern and characterized the genomic sequence by de novo assembly of PDR A. baumannii strain VJR422, which was isolated from a catheter-sputum specimen. The results showed that the VJR422 strain was resistant to any existing antibiotics. Based on de novo assembly, whole-genome sequences showed a total genome size of 3,924,675-bp. In silico and conventional MLST analysis of sequence type (ST) of this strain was new ST by Oxford MLST scheme and designated as ST1890. Moreover, we found 10,915 genes that could be classified into 45 categories by Gene Ontology (GO) analysis. There were 1,687 genes mapped to 34 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The statistics from Clusters of Orthologous Genes (COG) annotation identified 3,189 genes of the VJR422 strain. Regarding the existence of virulence factors, a total of 59 virulence factors were identified in the genome of the VJR422 strain by virulence factors of pathogenic bacteria databases (VFDB). The drug-resistant genes were investigated by searching in the Comprehensive Antibiotic Resistance Database (CARD). The strain harbored antibiotic-resistant genes responsible for aminoglycoside, β-lactam-ring-containing drugs, erythromycin, and streptogramin resistance. We also identified resistance-nodulation-cell division (RND) and the major facilitator superfamily (MFS) associated with the antibiotic efflux pump. Overall, this study focused on A. baumannii strain VJR422 at the genomic level data, i.e., GO, COG, and KEGG. The antibiotic-resistant genotype and phenotype as well as the presence of potential virulence associated factors were investigated.
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Pourhajibagher M, Talaei N, Bahador A. Evaluation of antimicrobial effects of photo-sonodynamic antimicrobial chemotherapy based on nano-micelle curcumin on virulence gene expression patterns in Acinetobacter baumannii. Infect Disord Drug Targets 2021; 22:e201221199163. [PMID: 34931970 DOI: 10.2174/1871526522666211220121725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/30/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Abaumannii baumannii rapidly resistance to a wide range of antimicrobial agents. The combination of antimicrobial photodynamic therapy (aPDT) and sonodynamic antimicrobial chemotherapy (SACT) known as photo-sonodynamic antimicrobial chemotherapy (PSACT) has received considerable attention as one of the emerging and promising strategies against microbial infections. OBJECTIVE This study aimed to investigate the antimicrobial effects of PSACT based on nano-micelle curcumin (N-MCur) on the virulence gene expression patterns in A. baumannii. MATERIALS AND METHODS N-MCur as a photo-sonosensitizer was synthesized and confirmed. To determine sub-significant reduction dose of PSACT, sub-significant reduction dose of N-MCur and blue laser light during aPDT, and ultrasound power output during SACT were assessed. Finally, changes in the expression of genes involved in treated A. baumannii by minimum sub-significant reduction dose of PSACT were determined using quantitative real-time-PCR (qRT-PCR). RESULTS PSACT using 12.5 mM N-MCur at the ultrasound power outputs of 28.7, 36.9, and 45.2 mW/cm2 with 4 min irradiation time of blue laser, as well as, 6.2 mM N-MCur at an ultrasound power output of 45.2 mW/cm2 plus 3 min blue laser irradiation time exhibited the significant dose-dependent reduction against A. baumannii cell viability compared to the control group (P<0.05). After treatment of A. baumannii using 3.1 mM N-MCur + 2 min blue laser irradiation time + 28.7 mW/cm2 ultrasound as the minimum sub-significant reduction doses of PSACT, mRNA expression was significantly upregulated to 6.0-, 11.2-, and 13.7-folds in recA, blsA, and dnaK and downregulated to 8.6-, 10.1-, and 14.5-folds in csuE, espA, and abaI, respectively. CONCLUSIONS N-MCur-mediated PSACT could regulate the expression of genes involved in A. baumannii pathogenesis. Therefore, PSACT can be proposed as a promising application to treat infections caused by A. baumannii.
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Affiliation(s)
- Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Narjes Talaei
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Wagner DD, Carleton HA, Trees E, Katz LS. Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks. PeerJ 2021; 9:e12446. [PMID: 34900416 PMCID: PMC8627651 DOI: 10.7717/peerj.12446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Background Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon WGS data quality. Methods Raw, unprocessed WGS reads from Escherichia coli, Salmonella enterica, and Shigella sonnei outbreak clusters were characterized for four quality metrics: PHRED score, read length, library insert size, and ambiguous nucleotide composition. PHRED scores were strongly correlated with improved SNPs analysis results in E. coli and S. enterica clusters. Results Assembly quality showed only moderate correlations with PHRED scores and library insert size, and then only for Salmonella. To improve SNP analyses and assemblies, we compared seven read-healing pipelines to improve these four quality metrics and to see how well they improved SNP analysis and genome assembly. The most effective read healing pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or both. The Lyve-SET SNPs pipeline showed a more marked improvement than the CFSAN SNP Pipeline, but the latter performed better on raw, unhealed reads. For genome assembly, SPAdes enabled significant improvements in healed E. coli reads only, while Skesa yielded no significant improvements on healed reads. Conclusions PHRED scores will continue to be a crucial quality metric albeit not of equal impact across all types of analyses for all enteric bacteria. While trimming-based read healing performed well for SNPs analyses, different read healing approaches are likely needed for genome assembly or other, emerging WGS analysis methodologies.
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Affiliation(s)
- Darlene D Wagner
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.,Eagle Medical Services, LLC, Atlanta, GA, United States of America
| | - Heather A Carleton
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Eija Trees
- Association of Public Health Laboratories, Silver Spring, MD, United States of America
| | - Lee S Katz
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.,Center for Food Safety, University of Georgia, Griffin, GA, United States of America
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Yang H, Huang J, Hu X, Hu M, Zhang Q, Jin M. Comparative Genome Analysis of Streptococcus suis Serotype 9 Isolates from China, The Netherland, and the U.K. Life (Basel) 2021; 11:life11121324. [PMID: 34947855 PMCID: PMC8707284 DOI: 10.3390/life11121324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Streptococcus suis (S. suis) is an important swine pathogen and an emerging zoonotic agent worldwide. Serotype 9 is the most prevalent serotype in several European countries but it is relatively rare in China. In this study, through the investigation of the serotypes of 279 S. suis strains isolated from China from 2015 to 2017, it was found that serotype 9 is the second most prevalent serotype (43 out of 279), behind serotype 2 (83 out of 279). Next, the 43 serotype 9 isolates were sequenced and compared with those from the Netherland (28) and the U.K. (eight). For the purpose of comparison, the strain D12 (GCA_000231905), which has completed genome sequences, was also incorporated. Phylogenetic tree analysis showed that the strains from China and the U.K. were heterogeneous. In contrast, all but one from the Netherland belonged to the same clade. The dominant clades of Chinese strains (33) and strains from the Netherland (27) were very similar. Both of them may have originated from the same strain about 70 years ago. Then, the distributions of virulence-associated genes and antibiotic resistance genes among different clades and sources were analyzed. By comparison, strains from the Netherland carried more virulence-associated genes and those from the U.K. had more antibiotic resistance genes. Additionally, some virulence-associated genes (salK and salR) and antibiotic resistance genes (lincomycin and spectinomycin) existed only in several Chinese strains. In conclusion, our data displayed the population characteristics and differences of S. suis serotype 9 between China and Europe, suggesting that they have taken different evolutionary paths.
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Affiliation(s)
- Huanhuan Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (H.Y.); (J.H.); (X.H.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jingjing Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (H.Y.); (J.H.); (X.H.)
| | - Xiaotong Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (H.Y.); (J.H.); (X.H.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
| | - Min Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
| | - Qiang Zhang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (Q.Z.); (M.J.)
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (H.Y.); (J.H.); (X.H.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan 430070, China
- Correspondence: (Q.Z.); (M.J.)
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Chen H, Li J, Yan S, Sun H, Tan C, Liu M, Liu K, Zhang H, Zou M, Xiao X. Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study. PeerJ 2021; 9:e11699. [PMID: 34249516 PMCID: PMC8253115 DOI: 10.7717/peerj.11699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/08/2021] [Indexed: 02/01/2023] Open
Abstract
Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.
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Affiliation(s)
- Huan Chen
- Postdoctoral Research Station of Clinical Medicine & Department of Hematology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Shanshan Yan
- Department of Intensive Medicine, Third Xiangya Hospital, Central South University, Changsha, China
| | - Hui Sun
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Chuyi Tan
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Meidong Liu
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ke Liu
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Huali Zhang
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Mingxiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Xianzhong Xiao
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, China
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Pan-Resistome Insights into the Multidrug Resistance of Acinetobacter baumannii. Antibiotics (Basel) 2021; 10:antibiotics10050596. [PMID: 34069870 PMCID: PMC8157372 DOI: 10.3390/antibiotics10050596] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 02/02/2023] Open
Abstract
Acinetobacter baumannii is an important Gram-negative opportunistic pathogen that is responsible for many nosocomial infections. This etiologic agent has acquired, over the years, multiple mechanisms of resistance to a wide range of antimicrobials and the ability to survive in different environments. In this context, our study aims to elucidate the resistome from the A. baumannii strains based on phylogenetic, phylogenomic, and comparative genomics analyses. In silico analysis of the complete genomes of A. baumannii strains was carried out to identify genes involved in the resistance mechanisms and the phylogenetic relationships and grouping of the strains based on the sequence type. The presence of genomic islands containing most of the resistance gene repertoire indicated high genomic plasticity, which probably enabled the acquisition of resistance genes and the formation of a robust resistome. A. baumannii displayed an open pan-genome and revealed a still constant genetic permutation among their strains. Furthermore, the resistance genes suggest a specific profile within the species throughout its evolutionary history. Moreover, the current study performed screening and characterization of the main genes present in the resistome, which can be used in applied research to develop new therapeutic methods to control this important bacterial pathogen.
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Acinetobacter baumannii Antibiotic Resistance Mechanisms. Pathogens 2021; 10:pathogens10030373. [PMID: 33808905 PMCID: PMC8003822 DOI: 10.3390/pathogens10030373] [Citation(s) in RCA: 190] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative ESKAPE microorganism that poses a threat to public health by causing severe and invasive (mostly nosocomial) infections linked with high mortality rates. During the last years, this pathogen displayed multidrug resistance (MDR), mainly due to extensive antibiotic abuse and poor stewardship. MDR isolates are associated with medical history of long hospitalization stays, presence of catheters, and mechanical ventilation, while immunocompromised and severely ill hosts predispose to invasive infections. Next-generation sequencing techniques have revolutionized diagnosis of severe A. baumannii infections, contributing to timely diagnosis and personalized therapeutic regimens according to the identification of the respective resistance genes. The aim of this review is to describe in detail all current knowledge on the genetic background of A. baumannii resistance mechanisms in humans as regards beta-lactams (penicillins, cephalosporins, carbapenems, monobactams, and beta-lactamase inhibitors), aminoglycosides, tetracyclines, fluoroquinolones, macrolides, lincosamides, streptogramin antibiotics, polymyxins, and others (amphenicols, oxazolidinones, rifamycins, fosfomycin, diaminopyrimidines, sulfonamides, glycopeptide, and lipopeptide antibiotics). Mechanisms of antimicrobial resistance refer mainly to regulation of antibiotic transportation through bacterial membranes, alteration of the antibiotic target site, and enzymatic modifications resulting in antibiotic neutralization. Virulence factors that may affect antibiotic susceptibility profiles and confer drug resistance are also being discussed. Reports from cases of A. baumannii coinfection with SARS-CoV-2 during the COVID-19 pandemic in terms of resistance profiles and MDR genes have been investigated.
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Esmaeili A, Hosseini S, Baghaban Eslaminejad M. Engineered-extracellular vesicles as an optimistic tool for microRNA delivery for osteoarthritis treatment. Cell Mol Life Sci 2021; 78:79-91. [PMID: 32601714 PMCID: PMC11072722 DOI: 10.1007/s00018-020-03585-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 06/13/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
Worldwide, osteoarthritis (OA) is one of the most common chronic diseases. In OA, profiling gene expression changes occur and cartilage tissue homeostasis is lost. Suggestions for OA treatment include regulation of gene expressions via the use of microRNAs (miRNAs). However, problems exist with the use of miRNAs, the most important of which is the delivery of sufficient amounts of effective miRNAs to save cartilage tissue. The engineering of extracellular vesicles (EVs) with the use of advanced techniques would be an efficient OA treatment. Therefore, we discuss the importance of miRNAs in terms of cartilage tissue regeneration and review recent advances in production of enriched EVs and miRNA delivery by EVs for future clinical applications.
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Affiliation(s)
- Abazar Esmaeili
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Samaneh Hosseini
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Cell Engineering, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mohamadreza Baghaban Eslaminejad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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Acinetobacter baumannii as a community foodborne pathogen: Peptide mass fingerprinting analysis, genotypic of biofilm formation and phenotypic pattern of antimicrobial resistance. Saudi J Biol Sci 2020; 28:1158-1166. [PMID: 33424412 PMCID: PMC7783781 DOI: 10.1016/j.sjbs.2020.11.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 01/02/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common Gram-negative pathogens that represent a major threat to human life. Because the prevalence of Multidrug-resistant biofilm-forming A. baumannii is increasing all over the world, this may lead to outbreaks of hospital infections. Nonetheless, the role of raw meat as a reservoir for A. baumannii remains unclear. Here our research was aimed to exhibit the frequency, precise identification, and genotyping of biofilm-related genes as well as antimicrobial resistance of A. baumannii isolates of raw meat specimens. Fifty-five A. baumannii strains were recovered from 220 specimens of different animal meat and then identified by Peptide Mass Fingerprinting Technique (PMFT). All identified isolates were genotyped by the qPCR method for the existence of biofilm-related genes (ompA, bap, blaPER-1, csuE, csgA, and fimH). In addition, the antimicrobial resistance against A. baumannii was detected by the Kirby-Bauer method. Based on our findings, the frequency rate of 55 A. baumannii isolates was 46.55%, 32.50%, 15.00%, and 9.68% of sheep, chicken, cow, and camel raw meat samples, respectively. The PMFT was able to identify all strains by 100%. the percentages of csuE, ompA, blaPER-1, bap, and csgA genes in biofilm and non-biofilm producer A. baumannii were 72.73%, 60%, 58.2%, 52.74%, and 25.45%, respectively. In contrast, the fimH was not detected in all non-biofilm and biofilm producer strains. The ompA, bap, blaPER-1, csgA were detected only in biofilm-producing A. baumannii isolates. The maximum degree of resistance was observed against amoxicillin/clavulanic acid (89.10%), gentamicin (74.55%), tetracycline (72.73%), ampicillin (65.45%), and tobramycin (52.73%). In conclusion, our investigation demonstrated the high incidence of multi-drug resistant A. baumannii in raw meat samples, with a high existence of biofilm-related virulence genes of ompA, bap, blaPER-1, csgA. Therefore, it has become necessary to take the control measures to limit the development of A. baumannii.
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Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii. Microorganisms 2020; 8:microorganisms8060935. [PMID: 32575913 PMCID: PMC7355832 DOI: 10.3390/microorganisms8060935] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/19/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections.
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Lal Gupta C, Kumar Tiwari R, Cytryn E. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes. ENVIRONMENT INTERNATIONAL 2020; 138:105667. [PMID: 32234679 DOI: 10.1016/j.envint.2020.105667] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.
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Affiliation(s)
- Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel
| | - Rohit Kumar Tiwari
- Department of Biosciences, Integral University, Lucknow 226026, UP, India
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel.
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Ganeshbabu M, Kannan N, Venkatesh PS, Paulraj G, Jeganathan K, MubarakAli D. Synthesis and characterization of BiVO4 nanoparticles for environmental applications. RSC Adv 2020; 10:18315-18322. [PMID: 35517221 PMCID: PMC9053757 DOI: 10.1039/d0ra01065k] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/27/2020] [Indexed: 11/21/2022] Open
Abstract
In the present study, a chemical precipitation method is adopted to synthesize bismuth vanadate nanoparticles. The calcination temperature dependent photocatalytic and antibacterial activities of BiVO4 nanoparticles are examined. The structural analysis evidences the monoclinic phase of BiVO4 nanoparticles, where the grain size increases with calcination temperature. Interestingly, BiVO4 nanoparticles calcined at 400 °C exhibit superior photocatalytic behaviour against methylene blue dye (K = 0.02169 min−1) under natural solar irradiation, which exhibits good stability for up to three cycles. The evolution of antibacterial activity studies using a well diffusion assay suggest that the BiVO4 nanoparticles calcined at 400 °C can act as an effective growth inhibitor of pathogenic Gram-negative (P. aeruginosa & A. baumannii) and Gram-positive bacteria (S. aureus). In the present study, a chemical precipitation method is adopted to synthesize bismuth vanadate nanoparticles.![]()
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Affiliation(s)
- M. Ganeshbabu
- Nanomaterials Laboratory
- Department of Physics
- Sri S. Ramasamy Naidu Memorial College
- Sattur-626 203
- India
| | - N. Kannan
- Nanomaterials Laboratory
- Department of Physics
- Sri S. Ramasamy Naidu Memorial College
- Sattur-626 203
- India
| | - P. Sundara Venkatesh
- Nanomaterials Laboratory
- Department of Physics
- Sri S. Ramasamy Naidu Memorial College
- Sattur-626 203
- India
| | - G. Paulraj
- Centre for Nanoscience and Nanotechnology
- Department of Physics
- Bharathidasan University
- Tiruchirappalli-620 024
- India
| | - K. Jeganathan
- Centre for Nanoscience and Nanotechnology
- Department of Physics
- Bharathidasan University
- Tiruchirappalli-620 024
- India
| | - D. MubarakAli
- School of Life Sciences
- B. S. Abdul Rahman Crescent Institute of Science and Technology
- Chennai-600 048
- India
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Sprigg K, Pietrangeli CE. Bacterial Antibiotic Resistance: on the Cusp of a Post-antibiotic World. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2019. [DOI: 10.1007/s40506-019-0181-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tavakol M, Momtaz H, Mohajeri P, Shokoohizadeh L, Tajbakhsh E. Genotyping and distribution of putative virulence factors and antibiotic resistance genes of Acinetobacter baumannii strains isolated from raw meat. Antimicrob Resist Infect Control 2018; 7:120. [PMID: 30323923 PMCID: PMC6172801 DOI: 10.1186/s13756-018-0405-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Background Acinetobacter baumannii strains with multiple antimicrobial resistance are primarily known as opportunistic nosocomial bacteria but they may also be regarded as emerging bacterial contaminants of food samples of animal origin. Here we aimed to study the molecular characteristics of the A. baumanni strains isolated from raw meat samples. Methods A total of 22 A. baumanni strains were isolated from 126 animal meat samples and were genotyped by ERIC-PCR method and by PCR detection of their virulence and antimicrobial resistance determinants. A. baumannii strains with 80% and more similarities were considered as one cluster. Results Sixteen different genetic clusters were found amongst the 22 A. baumanni strains. Of the 22 strains, 12 (54.54%) had similar genetic cluster. A. baumannii strains exhibited the highest percentage of resistance against tetracycline (90.90%), trimethoprim (59.09%), cotrimoxazole (54.54%) and gentamicin (50.00%). TetA (81.81%), tetB (72.72%), dfrA1 (63.63%), aac(3)-IV (63.63%), sul1 (63.63%) and aadA1 (45.45%) were the most commonly detected antibiotic resistance genes. FimH (81.81%), afa/draBC (63.63%), csgA (63.63%), cnf1 (59.09%), cnf2 (54.54%) and iutA (50.00%) were the most commonly detected virulence factors. A. baumannii strains isolated from the chicken meat samples had the highest similarities in the genetic cluster. Conclusions A. baumannii strains with similar genetic cluster (ERIC-Type) had the same prevalence of antibiotic resistance, antibiotic resistance genes and virulence factors. Genetic cluster of the A. baumannii strains is the main factor affected the similarities in the genotypic and phenotypic properties of the A. baumannii strains.
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Affiliation(s)
- Marziyeh Tavakol
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, PO. Box: 166, Shahrekord, Iran
| | - Hassan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, PO. Box: 166, Shahrekord, Iran
| | - Parviz Mohajeri
- 2Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.,3Nosocomial Infection Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Leili Shokoohizadeh
- 4Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Elahe Tajbakhsh
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, PO. Box: 166, Shahrekord, Iran
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Aslam F, Yasmin A, Thomas T. Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation. Curr Microbiol 2018; 75:1484-1492. [DOI: 10.1007/s00284-018-1549-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 08/06/2018] [Indexed: 11/28/2022]
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Almeida F, Seribelli AA, Medeiros MIC, Rodrigues DDP, de MelloVarani A, Luo Y, Allard MW, Falcão JP. Phylogenetic and antimicrobial resistance gene analysis of Salmonella Typhimurium strains isolated in Brazil by whole genome sequencing. PLoS One 2018; 13:e0201882. [PMID: 30102733 PMCID: PMC6089434 DOI: 10.1371/journal.pone.0201882] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/24/2018] [Indexed: 12/02/2022] Open
Abstract
Whole genome sequencing (WGS) has been used as a powerful technology for molecular epidemiology, surveillance, identification of species and serotype, identification of the sources of outbreaks, among other purposes. In Brazil, there is relatively few epidemiological data on Salmonella. In this study, 90 Salmonella Typhimurium strains had their genome sequenced to uncover the diversity of Salmonella Typhimurium isolated from humans and food, between 1983 and 2013, from different geographic regions in Brazil based on single nucleotide polymorphism (SNP) analysis. A total of 39 resistance genes were identified, such as aminoglycoside, tetracycline, sulfonamide, trimethoprim, beta-lactam, fluoroquinolone, phenicol and macrolide, as well as the occurrence of point mutations in some of the genes such as gyrA, gyrB, parC and parE. A total of 65 (72.2%) out of 90 S. Typhimurium strains studied were phenotypically resistant to sulfonamides, 44 (48.9%) strains were streptomycin resistant, 27 (30%) strains were resistant to tetracycline, 21 (23.3%) strains were gentamicin resistant, and seven (7.8%) strains were resistant to ceftriaxone. In the gyrA gene, it was observed the following amino acid substitutions: Asp(87)→Gly, Asp(87)→Asn, Ser(83)→Phe, Ser(83)→Tyr. Phylogenetic results placed the 90 S. Typhimurium strains into two major clades suggesting the existence of a prevalent subtype, likely more adapted, among strains isolated from humans, with some diversity in subtypes in foods. The variety and prevalence of resistant genes found in these Salmonella Typhimurium strains reinforces their potential hazard for humans and the risk in foods in Brazil.
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Affiliation(s)
- Fernanda Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas–Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/ nº, Ribeirão Preto, SP Brasil
| | - Amanda Aparecida Seribelli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas–Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/ nº, Ribeirão Preto, SP Brasil
| | | | - Dália dos Prazeres Rodrigues
- Laboratório de Enterobactérias, FIOCRUZ/Fundação Instituto Oswaldo Cruz, Avenida Brasil, Pavilhão Rocha Lima, 3°andar, Manguinhos, Rio de Janeiro, RJ, Brasil
| | - Alessandro de MelloVarani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Yan Luo
- Division of Microbiology, Office of Regular Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc W. Allard
- Division of Microbiology, Office of Regular Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
- * E-mail: (JPF); (MA)
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas–Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/ nº, Ribeirão Preto, SP Brasil
- * E-mail: (JPF); (MA)
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Salto IP, Torres Tejerizo G, Wibberg D, Pühler A, Schlüter A, Pistorio M. Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats. Sci Rep 2018; 8:7783. [PMID: 29773850 PMCID: PMC5958079 DOI: 10.1038/s41598-018-26180-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/27/2018] [Indexed: 12/20/2022] Open
Abstract
Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.
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Affiliation(s)
- Ileana P Salto
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
| | - Gonzalo Torres Tejerizo
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstr. 27, D-33615, Bielefeld, Germany
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina.
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Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland. Genes (Basel) 2018; 9:genes9030171. [PMID: 29558450 PMCID: PMC5867892 DOI: 10.3390/genes9030171] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 01/18/2023] Open
Abstract
Listeria monocytogenes is a major human foodborne pathogen that is prevalent in the natural environment and has a high case fatality rate. Whole genome sequencing (WGS) analysis has emerged as a valuable methodology for the classification of L. monocytogenes isolates and the identification of virulence islands that may influence infectivity. In this study, WGS was used to provide an insight into 25 L. monocytogenes isolates from cases of clinical infection in Ireland between 2013 and 2015. Clinical strains were either lineage I (14 isolates) or lineage II (11 isolates), with 12 clonal complexes (CC) represented, of which CC1 (6) and CC101 (4) were the most common. Single nucleotide polymorphism (SNP) analysis demonstrated that clinical isolates from mother-infant pairs (one isolate from the mother and one from the infant) were highly related (3 SNP differences in each) and also identified close similarities between isolates from otherwise distinct cases (1 SNP difference). Clinical strains were positive for common virulence-associated loci and 13 isolates harbour the LIPI-3 locus. Pulsed-field gel electrophoresis (PFGE) was used to compare strains to a database of 1300 Irish food and food processing environment isolates and determined that 64% of clinical pulsotypes were previously encountered in the food or food processing environment. Five of the matching food and food processing environment isolates were sequenced and results demonstrated a correlation between pulsotype and genotype. Overall, the work provides insights into the nature of L. monocytogenes strains currently causing clinical disease in Ireland and indicates that similar isolates can be found in the food or food processing environment.
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Si-Tuan N, Ngoc HM, Hang PTT, Nguyen C, Van PH, Huong NT. New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital. Ann Clin Microbiol Antimicrob 2017; 16:74. [PMID: 29137647 PMCID: PMC5686800 DOI: 10.1186/s12941-017-0250-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
Background Acinetobacter baumannii is an important nosocomial pathogen that can develop multidrug resistance. In this study, we characterized the genome of the A. baumannii strain DMS06669 (isolated from the sputum of a male patient with hospital-acquired pneumonia) and focused on identification of genes relevant to antibiotic resistance. Methods Whole genome analysis of A. baumannii DMS06669 from hospital-acquired pneumonia patients included de novo assembly; gene prediction; functional annotation to public databases; phylogenetics tree construction and antibiotics genes identification. Results After sequencing the A. baumannii DMS06669 genome and performing quality control, de novo genome assembly was carried out, producing 24 scaffolds. Public databases were used for gene prediction and functional annotation to construct a phylogenetic tree of the DMS06669 strain with 21 other A. baumannii strains. A total of 18 possible antibiotic resistance genes, conferring resistance to eight distinct classes of antibiotics, were identified. Eight of these genes have not previously been reported to occur in A. baumannii. Conclusions Our results provide important information regarding mechanisms that may contribute to antibiotic resistance in the DMS06669 strain, and have implications for treatment of patients infected with A. baumannii. Electronic supplementary material The online version of this article (10.1186/s12941-017-0250-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nguyen Si-Tuan
- Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, HCM National University, Ho Chi Minh City, Vietnam. .,Molecular Medicine Laboratory, Faculty of Medical Microbiology, Thong Nhat Dong Nai General Hospital, Bien Hoa City - Dong Nai Province, Vietnam.
| | - Hua My Ngoc
- Faculty of Medical Biochemistry, Thong Nhat Dong Nai General Hospital, Bien Hoa City - Dong Nai Province, Vietnam
| | - Pham Thi Thu Hang
- Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, HCM National University, Ho Chi Minh City, Vietnam.,Department of Microbiology, Faculty of Biology, Ho Chi Minh City University of Natural Science, HCM National University, Ho Chi Minh City, Vietnam
| | - Cuong Nguyen
- Department of Bioinformatics and Medical Statistics, Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Pham Hung Van
- The HCM Society of Clinical Microbiologists, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Huong
- Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology, HCM National University, Ho Chi Minh City, Vietnam
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