1
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Klein JA, Predeus AV, Greissl AR, Clark-Herrera MM, Cruz E, Cundiff JA, Haeberle AL, Howell M, Lele A, Robinson DJ, Westerman TL, Wrande M, Wright SJ, Green NM, Vallance BA, McClelland M, Mejia A, Goodman AG, Elfenbein JR, Knodler LA. Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system. Infect Immun 2024:e0031424. [PMID: 39254346 DOI: 10.1128/iai.00314-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
Providencia alcalifaciens is a Gram-negative bacterium found in various water and land environments and organisms, including insects and mammals. Some P. alcalifaciens strains encode gene homologs of virulence factors found in pathogenic Enterobacterales members, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are pathogenic determinants in P. alcalifaciens is not known. In this study, we investigated P. alcalifaciens-host interactions at the cellular level, focusing on the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1b is widespread in Providencia spp. and encoded on the chromosome. A large plasmid that is present in a subset of P. alcalifaciens strains, primarily isolated from diarrheal patients, encodes for T3SS1a. We show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, lyses its internalization vacuole, and proliferates in the cytosol. This triggers caspase-4-dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1a in entry, vacuole lysis, and cytosolic proliferation is host cell type-specific, playing a more prominent role in intestinal epithelial cells than in macrophages or insect cells. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa and induces mild epithelial damage with negligible fluid accumulation in a T3SS1a- and T3SS1b-independent manner. However, T3SS1b was required for the rapid killing of Drosophila melanogaster. We propose that the acquisition of two T3SS has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.
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Affiliation(s)
- Jessica A Klein
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | | | - Aimee R Greissl
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Mattie M Clark-Herrera
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Eddy Cruz
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jennifer A Cundiff
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Amanda L Haeberle
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Maya Howell
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Aaditi Lele
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Donna J Robinson
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Trina L Westerman
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Marie Wrande
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Sarah J Wright
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Nicole M Green
- Public Health Laboratory, Los Angeles County Department of Public Health, Downey, California, USA
| | - Bruce A Vallance
- Division of Gastroenterology, Hepatology and Nutrition, BC Children's Hospital and the University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California, USA
| | - Andres Mejia
- Comparative Pathology Laboratory, Research Animal Resources and Compliance, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alan G Goodman
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Johanna R Elfenbein
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Leigh A Knodler
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
- Department of Microbiology and Molecular Genetics, Robert Larner College of Medicine at The University of Vermont, Burlington, Vermont, USA
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2
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Bhattacharjee A, Singh AK. Delineating the Acquired Genetic Diversity and Multidrug Resistance in Alcaligenes from Poultry Farms and Nearby Soil. J Microbiol 2024; 62:511-523. [PMID: 38904697 DOI: 10.1007/s12275-024-00129-w] [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: 12/08/2023] [Revised: 01/25/2024] [Accepted: 02/22/2024] [Indexed: 06/22/2024]
Abstract
Alcaligenes faecalis is one of the most important and clinically significant environmental pathogens, increasing in importance due to its isolation from soil and nosocomial environments. The Gram-negative soil bacterium is associated with skin endocarditis, bacteremia, dysentery, meningitis, endophthalmitis, urinary tract infections, and pneumonia in patients. With emerging antibiotic resistance in A. faecalis, it has become crucial to understand the origin of such resistance genes within this clinically significant environmental and gut bacterium. In this research, we studied the impact of antibiotic overuse in poultry and its effect on developing resistance in A. faecalis. We sampled soil and faecal materials from five poultry farms, performed whole genome sequencing & analysis and identified four strains of A. faecalis. Furthermore, we characterized the genes in the genomic islands of A. faecalis isolates. We found four multidrug-resistant A. faecalis strains that showed resistance against vancomycin (MIC >1000 μg/ml), ceftazidime (50 μg/ml), colistin (50 μg/ml) and ciprofloxacin (50 μg/ml). From whole genome comparative analysis, we found more than 180 resistance genes compared to the reference sequence. Parts of our assembled contigs were found to be similar to different bacteria which included pbp1A and pbp2 imparting resistance to amoxicillin originally a part of Helicobacter and Bordetella pertussis. We also found the Mycobacterial insertion element IS6110 in the genomic islands of all four genomes. This prominent insertion element can be transferred and induce resistance to other bacterial genomes. The results thus are crucial in understanding the transfer of resistance genes in the environment and can help in developing regimes for antibiotic use in the food and poultry industry.
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Affiliation(s)
- Abhilash Bhattacharjee
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India
- Department of Botany, Dibrugarh Hanumanbax Surajmall Kanoi College, Dibrugarh, 786001, Assam, India
| | - Anil Kumar Singh
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 220002, India.
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3
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Klein JA, Predeus AV, Greissl AR, Clark-Herrera MM, Cruz E, Cundiff JA, Haeberle AL, Howell M, Lele A, Robinson DJ, Westerman TL, Wrande M, Wright SJ, Green NM, Vallance BA, McClelland M, Mejia A, Goodman AG, Elfenbein JR, Knodler LA. Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.595826. [PMID: 38895369 PMCID: PMC11185699 DOI: 10.1101/2024.06.07.595826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Providencia alcalifaciens is a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. Specific P. alcalifaciens strains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are also pathogenic determinants in P. alcalifaciens is not known. Here we have used P. alcalifaciens 205/92, a clinical isolate, with in vitro and in vivo infection models to investigate P. alcalifaciens -host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS 1b is widespread in Providencia spp. and encoded on the chromosome. T3SS 1a is encoded on a large plasmid that is present in a subset of P. alcalifaciens strains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS 1a in entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS 1a or T3SS 1b was seen in the calf infection model. However, T3SS 1b was required for the rapid killing of Drosophila melanogaster . We propose that the acquisition of two T3SS by horizontal gene transfer has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.
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Dong X, Jia H, Yu Y, Xiang Y, Zhang Y. Genomic revisitation and reclassification of the genus Providencia. mSphere 2024; 9:e0073123. [PMID: 38412041 PMCID: PMC10964429 DOI: 10.1128/msphere.00731-23] [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: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Members of Providencia, although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds. Interestingly, we found that Providencia stuartii and Providencia thailandensis actually fall under the same species, evidenced by an ANI of 98.59% and a dDDH value of 90.4%. By fusing ANI with phylogeny, we have reclassified 545 genomes within this genus into 20 species, including seven unnamed taxa (provisionally titled Taxon 1-7), which can be further subdivided into 23 lineages. Pangenomic analysis identified 1,550 genus-core genes in Providencia, with coenzymes being the predominant category at 10.56%, suggesting significant intermediate metabolism activity. Resistance analysis revealed that most lineages of the genus (82.61%, 19/23) carry a high number of antibiotic-resistance genes (ARGs) and display diverse resistance profiles. Notably, the majority of ARGs are located on plasmids, underscoring the significant role of plasmids in the resistance evolution within this genus. Three species or lineages (P. stuartii, Taxon 3, and Providencia hangzhouensis L12) that possess the highest number of carbapenem-resistance genes suggest their potential influence on clinical treatment. These findings underscore the need for continued surveillance and study of this genus, particularly due to their role in harboring antibiotic-resistance genes. IMPORTANCE The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.
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Affiliation(s)
- Xu Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Guangzhou, China
| | - Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuyun Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanghui Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Guangzhou, China
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5
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Wang P, Li C, Yin Z, Jiang X, Li X, Mu X, Wu N, Chen F, Zhou D. Genomic epidemiology and heterogeneity of Providencia and their blaNDM-1-carrying plasmids. Emerg Microbes Infect 2023; 12:2275596. [PMID: 37874004 PMCID: PMC10796120 DOI: 10.1080/22221751.2023.2275596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Providencia as an opportunistic pathogen can cause serious infection, and moreover the emergence of multi-drug-resistant Providencia strains poses a potentially life-threatening risk to public health. However, a comprehensive genomic study to reveal the population structure and dissemination of Providencia is still lacking. In this study, we conducted a genomic epidemiology analysis on the 580 global sequenced Providencia isolates, including 257 ones sequenced in this study (42 ones were fully sequenced). We established a genome sequence-based species classification scheme for Providencia, redefining the conventional 11 Providencia species into seven genocomplexes that were further divided into 18 genospecies, providing an extensively updated reference for Providencia species discrimination based on the largest Providencia genome dataset to date. We then dissected the profile of antimicrobial resistance genes and the prevalence of multi-drug-resistant Providencia strains among these genocomplexes/genospecies, disclosing the presence of diverse and abundant antimicrobial resistance genes and high resistance ratios against multiple classes of drugs in Providencia. We further dissected the genetic basis for the spread of blaNDM-1 in Providencia. blaNDM-1 genes were mainly carried by five incompatible (Inc) groups of plasmids: IncC, IncW, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001, and the last three were newly designated in this study. By tracking the spread of blaNDM-1-carrying plasmids, IncC, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001 plasmids were found to be highly involved in parallel horizontal transfer or vertical clonal expansion of blaNDM-1 among Providencia. Overall, our study provided a comprehensive genomic view of species differentiation, antimicrobial resistance prevalence, and plasmid-mediated blaNDM-1 dissemination in Providencia.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, People’s Republic of China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiaoyuan Jiang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, People’s Republic of China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Nier Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
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6
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Khataniar A, Das A, Baruah MJ, Bania KK, Rajkhowa S, Al-Hussain SA, Zaki MEA. An Integrative Approach to Study the Inhibition of Providencia vermicola FabD Using C2-Quaternary Indolinones. Drug Des Devel Ther 2023; 17:3325-3347. [PMID: 38024529 PMCID: PMC10657194 DOI: 10.2147/dddt.s427193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Background The present study investigates the potential bioactivity of twelve experimentally designed C-2 quaternary indolinones against Providencia spp., a bacterial group of the Enterobacteriaceae family known to cause urinary tract infections. The study aims to provide insights into the bioactive properties of the investigated compounds and their potential use in developing novel treatments against Providencia spp. The experimental design of indolinones, combined with their unique chemical structure, makes them attractive candidates for further investigation. The results of this research may contribute to the development of novel therapeutic agents to combat Providencia spp. infections. Methods The synthesized indolinones (moL1-moL12) are evaluated to identify any superior activity, particularly focusing on moL12, which possesses aza functionality. The antimicrobial activities of all twelve compounds are tested in triplicates against six different Gram-positive and Gram-negative organisms, including P. vermicola (P<0.05). Computational methods have been employed to assess the pharmacokinetic properties of the compounds. Results Among the synthesized indolinones, moL12 exhibits superior activity compared to the other compounds with similar skeleton but different functional moieties. All six strains tested, including P. vermicola, demonstrated sensitivity to moL12. Computational studies support the pharmacokinetic properties of moL12, indicating acceptable absorption, distribution, metabolism, excretion, and toxicity characteristics. Conclusion Utilizing the PPI approach, we have identified a promising target, FabD, in Gram-negative bacteria. Our analysis has shown that moL12 exhibits significant potential in binding with FabD, thereby, might inhibit cell wall formation, and display superior antimicrobial activity compared to other compounds. Consequently, moL12 may be a potential therapeutic agent that could be used to combat urinary tract infections caused by Providencia spp. The findings of this research hold significant promise for the development of new and effective treatments for bacterial infections.
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Affiliation(s)
- Ankita Khataniar
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, As-786004, India
| | - Abhichandan Das
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, As-786004, India
| | - Manash J Baruah
- Department of Chemical Sciences, Tezpur University, Tezpur, As-784028, India
| | - Kusum K Bania
- Department of Chemical Sciences, Tezpur University, Tezpur, As-784028, India
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, As-786004, India
| | - Sami A Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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7
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El-Sabeh A, Mlesnita AM, Munteanu IT, Honceriu I, Kallabi F, Boiangiu RS, Mihasan M. Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster. BMC Genomics 2023; 24:536. [PMID: 37697273 PMCID: PMC10494377 DOI: 10.1186/s12864-023-09644-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids. RESULTS In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway. CONCLUSIONS The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.
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Affiliation(s)
- Amada El-Sabeh
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | | | | | - Iasmina Honceriu
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
| | - Fakhri Kallabi
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Marius Mihasan
- Faculty of Biology, Alexandru Ioan Cuza University of Iași, Iași, Romania.
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Li Z, Liao F, Ding Z, Chen S, Li D. Providencia manganoxydans sp. nov., a Mn(II)-oxidizing bacterium isolated from heavy metal contaminated soils in Hunan Province, China. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, Gram-negative, rod-shaped bacterial strain designated as LLDRA6T, was isolated from heavy metal contaminated soils collected near a ceased smelting factory at Zhuzhou, Hunan Province, China. Strain LLDRA6T has the ability to oxidize Mn(II) and generate biogenic manganese oxides. The strain can grow in a wide range of temperature from 10–42°C and pH from 5 to 10. Comparative analysis of its complete 16S rRNA gene sequence suggests that strain LLDRA6T is highly similar to species within the genus
Providencia
. The complete genome of LLDRA6T is 4 342 370 bp with 40.18 mol% of G+C content and contains no plasmids. In comparison to the genomes of type strains in
Providencia
, LLDRA6T shows average nucleotide identity values between 76.60 and 80.89 %, and digital DNA–DNA hybridization values in a range of 21.2–24.6 %. Both multilocus sequence analysis and genomic phylogenetics indicate a new taxonomic status for LLDRA6T in
Providencia
. Chemotaxonomic analyses for LLDRA6T show that the predominant cellular fatty acids are C16 : 0, C14 : 0 and cyclo-C17 : 0, accounting for 32.7, 16.1 and 10.3 % of total fatty acids, respectively. The polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids, one unidentified phospholipid and three unidentified lipids. Within the cell wall, ribose and meso-diaminopimelic acid are the characteristic constituents for saccharides and amino acids, respectively. Respiratory quinones on cell membranes are composed of menaquinone (MK) and ubiquinone (coenzyme Q), including MK-8 (100.0 %), Q-7 (13.7 %) and Q-8 (86.3 %). Moreover, the positive results from d-lyxose and d-mannitol fermentation tests indicate that LLDRA6T is totally different from all the type strains within the genus
Providencia
. In summary, strain LLDRA6T represents a novel species in the genus
Providencia
, for which the name Providencia manganoxydans sp. nov. (type strain LLDRA6T=CCTCC AB 2021154T=KCTC 92091T) is proposed.
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Affiliation(s)
- Zongpei Li
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou 412007, PR China
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Fengfeng Liao
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou 412007, PR China
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Zhexu Ding
- Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Sha Chen
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou 412007, PR China
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Ding Li
- Hunan Provincial Engineering Research Center of Lily Germplasm Resource Innovation and Deep Processing, Hunan University of Technology, Zhuzhou 412007, PR China
- School of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China
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Chen W, Liu Z, Lin H, Yang J, Liu T, Zheng J, Long X, Sun Z, Li J, Chen X. Occurrence of blaNDM-1-Positive Providencia spp. in a Pig Farm of China. Antibiotics (Basel) 2022; 11:antibiotics11060713. [PMID: 35740120 PMCID: PMC9219741 DOI: 10.3390/antibiotics11060713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
Antibiotics have been extensively used to ensure the productivity of animals on intensive livestock farms. Accordingly, antimicrobial-resistant organisms, which can be transmitted to humans via the food chain, pose a threat to public health. The Enterobacterium antimicrobial resistance gene, blaNDM-1, is a transmissible gene that has attracted widespread attention. Here, we aimed to investigate the prevalence of Enterobacteriaceae carrying blaNDM-1 on an intensive pig farm. A total of 190 samples were collected from a pig farm in Hunan Province, China. Resistant isolates were selected using MacConkey agar with meropenem and PCR to screen for blaNDM-1-positive isolates. Positive strains were tested for conjugation, antimicrobial susceptibility, and whole-genome sequencing. Four blaNDM-1-positive Providencia strains were obtained, and multidrug resistance was observed in these strains. The structure carrying blaNDM-1 did not conjugate to E. coli J53 after three repeated conjugation assays. This suggests that, in intensive farming, attention should be focused on animal health and welfare to reduce the frequency of antibiotic usage. Carbapenem-resistant Enterobacteriaceae in the breeding industry should be included in systematic monitoring programs, including animal, human, and environmental monitoring programs.
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Affiliation(s)
- Wenxin Chen
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
| | - Zhihong Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
| | - Hongguang Lin
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
| | - Jie Yang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
| | - Ting Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
| | - Jiaomei Zheng
- Changsha Animal and Plant Disease Control Center, Changsha 410003, China;
| | - Xueming Long
- Hunan Provincial Institution of Veterinary Drug and Feed Control, Changsha 410006, China;
| | - Zhiliang Sun
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
| | - Jiyun Li
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (J.L.); (X.C.)
| | - Xiaojun Chen
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China; (W.C.); (Z.L.); (H.L.); (J.Y.); (T.L.); (Z.S.)
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (J.L.); (X.C.)
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