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Liu M, Wang M, Huang M, Gao Q, Zhu D, Wang M, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Mao S, Tian B, Sun D, Cheng A. Iron efflux by IetA enhances β-lactam aztreonam resistance and is linked to oxidative stress through cellular respiration in Riemerella anatipestifer. J Antimicrob Chemother 2024; 79:1385-1396. [PMID: 38629469 DOI: 10.1093/jac/dkae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/20/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Riemerella anatipestifer encodes an iron acquisition system, but whether it encodes the iron efflux pump and its role in antibiotic resistance are largely unknown. OBJECTIVES To screen and identify an iron efflux gene in R. anatipestifer and determine whether and how the iron efflux gene is involved in antibiotic resistance. METHODS In this study, gene knockout, streptonigrin susceptibility assay and inductively coupled plasma mass spectrometry were used to screen for the iron efflux gene ietA. The MIC measurements, scanning electron microscopy and reactive oxygen species (ROS) detection were used to verify the role of IetA in aztreonam resistance and its mechanism. Mortality and colonization assay were used to investigate the role of IetA in virulence. RESULTS The deletion mutant ΔietA showed heightened susceptibility to streptonigrin, and prominent intracellular iron accumulation was observed in ΔfurΔietA under excess iron conditions. Additionally, ΔietA exhibited increased sensitivity to H2O2-produced oxidative stress. Under aerobic conditions with abundant iron, ΔietA displayed increased susceptibility to the β-lactam antibiotic aztreonam due to heightened ROS production. However, the killing efficacy of aztreonam was diminished in both WT and ΔietA under anaerobic or iron restriction conditions. Further experiments demonstrated that the efficiency of aztreonam against ΔietA was dependent on respiratory complexes Ⅰ and Ⅱ. Finally, in a duckling model, ΔietA had reduced virulence compared with the WT. CONCLUSION Iron efflux is critical to alleviate oxidative stress damage and β-lactam aztreonam killing in R. anatipestifer, which is linked by cellular respiration.
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Affiliation(s)
- Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Mengying Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Mi Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Qun Gao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Sai Mao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu 611130, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611130, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu 611130, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
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Wang M, Wang S, Wang M, Zhu D, Jia R, Chen S, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Liu M, Cheng A. Functional characterization of RhuB as a second TonB2-dependent hemin receptor in Riemerella anatipestifer CH-1. Microbiol Spectr 2024; 12:e0313323. [PMID: 38376226 PMCID: PMC10986502 DOI: 10.1128/spectrum.03133-23] [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: 08/20/2023] [Accepted: 01/14/2024] [Indexed: 02/21/2024] Open
Abstract
In the previous study, it was shown that Riemerella anatipestifer (R. anatipestifer, RA), a pathogen in ducks and some other birds, encodes a hemin uptake system. The R. anatipestifer hemin uptake receptor RhuR is a TonB2-dependent hemin transporter. However, it remains unclear whether R. anatipestifer encodes additional TonB-dependent hemin transporters. Herein, we demonstrated that R. anatipestifer hemin uptake receptor B (RhuB) of R. anatipestifer CH-1 (RA CH-1) was negatively regulated by iron and mediated by the Fur protein, and knocking out rhuB damaged the ability of RA CH-1 to utilize iron from duck hemoglobin (Hb) but not that from duck serum. Moreover, the ability to use iron from Hb was restored by the expression rhuB in trans. Furthermore, the RhuB of RA CH-1 is a membrane protein, and recombinant RhuB could bind hemin at a 1:1 molar ratio in vitro. Compared to that of ΔtonB1ΔrhuR, the ability of ΔtonB1ΔrhuRΔrhuB to utilize hemin was impaired; meanwhile, compared to that of ΔtonB2ΔrhuR, the hemin utilization ability of ΔtonB2ΔrhuRΔrhuB was not affected, indicating that RhuB is a TonB2-dependent receptor. Compared to ΔrhuB, ΔrhuBΔrhuA did not affect hemin utilization. However, compared to ΔrhuA, ΔrhuBΔrhuA had reduced ability to utilize hemin, suggesting that RhuA relies on RhuB for its activity. Finally, the deletion of rhuB did not affect the virulence of RA CH-1. These results suggested that RhuB encodes a TonB2-dependent hemin receptor. The characterization of the second TonB-dependent receptor in R. anatipestifer enriches our understanding of the hemin uptake system of this bacterium.IMPORTANCEIron is essential for the survival of most bacteria, and hemin of hemoglobin can serve as an important iron source. In our previous studies, we showed that R. anatipestifer CH-1 encodes a TonB2-dependent hemin receptor RhuR, which is involved in hemin uptake. The deletion of rhuR did not abolish hemin utilization by RA CH-1. We hypothesized that additional hemin uptake systems exist in this bacterium. In this study, we identified the second TonB2-dependent hemin receptor RhuB in RA CH-1 through hemin utilization, protein localization, and hemin-binding experiments. The duck infection model showed that the deletion of rhuB did not affect the virulence of RA CH-1. This study is not only important for further understanding the hemin utilization mechanism of R. anatipestifer, but also for enriching the hemin uptake transporters of gram-negative bacteria.
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Affiliation(s)
- Mengying Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Siyi Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Burbick CR, Lawhon SD, Munson E, Thelen E, Zapp A, Wilson A. An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022. J Clin Microbiol 2023; 61:e0084023. [PMID: 37888990 PMCID: PMC10741638 DOI: 10.1128/jcm.00840-23] [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] [Indexed: 10/28/2023] Open
Abstract
Numbers of new and revised microbial taxa are continuously expanding, and the rapid accumulation of novel bacterial species is challenging to keep up with in the best of circumstances. With that in mind, following the template of reports on prokaryotic species isolated from humans, this is now the second publication summarizing new and revised taxa in non-domestic animal species in the Journal of Clinical Microbiology. The majority of new taxa were obtained as part of programs to identify bacteria from mucosal surfaces and the gastrointestinal tract from healthy wildlife. A few notable bacteria included new Erysipelothrix spp. from mammalian and aquatic sources and a novel Bartonella spp. isolated from a rodent, both of which could be considered members of emerging and re-emerging genera with pathogenic potential in humans and animals.
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Affiliation(s)
- Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Anastasia Wilson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142622. [PMID: 36719221 PMCID: PMC9945501 DOI: 10.1128/jcm.01426-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.
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Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021. J Clin Microbiol 2023; 61:e0028222. [PMID: 36533910 PMCID: PMC9879126 DOI: 10.1128/jcm.00282-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
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Draft Genome Sequence of Mycolicibacterium smegmatis VKM Ac-1171 Contains Full Set of Sterol Catabolic Genes. Microbiol Resour Announc 2022; 11:e0077222. [DOI: 10.1128/mra.00772-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mycolicibacterium smegmatis
VKM Ac-1171 is a saprotrophic bacterium that was isolated several decades ago and is deposited in microbial collections around the world. We report here a draft genome sequence of the strain. Annotation of the genome revealed the presence of a complete set of genes related to the sterol catabolic pathway.
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Kim I, Chhetri G, Kim J, So Y, Seo T. Quadrisphaera setariae sp. nov., polyphosphate-accumulating bacterium occurring as tetrad or aggregate cocci and isolated from Setaria viridis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005465] [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 Gram-stain-positive, orange-pigmented, aerobic, cocci (occurring in tetrads), non-spore-forming, non-motile bacterium, designated as DD2AT, was isolated from Setaria viridis collected at Dongguk University, Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene revealed that strain DD2AT was most closely related to type strains of the genus
Quadrisphaera
. Strain DD2AT showed the highest 16S rRNA gene sequence similarities to
Quadrisphaera oryzae
TBRC 8486T (99.4 %) and
Quadrisphaera granulorum
JCM 16010T (98.8 %). Strain DD2AT also showed auto-aggregation ability. The digital DNA–DNA hybridization values between strain DD2AT and the reference strains,
Q. oryzae
TBRC 8486T and
Q. granulorum
JCM 16010T were 31.1 and 27.4 %, respectively. The average nucleotide identity values between strain DD2AT and
Q. oryzae
TBRC 8486T and
Q. granulorum
JCM 16010T were 86.3 and 84.1 %, respectively. The major polar lipids of strain DD2AT were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acid of strain DD2AT was anteiso-C15 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid (which is a diagnostic cell-wall diamino acid), alanine and glutamic acid. The respiratory quinones was found to be menaquinone-8. The DNA G+C content of strain DD2AT was 74.8 mol%. On the basis of the findings of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain DD2AT was considered to represent a novel member in the genus
Quadrisphaera
, for which the name Quadrisphaera setariae sp. nov. is proposed. The type strain of Quadrisphaera setariae is DD2AT (=KACC 21165T=NBRC 113770T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
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Abstract
The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice while minimizing difficulties. Adoption of linguistic pragmatism-obeying the rules while treating recommendations as merely optional-will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.
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Affiliation(s)
- M.J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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Gnangui SLE, Fossou RK, Ebou A, Amon CER, Koua DK, Kouadjo CGZ, Cowan DA, Zézé A. The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d'Ivoire. Microorganisms 2021; 9:microorganisms9091842. [PMID: 34576737 PMCID: PMC8472840 DOI: 10.3390/microorganisms9091842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/17/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023] Open
Abstract
Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.
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Affiliation(s)
- Sara Laetitia Elphège Gnangui
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Correspondence:
| | - Anicet Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
| | - Dominique Kadio Koua
- Équipe Bioinformatique, Département de Formation et de Recherche Agriculture et Ressources Animales, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro 1313, Côte d’Ivoire;
| | - Claude Ghislaine Zaka Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, 01 Abidjan 1740, Côte d’Ivoire;
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa;
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne (LBVM), Unité Mixte de Recherche et d’Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Felix Houphouët-Boigny, Yamoussoukro 1093, Côte d’Ivoire; (S.L.E.G.); (A.E.); (C.E.R.A.); (A.Z.)
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