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Liu J, Hao D, Ding X, Shi M, Wang Q, He H, Cheng B, Wang M, Wang Q, Xiang Y, Chen L. Epidemiological investigation and β-lactam antibiotic resistance of Riemerella anatipestifer isolates with waterfowl origination in Anhui Province, China. Poult Sci 2024; 103:103490. [PMID: 38387287 PMCID: PMC10899037 DOI: 10.1016/j.psj.2024.103490] [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: 12/01/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Riemerella anatipestifer (R. anatipestifer) is a highly pathogenic and complex serotypes waterfowl pathogen with inherent resistance to multiple antibiotics. This study was aimed to investigate the antibiotic resistance characteristics and genomic features of R. anatipestifer isolates in Anhui Province, China in 2023. A total of 287 cases were analysed from duck farms and goose farms, and the R. anatipestifer isolates were subjected to drug resistance tests for 30 antimicrobials. Whole genome sequencing (WGS) and bioinformatics analysis were performed on the bacterial genomes, targeting the β-lactam resistance genes. The results showed that a total of 74 isolates of R. anatipestifer were isolated from 287 cases, with a prevalence of 25.8%. The antimicrobial susceptibility testing (AST) revealed that all the 74 isolates were resistant to multiple drugs, ranging from 13 to 26 kinds of drugs. Notably, these isolates showed significant resistance to aminoglycosides and macrolides, which are also commonly used in clinical practices. Data revealed the presence of several β-lactamase-related genes among the isolates, including a novel blaRASA-1 variant (16.2%), the class A extended-spectrum β-lactamase blaRAA-1 (12.2%), and a blaOXA-209 variant (98.6%). Functional analysis of the variants blaRASA-1 and blaOXA-209 showed that the blaRASA-1 variant exhibited activity against various β-lactam antibiotics while their occurrence in R. anatipestifer were not common. The blaOXA-209 variant, on the other hand, did not perform any β-lactam antibiotic resistance. Furthermore, we observed that blaRAA-1 could undergo horizontal transmission among different bacteria via the insertion sequence IS982. In conclusion, this study delves into the high prevalence of R. anatipestifer infection in waterfowl in Anhui, China. The isolated strains exhibit severe drug resistance issues, closely associated with the prevalence of antibiotic resistance genes (ARG). Additionally, our research investigates the β-lactam antibiotic resistance mechanism in R. anatipestifer.
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Affiliation(s)
- Junfeng Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China; Anhui Qiangying Food Group, Suzhou City 234000, Anhui Province, China
| | - Dongmin Hao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Henan Key Laboratory of Animal Food Safety Zhengzhou City 450000, Henan Province, China; Anhui Qiangying Food Group, Suzhou City 234000, Anhui Province, China
| | - Xueyan Ding
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China
| | - Mingzhen Shi
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China
| | - Qiaojun Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou City 225000, Jiangsu Province, China
| | - Hengxu He
- College of Veterinary Medicine, Yangzhou University, Yangzhou City 225000, Jiangsu Province, China
| | - Binghua Cheng
- Anhui Qiangying Food Group, Suzhou City 234000, Anhui Province, China
| | - Mengping Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China
| | - Qingxiu Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China
| | - Yuqiang Xiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China
| | - Liying Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou City 450000, Henan Province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou City 450000, China; Henan Key Laboratory of Animal Food Safety Zhengzhou City 450000, Henan Province, China.
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Apostolakos I, Skarlatoudi T, Vatavali K, Giannouli A, Bosnea L, Mataragas M. Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep's Milk. Int J Mol Sci 2023; 24:13883. [PMID: 37762186 PMCID: PMC10530712 DOI: 10.3390/ijms241813883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Dairy products play a crucial role in human nutrition as they provide essential nutrients. However, the presence of diverse microorganisms in these products can pose challenges to food safety and quality. Here, we provide a comprehensive molecular characterization of a diverse collection of lactic acid bacteria (LAB) and staphylococci isolated from raw sheep's milk. Whole-genome sequencing, phenotypic characterization, and bioinformatics were employed to gain insight into the genetic composition and functional attributes of these bacteria. Bioinformatics analysis revealed the presence of various genetic elements. Important toxin-related genes in staphylococci that contribute to their pathogenic potential were identified and confirmed using phenotypic assays, while adherence-related genes, which are essential for attachment to host tissues, surfaces in the dairy environment, and the creation of biofilms, were also present. Interestingly, the Staphylococcus aureus isolates belonged to sequence type 5, which largely consists of methicillin-susceptible isolates that have been involved in severe nosocomial infections. Although genes encoding methicillin resistance were not identified, multiple resistance genes (RGs) conferring resistance to aminoglycosides, macrolides, and fluroquinolones were found. In contrast, LAB had few inherently present RGs and no virulence genes, suggesting their likely safe status as food additives in dairy products. LAB were also richer in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrate substrates, respectively. Additionally, mobile genetic elements, present in both LAB and staphylococci, may facilitate the acquisition and dissemination of genetic traits, including RGs, virulence genes, and metabolic factors, with implications for food quality and public health. The molecular and phenotypic characterization presented herein contributes to the effort to mitigate risks and infections (e.g., mastitis) and enhance the safety and quality of milk and products thereof.
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Affiliation(s)
| | | | | | | | | | - Marios Mataragas
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece; (I.A.); (T.S.); (K.V.); (A.G.); (L.B.)
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RAA enzyme is a new family of class A extended-spectrum β-lactamase from the
Riemerella anatipestifer
RCAD0122 strain. Antimicrob Agents Chemother 2022; 66:e0175721. [DOI: 10.1128/aac.01757-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole genome sequencing of
Riemerella anatipestifer
isolate RCAD0122 revealed a chromosomally-located β-lactamases gene,
bla
RAA-1
, which encoded a novel class A extended-spectrum β-lactamases (ESBL), RAA-1. The RAA-1 shared ≤ 65% amino acid sequence identity with other characterized β-lactamases. The kinetic assay of native purified RAA-1 revealed ESBL-like hydrolysis activity. Furthermore,
bla
RAA-1
could be transferred to a homologous strain by natural transformation. However, the epidemiological study showed that the
bla
RAA-1
gene is not prevalent currently.
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Yayo J, Kuil T, Olson DG, Lynd LR, Holwerda EK, van Maris AJA. Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose. Appl Environ Microbiol 2021; 87:e03017-20. [PMID: 33608285 PMCID: PMC8091016 DOI: 10.1128/aem.03017-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/10/2021] [Indexed: 02/04/2023] Open
Abstract
The native ability of Clostridium thermocellum to efficiently solubilize cellulose makes it an interesting platform for sustainable biofuel production through consolidated bioprocessing. Together with other improvements, industrial implementation of C. thermocellum, as well as fundamental studies into its metabolism, would benefit from improved and reproducible consumption of hexose sugars. To investigate growth of C. thermocellum on glucose or fructose, as well as the underlying molecular mechanisms, laboratory evolution was performed in carbon-limited chemostats with increasing concentrations of glucose or fructose and decreasing cellobiose concentrations. Growth on both glucose and fructose was achieved with biomass yields of 0.09 ± 0.00 and 0.18 ± 0.00 gbiomass gsubstrate-1, respectively, compared to 0.15 ± 0.01 gbiomass gsubstrate-1 for wild type on cellobiose. Single-colony isolates had no or short lag times on the monosaccharides, while wild type showed 42 ± 4 h on glucose and >80 h on fructose. With good growth on glucose, fructose, and cellobiose, the fructose isolates were chosen for genome sequence-based reverse metabolic engineering. Deletion of a putative transcriptional regulator (Clo1313_1831), which upregulated fructokinase activity, reduced lag time on fructose to 12 h with a growth rate of 0.11 ± 0.01 h-1 and resulted in immediate growth on glucose at 0.24 ± 0.01 h-1 Additional introduction of a G-to-V mutation at position 148 in cbpA resulted in immediate growth on fructose at 0.32 ± 0.03 h-1 These insights can guide engineering of strains for fundamental studies into transport and the upper glycolysis, as well as maximizing product yields in industrial settings.IMPORTANCEC. thermocellum is an important candidate for sustainable and cost-effective production of bioethanol through consolidated bioprocessing. In addition to unsurpassed cellulose deconstruction, industrial application and fundamental studies would benefit from improvement of glucose and fructose consumption. This study demonstrated that C. thermocellum can be evolved for reproducible constitutive growth on glucose or fructose. Subsequent genome sequencing, gene editing, and physiological characterization identified two underlying mutations with a role in (regulation of) transport or metabolism of the hexose sugars. In light of these findings, such mutations have likely (and unknowingly) also occurred in previous studies with C. thermocellum using hexose-based media with possible broad regulatory consequences. By targeted modification of these genes, industrial and research strains of C. thermocellum can be engineered to (i) reduce glucose accumulation, (ii) study cellodextrin transport systems in vivo, (iii) allow experiments at >120 g liter-1 soluble substrate concentration, or (iv) reduce costs for labeling studies.
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Affiliation(s)
- Johannes Yayo
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Teun Kuil
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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