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Zhang S, Hu L, Xue Y, Zhang D, Zhang Y, Wang S. Development of a real-time loop-mediated isothermal amplification method for monitoring Pseudomonas lurida in raw milk throughout the year of pasture. Front Microbiol 2023; 14:1133077. [PMID: 37125188 PMCID: PMC10130427 DOI: 10.3389/fmicb.2023.1133077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction The psychrophilic bacterium Pseudomonas lurida (P. lurida) and its thermostable alkaline proteases can seriously damage raw milk quality. Methods In this study, specific primers were designed for P. lurida's gyrB and aprX genes, and a real-time loop-mediated isothermal amplification (RealAmp) rapid detection method was developed for the early monitoring of P. lurida and its proteases in raw milk. A phylogenetic tree of the gyrB and aprX genes of P. lurida was constructed to analyze the homology of the design sequence of the RealAmp primer. The DNA of 2 strains of P. lurida and 44 strains of non-P. lurida were detected via RealAmp to analyze the specificity of the primer. Results It was found that aprX-positive proteases were produced by P. lurida-positive strains only when Pseudomonas fluorescens was negative. The dissociation temperatures of gyrB and aprX in the RealAmp-amplified products were approximately 85.0°C and 90.0°C, respectively. Moreover, DNA was detected through a 10-fold dilution of P. lurida in a pure bacterial solution and artificially contaminated skimmed milk. The limit of detection of P. lurida DNA copy number in the pure bacterial solution was 8.6 copies/μL and that in the 10% skimmed milk was 5.5 copies/μL. Further, 144 raw milk samples throughout the year from three farms in Hebei province were analyzed using RealAmp. The highest detection rate of P. lurida was 56% in the first and third quarters, and that of proteases was 36% in the second quarter. The detection rates of P. lurida and its proteases were the highest in samples collected from pasture 2 (52 and 46%, respectively), and the ability of P. lurida to produce proteases reached 88%. Discussion In conclusion, RealAmp established an early and rapid method for the detection of P. lurida and its proteases in raw milk samples, allowing the identification and control of contamination sources in a timely manner to ensure the quality of milk and dairy products.
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Affiliation(s)
- Shufei Zhang
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang, Hebei, China
| | - Lianxia Hu
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, Hebei, China
| | - Yuling Xue
- Junlebao Dairy Group Co., Ltd., Shijiazhuang, Hebei, China
| | - Dong Zhang
- Junlebao Dairy Group Co., Ltd., Shijiazhuang, Hebei, China
| | - Yaoguang Zhang
- Junlebao Dairy Group Co., Ltd., Shijiazhuang, Hebei, China
| | - Shijie Wang
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang, Hebei, China
- Junlebao Dairy Group Co., Ltd., Shijiazhuang, Hebei, China
- *Correspondence: Shijie Wang,
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Yan Q, Song J, Zhou J, Han Y, Cai Z. Biodeposition of oysters in an urbanized bay area alleviates the black-malodorous compounds in sediments by altering microbial sulfur and iron metabolism. Sci Total Environ 2022; 817:152891. [PMID: 34995586 DOI: 10.1016/j.scitotenv.2021.152891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
The occurrence of the 'black-malodorous phenomenon' in a waterbody is a clear sign of a highly eutrophic bay, the formation of which is associated with microbial sulfur and iron metabolism in the sediments. Oyster farming restoration has been widely studied as an important method for treating eutrophication and related ecological problems. However, few studies focus on the ecosystem-level consequences of oyster farming concerning microbial sulfur and iron cycles in the sediment. Here, we compared the physicochemical features and microbial functions of oyster farms with those of reference areas using the Geochip5.0 technique. Our results showed a significant reduction of acid volatile sulfide (AVS) content associated with oyster farming, thus alleviating the black-malodorous status of Shenzhen Bay in China. Oyster farming created loose and porous sedimentary structures and stimulated the oxidation of black-odorous compounds. Moreover, we observed that the introduction of oysters changed microbial biodiversity significantly based on gyrB gene structure, with typical sulfur- and iron-cycling microbes being enriched. We also demonstrated that microbial abilities involved in sulfur and iron metabolism were greatly increased in oyster farming areas compared with reference areas. Under such circumstances, some cascading processes (AVS uptake and rates of organic matter turnover) were improved, which eventually contributed to black odor reduction. From the microecological perspective, we conclude that the biodeposition of oysters was the key factor for water retention and improvement of microbial metabolism. This study suggests that biodeposition shapes the microbial functional communities in adjacent territories and presumably alleviates the black-malodorous compounds in sediments.
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Affiliation(s)
- Qi Yan
- School of Life Science, Tsinghua University, Beijing 100083, PR China
| | - Junting Song
- The Institute for Ocean Engineering, Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Jin Zhou
- The Institute for Ocean Engineering, Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Yilin Han
- The Institute for Ocean Engineering, Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- The Institute for Ocean Engineering, Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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Sun X, Qiu S, Luo X, Jin P, Zhao J, Wu X, Yang J, Wang X, Song J, Xiang W. Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin. Antonie Van Leeuwenhoek 2021; 114:697-708. [PMID: 33666807 DOI: 10.1007/s10482-021-01550-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/20/2021] [Indexed: 11/28/2022]
Abstract
A novel actinobacterium, designated strain NEAU-HG-1T, was isolated from soil collected from Harbin, Heilongjiang Province, Northeast China and characterised using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-HG-1T belonged to the genus Micromonospora, and shared high sequence similarities with Micromonospora auratinigra DSM 44815T (98.9%) and Micromonospora coerulea DSM 43143T (98.7%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Micromonospora. Cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The polar lipid contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipid and phosphatidylinositol. The predominant menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). The major fatty acids were C17:0 cycle, iso-C15:0, and iso-C16:0. Furthermore, strain NEAU-HG-1T displayed a DNA-DNA relatedness of 33.8 ± 2.2% with M. coerulea DSM 43143T. The level of digital DNA-DNA hybridization between strain NEAU-HG-1T and M. auratinigra DSM 44815T was 27.2% (24.8-29.7%). The value was well below the criteria for species delineation of 70% for dDDH. Whole-genome average nucleotide identity analyses result also indicated that the isolate should be assigned to a new species under the genus Micromonospora. Therefore, it is concluded that strain NEAU-HG-1T represents a novel species of the genus Micromonospora, for which the name Micromonospora rubida sp. nov. is proposed, with NEAU-HG-1T (= CGMCC 4.7479T = JCM 32386T) as the type strain.
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Affiliation(s)
- Xiujun Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Shiwen Qiu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xianxian Luo
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Pinjiao Jin
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xianyao Wu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Jize Yang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
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Ahmed LM, Sayed ASM, ElKader HAA, Faddan NHA, Al Hosary AAT. Phylogenetic analysis of Salmonella species isolated from cows, buffaloes, and humans based on gyrB gene sequences. Trop Anim Health Prod 2020; 52:1487-92. [PMID: 31898024 DOI: 10.1007/s11250-019-02155-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
This study aimed to investigate the role of dairy cows and buffaloes as reservoirs of nontyphoidal salmonelloses (NTS), to reveal the occurrence of NTS among dairy workers and children with acute diarrhea and to study the gyrB gene phylogenetic relations of the obtained Salmonella strains, 300 samples were chosen randomly from clinically infected animals, including 100 feces and 50 raw milk from buffaloes and cows. Five hundred samples were chosen randomly from healthy animals, including 150 feces and 100 raw milk from buffaloes and cows. A total of 160 stool samples were randomly chosen from healthy workers (60) and children with acute diarrhea (100). Salmonella species were isolated from the examined samples and identified by polymerase chain reaction. Sequencing and phylogenetic analyses of gyrB gene were also performed. S. enteritidis and S.typhimurium were isolated from 0.5% (2/400) of the cows and buffaloes, respectively. Dairy workers were found to be at greater risk of exposure to Salmonella infection (5%) than children (1%). S. enteritidis was isolated from 1.7% (1/60) of dairy workers. S. typhimurium was isolated from 3.33% (2/60) and 1% (1/100) of dairy workers and children, respectively. Phylogenetic analysis of Salmonella species gyrB gene sequences from both animals and humans falls inside one clade, and all of them were closely related to each other with less significant genetic distance (99.9:100). In conclusion, cows and buffaloes act as reservoirs of Salmonella infection in dairy farms in Egypt and contribute a risk of zoonotic transmission to human.
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Chen F, Sun J, Han Z, Yang X, Xian JA, Lv A, Hu X, Shi H. Isolation, Identification and Characteristics of Aeromonas veronii From Diseased Crucian Carp ( Carassius auratus gibelio). Front Microbiol 2019; 10:2742. [PMID: 32038507 PMCID: PMC6988821 DOI: 10.3389/fmicb.2019.02742] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/11/2019] [Indexed: 11/13/2022] Open
Abstract
Aeromonas species often cause disease in farmed fish. In the present study, dominant bacteria were isolated from diseased crucian carp (Carassius auratus gibelio). Based on this, a bacterial isolate was tentatively named CFJY-623. This isolate was identified as Aeromonas veronii based on analysis of its morphological, physiological, and biochemical features, as well as 16S rRNA and gyrB gene sequences. Six virulence genes related to pathogenicity including aerolysin, cytotonic enterotoxins, elastase, glycerophospholipid: cholesterol acyltransferase, lipase, and serine protease were identified in this A. veronii isolate. The median lethal dosage (LD50) of the CFJY-623 isolate for crucian carp was determined as 1.31 × 107 CFU/mL. Artificial experimental infection showed that the CFJY-623 isolate caused considerable histological lesions in the fish, including tissue cell degeneration, necrosis, and inflammatory cell infiltrating. Drug sensitivity testing showed that the isolate was susceptible to aminoglycosides, carbapenemes, and nitrofurans. Exploring its growing features showed that this isolate exhibited a high level of environmental adaptability. These results provided a scientific basis for the identification of A. veronii and treatment for fish infected by this pathogen.
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Affiliation(s)
- Feng Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Jingfeng Sun
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Zhuoran Han
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Xijun Yang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Jian-an Xian
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Xiucai Hu
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
| | - Hongyue Shi
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, China
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Negishi T, Matsumoto T, Shinagawa J, Kasuga E, Horiuchi K, Natori T, Sugano M, Uehara T, Honda T. A case of cervical subcutaneous abscess due to Bordetella hinzii. Diagn Microbiol Infect Dis 2019; 95:114865. [PMID: 31405631 DOI: 10.1016/j.diagmicrobio.2019.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/25/2022]
Abstract
We present a case of subcutaneous infection caused by Bordetella hinzii in a healthy male. The isolate was successfully identified by gyrB gene sequencing. B. hinzii cannot be distinctively identified using 16S rRNA gene sequencing or by biochemical methods. The number of cases infected with B. hinzii might be underestimated owing to the difficulty in accurate identification, which can be achieved by gyrB gene sequencing to gain knowledge about the species.
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Affiliation(s)
- Tatsuya Negishi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takehisa Matsumoto
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi 371-8514, Gunma, Japan.
| | - Jun Shinagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Nagano, Japan
| | - Eriko Kasuga
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Kazuki Horiuchi
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Tatsuya Natori
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Mitsutoshi Sugano
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Takayuki Honda
- Department of Laboratory Medicine, Shinshu University Hospital, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
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Zhang L, Gao W, Yin Y, Wang Z. Discrimination of Burkholderia gladioli pv. alliicola and B. cepacia complex using the gyrB gene of B. gladioli pv. alliicola. Exp Ther Med 2019; 17:1870-1876. [PMID: 30783462 DOI: 10.3892/etm.2018.7137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/22/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the efficiency of the gyrB gene derived from Burkholderia gladioli pv.Alliicola (Bga) on the identification of Bga from the B. cepacia complex (Bcc) based on the COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy. A set of primers used for the specific amplification of the gyrB gene in Bga were designed according to the CODEHOP principle. A total of 1,644 bp of the gyrB gene sequence of Bga were acquired by CODEHOP amplification. The sequence was blasted in GenBank and it revealed an average of 86% similarity with the gyrB gene of nine genomovars of Bcc. A phylogenetic tree was constructed using the gyrB gene sequences. The microarray method was adopted to discriminate Bga from Bcc based on the specific probes designed upon the gyrB gene, and five genomovars of Bcc demonstrated a good discrimination from Bga on the microarray chip. CODEHOP strategy succeeded in amplification of the gyrB gene of Bga, which made it possible for the identification of Bga from five genomovars of Bcc.
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Affiliation(s)
- Lun Zhang
- School of Life Sciences, Chongqing University, Shapingba, Chongqing 400030, P.R. China
| | - Wenna Gao
- Beijing Entry-Exit Inspection and Quarantine Bureau, Beijing 100026, P.R. China
| | - Youping Yin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing 400030, P.R. China
| | - Zhongkang Wang
- School of Life Sciences, Chongqing University, Shapingba, Chongqing 400030, P.R. China
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Marcos LA, Spitzer ED, Mahapatra R, Ma Y, Halse TA, Shea J, Isabelle M, Lapierre P, Escuyer VE. Mycobacterium orygis Lymphadenitis in New York, USA. Emerg Infect Dis 2018; 23:1749-1751. [PMID: 28930016 PMCID: PMC5621560 DOI: 10.3201/eid2310.170490] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We report a case of lymphadenitis caused by Mycobacterium orygis in an immunocompetent person in Stony Brook, New York, USA. Initial real-time PCR assay failed to provide a final subspecies identification within the M. tuberculosis complex, but whole-genome sequencing characterized the isolate as M. orygis.
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Bunpa S, Nishibuchi M, Thawonsuwan J, Sermwittayawong N. Genetic heterogeneity among Vibrio alginolyticus strains, and design of a PCR-based identification method using gyrB gene sequence. Can J Microbiol 2017; 64:1-10. [PMID: 29017024 DOI: 10.1139/cjm-2017-0269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vibrio alginolyticus, a pathogen among humans and marine animals, is ubiquitous in marine environments. The aims of this study were to analyze the relationships between genetic diversity and origins, and to develop new primers based on the gyrB sequence to identify V. alginolyticus isolated from various sources. To determine the genetic diversity of this bacterium, an arbitrarily primed polymerase chain reaction (AP-PCR) technique was performed on 36 strains of V. alginolyticus isolated from diarrhea patients and from diseased marine animals and environments in southern Thailand. The results showed distinct DNA fingerprints of all strains, indicating that they are genetically heterogeneous. For species-specific identification of V. alginolyticus, primers targeting the gyrB gene of V. alginolyticus were developed. Thirty reference Vibrio spp., 13 non-Vibrio spp., and 160 strains of V. alginolyticus isolated from various sources in southern Thailand were used to evaluate the specificity of these primers. Our results showed that the gyrB primers could specifically identify V. alginolyticus from all sample types. In addition, the detection limit of the PCR was at least 95 pg of DNA template. Therefore, we concluded that the newly designed gyrB primers are rapid, highly sensitive, and specific to identify V. alginolyticus isolated from various sources.
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Affiliation(s)
- Supansa Bunpa
- a Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand.,b Food Safety and Health Research Unit, Prince of Songkla University, Songkhla 90110, Thailand
| | - Mitsuaki Nishibuchi
- c Center for Southeast Asian Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Jumroensri Thawonsuwan
- d Coastal Aquatic Animal Health Research Institute, Coastal Fisheries Research and Development Division, Department of Fisheries, Songkhla 90100, Thailand
| | - Natthawan Sermwittayawong
- a Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand.,b Food Safety and Health Research Unit, Prince of Songkla University, Songkhla 90110, Thailand
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Hu LX, Yang ZH, Zhang D, Zhao DM, Zhu JH. Sensitive and rapid detection of Pectobacterium atrosepticum by targeting the gyrB gene using a real-time loop-mediated isothermal amplification assay. Lett Appl Microbiol 2017; 63:289-96. [PMID: 27450435 DOI: 10.1111/lam.12618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 11/29/2022]
Abstract
UNLABELLED This study reports the development of a real-time, loop-mediated isothermal amplification (RealAmp) assay for the detection of Pectobacterium atrosepticum (P. atrosepticum). A phylogenetic tree was constructed based on the gyrB gene of P. atrosepticum and related species. Pectobacterium atrosepticum from different sources can be clustered in the same branch with 100% support rate. The RealAmp primers targeting the gyrB gene of P. atrosepticum worked most efficiently at 61·0°C. Compared with 55 related bacterial strains, the eight P. atrosepticum strains displayed positive reaction in the RealAmp assay. The melting temperature (Tm) of P. atrosepticum amplified products was about 85·0°C. The detection limit of the RealAmp assay for the detection of P. atrosepticum in pure culture was approx. 3 CFU reaction(-1) . The detection limit of the RealAmp assay for the detection of P. atrosepticum in artificially contaminated samples was 22 CFU reaction(-1) . The detection rate of the RealAmp assay for the detection of potato tubers was 28·5-32·0% higher than that of the conventional PCR. In summary, a specific, sensitive and rapid RealAmp assay based on the gyrB gene of P. atrosepticum, which can be easily performed and real-time monitored, was established. SIGNIFICANCE AND IMPACT OF THE STUDY Potato blackleg caused by Pectobacterium atrosepticum (P. atrosepticum) which is mainly transmitted through the seed potato leads to the decline in potato production. To reduce yield loss, rapid detection of P. atrosepticum in seed potato remains essential. Based on the gyrB gene of P. atrosepticum, species-specific primers were designed. A real-time, loop-mediated isothermal amplification (RealAmp) assay was established for the detection of P. atrosepticum. The RealAmp assay is a specific, rapid and sensitive method for P. atrosepticum detection. Therefore, it provides an effective diagnosis of potato blackleg in both the growing and stored potato.
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Affiliation(s)
- L X Hu
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - Z H Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - D Zhang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - D M Zhao
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - J H Zhu
- College of Plant Protection, Agricultural University of Hebei, Baoding, China.
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Kang CH, Shin Y, Jang S, Jung Y, So JS. Antimicrobial susceptibility of Vibrio alginolyticus isolated from oyster in Korea. Environ Sci Pollut Res Int 2016; 23:21106-21112. [PMID: 27543129 DOI: 10.1007/s11356-016-7426-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 08/04/2016] [Indexed: 06/06/2023]
Abstract
Pathogenic Vibrio alginolyticus, a cause of severe infection in shellfish, as well as in humans, has been found at high frequency around all coastal areas of Korea. The aim of this study was to determine the occurrence of V. alginolyticus, to identify the strains isolated from oysters in West Sea, and to investigate their antimicrobial resistance profiles. Biochemical analyses of the 90 initially recovered presumptive V. alginolyticus colonies indicated that 16 isolates were V. alginolyticus. PCR analysis to detect the presence of the gyrB gene confirmed that 15 (93.8 %) of the 16 isolates were V. alginolyticus. These 15 isolates had the following profiles of resistance against 16 antibiotics: all isolates were resistant to ampicillin and vancomycin, and 26.7 % of the isolates exhibited resistance to cephalothin. A large number of isolates showed intermediate resistance to erythromycin (100 %) and rifampin (73.3 %). Five (33.3 %) of the V. alginolyticus isolates demonstrated multiple resistance to at least three antimicrobials.
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Affiliation(s)
- Chang-Ho Kang
- Department of Biological Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon, 402-751, South Korea
| | - YuJin Shin
- Department of Biological Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon, 402-751, South Korea
| | - SeokCheol Jang
- Department of Biological Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon, 402-751, South Korea
| | - Yeojung Jung
- Department of Biological Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon, 402-751, South Korea
| | - Jae-Seong So
- Department of Biological Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon, 402-751, South Korea.
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Zhou M, Yang Q, Kudinha T, Zhang L, Xiao M, Kong F, Zhao Y, Xu YC. Using Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Complemented with Selected 16S rRNA and gyrB Genes Sequencing to Practically Identify Clinical Important Viridans Group Streptococci (VGS). Front Microbiol 2016; 7:1328. [PMID: 27617008 PMCID: PMC5000867 DOI: 10.3389/fmicb.2016.01328] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/11/2016] [Indexed: 11/13/2022] Open
Abstract
There are challenges in viridans group streptococci (VGS) identification especially for the mitis group. Few studies have investigated the performance of MALDI-TOF MS system in VGS identification. Using 16S rRNA gene and gyrB gene sequencing as a gold standard, the performance of two MALDI-TOF MS instruments in the identification of 181 VGS clinical isolates was studied. The Bruker Biotyper and Vitek MS IVD systems correctly identified 88.4% and 98.9% of the 181 isolates, respectively. The Vitek MS RUO system was the least reliable, only correctly identifying 38.7% of the isolates to species level with several misidentifications and invalid results. The Bruker Biotyper system was very unreliable in the identification of species within the mitis group. Among 22 non-pneumococci isolates (S. mitis/S. oralis/S. pseudopneumoniae), Biotyper misidentified 21 of them as S. pneumoniae leading to a low sensitivity and low positive predictive value in these species. In contrast, the Vitek MS IVD demonstrated a better resolution for pneumococci and non-pneumococci despite the inability to distinguish between S. mitis/S. oralis. For more accurate species-level identification, further improvements in the VGS spectra databases are needed. Based on MALDI-TOF analysis and selected 16S rRNA gene plus gyrB genes sequencing, we designed a practical VGS identification algorithm.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University Orange, NSW, Australia
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital Westmead, NSW, Australia
| | - Yupei Zhao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
| | - Ying-Chun Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences Beijing, China
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Veyisoglu A, Carro L, Guven K, Cetin D, Spröer C, Schumann P, Klenk HP, Goodfellow M, Sahin N. Micromonospora yasonensis sp. nov., isolated from a Black Sea sediment. Antonie Van Leeuwenhoek 2016; 109:1019-28. [PMID: 27154186 DOI: 10.1007/s10482-016-0701-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
A Micromonospora strain, designated DS3186(T), isolated from sediment collected from the Black Sea off the Yason Peninsula, Ordu, Turkey, was examinated using a polyphasic approach. The strain was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its clasification in the genus Micromonospora. A comparative 16S rRNA gene sequence analysis showed that the strain was closely related to the type strains of Micromonospora olivasterospora (99.0 %), Micromonospora equina (98.8 %), Micromonospora rhizosphaerae (98.8 %) and Micromonospora viridifaciens (98.8 %); low levels of DNA-DNA relatednes were found between the isolate and the M. olivasterospora and M. rhizosphaerae strains. Corresponding phylogenetic analysis based on partial gyrB gene sequences showed that strain DS3186(T) formed a subclade with the type strains of Micromonospora eburnea, M. equina, Micromonospora narathiwatensis and M. viridifaciens. Strain DS3186(T) was distinguished from its close phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that strain DS3186(T) represents a novel Micromonospora species for which the name Micromonospora yasonensis sp. nov. is proposed. The type strain is DS3186(T) (=DSM 45980(T) = KCTC 29433(T)).
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Lidan C, Linhai L, Yang L, Zhaohui S, Xiaoyan H, Yuling S. Molecular characterization and antimicrobial susceptibility of tcdA-negative Clostridium difficile isolates from Guangzhou, China. Diagn Microbiol Infect Dis 2015; 84:361-5. [PMID: 26867962 DOI: 10.1016/j.diagmicrobio.2015.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/07/2015] [Accepted: 12/21/2015] [Indexed: 11/30/2022]
Abstract
This study aimed to investigate the molecular characteristics and antimicrobial susceptibility of Clostridium difficile clinical isolates in Guangzhou, China. One hundred twenty isolates were collected from Guangzhou General Hospital at the Guangzhou Military Command in China from March 2014 to April 2015, and 9 isolates were identified as tcdA-negative/tcdB-positive (A(-)B(+)) strains. Results showed that all of the strains were confirmed to be ST37 and 0 single nucleotide variants (SNVs) were found in the PaLoc region, and >60 SNVs were identified throughout the whole genome sequence. The results show the diversity of the antibiotic and gene mutations present in these strains. All of the A(-)B(+) isolates were highly resistant to clindamycin and erythromycin; showed an average sensitivity to fluoroquinolones; and maintained a high susceptibility to metronidazole, vancomycin, and tigecycline.
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Affiliation(s)
- Chen Lidan
- Graduate School of Southern Medical University, Guangzhou, Guangdong 510515, PR China; Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Li Linhai
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Liao Yang
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Sun Zhaohui
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Huang Xiaoyan
- Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China
| | - Shi Yuling
- Graduate School of Southern Medical University, Guangzhou, Guangdong 510515, PR China; Department of Laboratory Medicine, Guangzhou General Hospital of Guangzhou Military Command of PLA, Guangzhou, Guangdong 510010, PR China.
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Aghamollaei H, Moghaddam MM, Kooshki H, Heiat M, Mirnejad R, Barzi NS. Detection of Pseudomonas aeruginosa by a triplex polymerase chain reaction assay based on lasI/R and gyrB genes. J Infect Public Health 2015; 8:314-22. [PMID: 25863575 DOI: 10.1016/j.jiph.2015.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/24/2015] [Accepted: 03/08/2015] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is a nosocomial pathogen, which, due to its inherent and acquired resistance to a wide range of antibiotics, causes high mortality rates. Therefore, rapid detection of the bacterium with high specificity and sensitivity plays a critical role in the control of the pathogenic bacterium. The aim of this study was to evaluate the accuracy and specificity of a prompt detection of the bacterium based on a triplex polymerase chain reaction that amplifies the lasI, lasR and gyrB genes. For this purpose, 30 clinical isolates of P. aeruginosa and 30 wound biopsy samples were retrieved from clinical diagnostic laboratories. After the extraction of the chromosomal DNA, the desired genes were amplified using uniplex and triplex PCR with appropriate primers. The specificity of the primers was evaluated by a comparison of the PCR results for P. aeruginosa clinical samples and non-Pseudomonas species control samples. The sensitivity of the primers was determined using a serial dilution of the genomic DNA template (100 ng to 100 fg) and by a comparison of the PCR and bacterial culture results. The results showed that the triplex PCR assay was positive for all of the samples (100%), while the PCR identifications were negative for non-Pseudomonas species. Additionally, at 10(-4) and 10(-5) diluted genomic DNA from P. aeruginosa (10 pg and 1 pg), the triplex PCR test was positive for the Las and gyrB genes in all of the samples, respectively. Based on these results, the designed primers can be used for the rapid, specific and sensitive diagnosis of P. aeruginosa in a triplex PCR assay.
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Branquinho R, Meirinhos-Soares L, Carriço JA, Pintado M, Peixe LV. Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones. FEMS Microbiol Ecol 2014; 90:689-98. [PMID: 25230950 DOI: 10.1111/1574-6941.12426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 11/30/2022] Open
Abstract
Bacillus pumilus is a Gram-positive bacterium with a wide range of attributed applications, namely as a plant growth promoting rhizobacteria (PGPR), animal, and human probiotic. However, a rare putative role in human diseases has been reported, namely in food poisoning or as anthrax-like cutaneous infectious agent. This species is difficult to distinguish from its closely related species on the basis of phenotypic or biochemical characteristics and 16S rRNA gene sequences. In this study, the phylogenetic analysis of gyrB and rpoB gene sequences of a collection of isolates previously identified as B. pumilus, assigned most of them (93%, 38 of 41 isolates) to B. safensis or to the new recently described B. invictae. Moreover, we extended the previously reported recognized habitats of these species and unveiled a human health or biotechnological relevance (e.g. as implicated in food poisoning or PGPR) for them. Additionally, we demonstrated that both B. safensis and B. invictae species encompass a clonally diverse population, which can justify their great adaptation ability to different niches, with evidence of clonal-host specificity.
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Affiliation(s)
- Raquel Branquinho
- Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, REQUIMTE, Universidade do Porto, Porto, Portugal
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