1
|
Mostafa NF, Elkenany RM, Younis G. Characterization of Bacillus cereus isolated from contaminated foods with sequencing of virulence genes in Egypt. BRAZ J BIOL 2024; 84:e257516. [DOI: 10.1590/1519-6984.257516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/14/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract The current study describes the presence of Bacillus cereus (B. cereus) in contaminated foods of animal source and ready for human consumption with highlighting on their virulence contributing factors by detection of its virulence genes in addition to identification of their sequencing. Three hundred sixty food samples categorized as (228) meat products and (132) milk products were examined for B. cereus isolation and all of these isolates were confirmed by biochemical tests. Eighteen strains obtained from different food samples were examined for the attendance of a number of virulence genes (nheA, cytK, entFM, bceT and hblC genes) using uniplex PCR method. Furthermore, the B. cereus strains were valued for the sequencing of described genes. Generally 24.44% (88/360) food samples classified as 11.11% (40/360) meat products and 13.33% (48/360) milk products carried B. cereus according to cultural and biochemical properties, with geometric mean (1.5×107±0.15 CFU/g or mL) . The highest counts (above 105 CFU/g or mL) were originated from milk products (with geometric mean 2.2×107±0.22 CFU/g or mL) more than meat products (with geometric mean 1×107±0.19 CFU/g or mL). The results revealed that all of our isolates had one or more virulence (enterotoxin) genes. In our research, the most predominant genes were nheA (100%), followed by cytK (61.11%), entFM (33.33%), bceT (11.11%) then hblC (5.56%). Molecular method detected that overall, 5 strains (27.78%) harbored only 1 gene (nheA), 7 strains (38.88%) harbored 2 genes which classified as 5 strains (27.78%) (nheA and cytK), 2 strains (11.11%) have (nheA and entFM). Moreover, 5 strains (27.78%) have 3 genes classified as 3 strains (16.67%) harbored (nheA, cytK and entFM), 1 strain (5.56%) had (nheA, cytK and hblC), and 1 strain (5.56%) had (nheA, cytK and bceT). Only 1 strain (5.56%) carried 4 tested virulence genes (nheA, cytK, entFM and bceT) genes. The most prevalent gene in meat and dairy foods was nheA (100%). The nucleotide sequences of (bceT, cytK, entFM, hblC and nheA genes) of B. cereus strains were deposited in GenBank under accession no. (MW911824, MW911825, MW911826, MW911827 and MW911828), respectively. Our study was established to indicate the presence of virulent B. cereus in meat and milk products ready for human consumption as a result of deficient hygienic actions. So, a plain for good hygienic measures should be modified to avoid causing serious health problems to human due to ingestion of such products.
Collapse
|
2
|
Ateiah M, Gandalipov ER, Rubel AA, Rubel MS, Kolpashchikov DM. DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species. Int J Mol Sci 2023; 24:ijms24054473. [PMID: 36901903 PMCID: PMC10003685 DOI: 10.3390/ijms24054473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/12/2023] Open
Abstract
Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for "opening up" the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10-23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of B. thuringiensis 16S rRNA at fluorescein and B. mycoides at Cy5 channels with a limit of detection of 30 × 103 and 35 × 103 CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification.
Collapse
Affiliation(s)
- Muhannad Ateiah
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Erik R. Gandalipov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya enb. 7-9, St. Petersburg 199034, Russia;
| | - Maria S. Rubel
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
| | - Dmitry M. Kolpashchikov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, St. Petersburg 191002, Russia; (M.A.); (E.R.G.); (M.S.R.)
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- Correspondence:
| |
Collapse
|
3
|
Lin A, Deatherage Kaiser BL, Hutchison JR, Bilmes JA, Noble WS. MS1Connect: a mass spectrometry run similarity measure. Bioinformatics 2023; 39:7005198. [PMID: 36702456 PMCID: PMC9913042 DOI: 10.1093/bioinformatics/btad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
MOTIVATION Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols. RESULTS We propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though these data are not used by MS1Connect. AVAILABILITY AND IMPLEMENTATION The MS1Connect software is available at https://github.com/bmx8177/MS1Connect. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Andy Lin
- Chemical and Biological Signatures, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Janine R Hutchison
- Chemical and Biological Signatures, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jeffrey A Bilmes
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
4
|
Identification of Universally Applicable and Species-Specific Marker Peptides for Bacillus anthracis. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101549. [PMID: 36294983 PMCID: PMC9605612 DOI: 10.3390/life12101549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022]
Abstract
Anthrax is a zoonotic infection caused by the bacterium Bacillus anthracis (BA). Specific identification of this pathogen often relies on targeting genes located on two extrachromosomal plasmids, which represent the major pathogenicity factors of BA. However, more recent findings show that these plasmids have also been found in other closely related Bacillus species. In this study, we investigated the possibility of identifying species-specific and universally applicable marker peptides for BA. For this purpose, we applied a high-resolution mass spectrometry-based approach for 42 BA isolates. Along with the genomic sequencing data and by developing a bioinformatics data evaluation pipeline, which uses a database containing most of the publicly available protein sequences worldwide (UniParc), we were able to identify eleven universal marker peptides unique to BA. These markers are located on the chromosome and therefore, might overcome known problems, such as observable loss of plasmids in environmental species, plasmid loss during cultivation in the lab, and the fact that the virulence plasmids are not necessarily a unique feature of BA. The identified chromosomally encoded markers in this study could extend the small panel of already existing chromosomal targets and along with targets for the virulence plasmids, may pave the way to an even more reliable identification of BA using genomics- as well as proteomics-based techniques.
Collapse
|
5
|
Abril AG, Quintela-Baluja M, Villa TG, Calo-Mata P, Barros-Velázquez J, Carrera M. Proteomic Characterization of Virulence Factors and Related Proteins in Enterococcus Strains from Dairy and Fermented Food Products. Int J Mol Sci 2022; 23:ijms231810971. [PMID: 36142880 PMCID: PMC9503237 DOI: 10.3390/ijms231810971] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 01/23/2023] Open
Abstract
Enterococcus species are Gram-positive bacteria that are normal gastrointestinal tract inhabitants that play a beneficial role in the dairy and meat industry. However, Enterococcus species are also the causative agents of health care-associated infections that can be found in dairy and fermented food products. Enterococcal infections are led by strains of Enterococcus faecalis and Enterococcus faecium, which are often resistant to antibiotics and biofilm formation. Enterococci virulence factors attach to host cells and are also involved in immune evasion. LC-MS/MS-based methods offer several advantages compared with other approaches because one can directly identify microbial peptides without the necessity of inferring conclusions based on other approaches such as genomics tools. The present study describes the use of liquid chromatography−electrospray ionization tandem mass spectrometry (LC−ESI−MS/MS) to perform a global shotgun proteomics characterization for opportunistic pathogenic Enterococcus from different dairy and fermented food products. This method allowed the identification of a total of 1403 nonredundant peptides, representing 1327 proteins. Furthermore, 310 of those peptides corresponded to proteins playing a direct role as virulence factors for Enterococcus pathogenicity. Virulence factors, antibiotic sensitivity, and proper identification of the enterococcal strain are required to propose an effective therapy. Data are available via ProteomeXchange with identifier PXD036435. Label-free quantification (LFQ) demonstrated that the majority of the high-abundance proteins corresponded to E. faecalis species. Therefore, the global proteomic repository obtained here can be the basis for further research into pathogenic Enterococcus species, thus facilitating the development of novel therapeutics.
Collapse
Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
- Correspondence:
| |
Collapse
|
6
|
Detection of emetic Bacillus cereus and the emetic toxin cereulide in food matrices: Progress and perspectives. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
7
|
Novel Techniques for Microbiological Safety in Meat and Fish Industries. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app12010319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The consumer tendency towards convenient, minimally processed meat items has placed extreme pressure on processors to certify the safety of meat or meat products without compromising the quality of product and to meet consumer’s demand. This has prompted difficulties in creating and carrying out novel processing advancements, as the utilization of more up-to-date innovations may influence customer decisions and assessments of meat and meat products. Novel advances received by the fish and meat industries for controlling food-borne microbes of huge potential general wellbeing concern, gaps in the advancements, and the requirement for improving technologies that have been demonstrated to be effective in research settings or at the pilot scale shall be discussed. Novel preparing advancements in the meat industries warrant microbiological approval before being named as industrially suitable alternatives and authorizing infra-structural changes. This miniature review presents the novel techniques for the microbiological safety of meat products, including both thermal and non-thermal methods. These technologies are being successfully implemented and rationalized in subsisting processing surroundings.
Collapse
|
8
|
Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis. Foods 2021; 10:799. [PMID: 33917943 PMCID: PMC8068337 DOI: 10.3390/foods10040799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
Collapse
Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain;
| | - José-Luis R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| |
Collapse
|
9
|
Kong L, Yu S, Yuan X, Li C, Yu P, Wang J, Guo H, Wu S, Ye Q, Lei T, Yang X, Zhang Y, Wei X, Zeng H, Zhang J, Wu Q, Ding Y. An Investigation on the Occurrence and Molecular Characterization of Bacillus cereus in Meat and Meat Products in China. Foodborne Pathog Dis 2021; 18:306-314. [PMID: 33769083 DOI: 10.1089/fpd.2020.2885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bacillus cereus is a common foodborne pathogen that can cause both gastrointestinal and nongastrointestinal diseases. In this study, we collected 603 meat and meat products from 39 major cities in China. The positive contamination rate of B. cereus in the collected samples was 26.37% (159/603), and the contamination level in 5.03% (8/159) positive samples exceeded 1100 most probable number/g. The detection rates of virulence genes were 89.7% for the nheABC gene group, 37.1% for the hblACD gene cluster, 82.3% for cytK-2, and 2.9% for cesB. Notably, all isolates presented with multiple antibiotic resistance, and 99.43% of isolates were resistant to five classes of antibiotics. In addition, the multilocus sequence typing results indicated that all isolates were rich in genetic diversity. Collectively, we conducted a systematic investigation on the prevalence and characterization of B. cereus in meat and meat products in China, providing crucial information for assessing the risk of B. cereus occurrence in meat and meat products.
Collapse
Affiliation(s)
- Li Kong
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Shubo Yu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoming Yuan
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Chun Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Pengfei Yu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Hui Guo
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Haiyan Zeng
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| |
Collapse
|
10
|
Abril AG, Ortea I, Barros-Velázquez J, Villa TG, Calo-Mata P. Shotgun Proteomics for Food Microorganism Detection. Methods Mol Biol 2021; 2259:205-213. [PMID: 33687717 DOI: 10.1007/978-1-0716-1178-4_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) has been used for the analysis of bacterial pathogen strain-specific diagnostic peptides allowing the characterization of bacterial strains.Here, we describe the analysis of tryptic digestion peptides by LC-ESI-MS/MS to search for specific biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other hand, the physiological and biochemical characteristics such as the expression of virulence factors, including toxins, immune-modulatory factors, and exoenzymes.
Collapse
Affiliation(s)
- Ana G Abril
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Ignacio Ortea
- Institute Maimónides of Biomedica Investigation of Córdoba, Córdoba, Spain
| | - Jorge Barros-Velázquez
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, 27002, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Tomás G Villa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Pilar Calo-Mata
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, 27002, Universidad de Santiago de Compostela, A Coruña, Spain.
| |
Collapse
|
11
|
Shani N, Isolini D, Marzohl D, Berthoud H. Evaluation of a new culture medium for the enumeration and isolation of Streptococcus salivarius subsp. thermophilus from cheese. Food Microbiol 2020; 95:103672. [PMID: 33397607 DOI: 10.1016/j.fm.2020.103672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022]
Abstract
Enumeration and isolation of Streptococcus salivarius subsp. thermophilus from cheese is challenging, due to the relatively high number of species it may host. We describe medium SPY9.3 for the cultivation of S. salivarius subsp. thermophilus from cheese. The medium and related incubation conditions (SPY) was compared with 2 other protocols, M17 and ST: sensitivity was assessed by parallel cultivation of 55 strains of S. salivarius subsp. thermophilus, and selectivity by (i) parallel cultivation of 60 strains belonging to 20 different non-target species and sub-species and (ii) isolating bacteria from 3 raw-milk cheeses. Colony counts were similar on SPY9.3 and M17 (mean difference 0.07 log(cfu/mL), p > 0.001) and significantly higher on ST than on M17 and SPY9.3 (mean differences 0.42 and 0.48 log(cfu/mL), respectively, p < 0.001). SPY was more specific than ST and M17, with respectively 20%, 40%, and 50% of the investigated non-target species able to grow. S. salivarius subsp. thermophilus, Enterococcus spp., and Staphylococcus aureus were indistinguishable using all 3 protocols. Only SPY avoided growth of Lactobacillus delbrueckii subsp. lactis. Finally, ST and SPY displayed higher recoveries of S. salivarius subsp. thermophilus colonies from cheese than M17 (5.6, 5.5, and 3.0 adjusted log(cfu/mL), respectively) and the lowest proportion of non-specific isolates. The protocol described here and based on SPY9.3 presents a promising alternative to existing protocols for the enumeration and isolation of S salivarius subsp. thermophilus from cheese or other complex fermented products.
Collapse
Affiliation(s)
- Noam Shani
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, 3003, Bern, Switzerland.
| | - Dino Isolini
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, 3003, Bern, Switzerland
| | - Daniel Marzohl
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, 3003, Bern, Switzerland
| | - Hélène Berthoud
- Agroscope, Competence Division Methods Development and Analytics, Research Group Fermenting Organisms, Schwarzenburgstrasse 161, 3003, Bern, Switzerland
| |
Collapse
|
12
|
Rousset L, Alpha-Bazin B, Château A, Armengaud J, Clavel T, Berge O, Duport C. Groundwater promotes emergence of asporogenic mutants of emetic Bacillus cereus. Environ Microbiol 2020; 22:5248-5264. [PMID: 32815215 DOI: 10.1111/1462-2920.15203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023]
Abstract
Bacillus cereus is a ubiquitous endospore-forming bacterium, which mainly affects humans as a food-borne pathogen. Bacillus cereus can contaminate groundwater used to irrigate food crops. Here, we examined the ability of the emetic strain B. cereus F4810/72 to survive abiotic conditions encountered in groundwater. Our results showed that vegetative B. cereus cells rapidly evolved in a mixed population composed of endospores and asporogenic variants bearing spo0A mutations. One asporogenic variant, VAR-F48, was isolated and characterized. VAR-F48 can survive in sterilized groundwater over a long period in a vegetative form and has a competitive advantage compared to its parental strain. Proteomics analysis allowed us to quantify changes to cellular and exoproteins after 24 and 72 h incubation in groundwater, for VAR-F48 compared to its parental strain. The results revealed a significant re-routing of the metabolism in the absence of Spo0A. We concluded that VAR-F48 maximizes its energy use to deal with oligotrophy, and the emergence of spo0A-mutated variants may contribute to the persistence of emetic B. cereus in natural oligotrophic environments.
Collapse
Affiliation(s)
- Ludivine Rousset
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France.,INRAE, Pathologie Végétale, Montfavet, F-84140, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Thierry Clavel
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Odile Berge
- INRAE, Pathologie Végétale, Montfavet, F-84140, France
| | | |
Collapse
|
13
|
Characterization of Clostridium tyrobutyricum Strains Using Three Different Typing Techniques. Microorganisms 2020; 8:microorganisms8071057. [PMID: 32708607 PMCID: PMC7409188 DOI: 10.3390/microorganisms8071057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022] Open
Abstract
Clostridium tyrobutyricum is well known as one of the main causative agents of severe cheese spoilage. The metabolism of this anaerobic bacterium during ripening leads to textural and sensory defects in cheese and consequential loss of product value. The potential to induce cheese spoilage, however, may vary among different strains of the same species. Therefore, a better understanding of the intra-species diversity of C. tyrobutyricum may be of practical relevance for the dairy industry. In the present study, we compared the ability of three typing techniques to differentiate 95 C. tyrobutyricum strains on the subspecies level: (1) repetitive element palindromic PCR (rep-PCR) fingerprinting combined with conventional agarose gel electrophoresis, (2) hexaplex-PCR followed by an automated capillary electrophoresis and (3) matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) typing. MALDI-TOF MS fingerprinting provided only moderate reproducibility and low discriminatory power. Both PCR-based methods were highly reproducible and discriminative, with hexaplex-PCR fingerprinting being slightly more discriminative than rep-PCR typing. Overall, a high intra-species diversity was observed among the tested strains, indicating that further investigations on the strain level may be of interest.
Collapse
|
14
|
In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. Microorganisms 2020; 8:microorganisms8070966. [PMID: 32605102 PMCID: PMC7409220 DOI: 10.3390/microorganisms8070966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/22/2023] Open
Abstract
The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome’s annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, γ-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.
Collapse
|
15
|
Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Characterization of Bacteriophage Peptides of Pathogenic Streptococcus by LC-ESI-MS/MS: Bacteriophage Phylogenomics and Their Relationship to Their Host. Front Microbiol 2020; 11:1241. [PMID: 32582130 PMCID: PMC7296060 DOI: 10.3389/fmicb.2020.01241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/21/2023] Open
Abstract
The present work focuses on LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analysis of phage-origin tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2,546 non-redundant peptides belonging to 1,890 proteins were identified and analyzed. Among them, 65 phage-origin peptides were determined as specific Streptococcus spp. peptides. These peptides belong to proteins such as phage repressors, phage endopeptidases, structural phage proteins, and uncharacterized phage proteins. Studies involving bacteriophage phylogeny and the relationship between phages encoding the peptides determined and the bacteria they infect were also performed. The results show how specific peptides are present in closely related phages, and a link exists between bacteriophage phylogeny and the Streptococcus spp. they infect. Moreover, the phage peptide M∗ATNLGQAYVQIM∗PSAK is unique and specific for Streptococcus agalactiae. These results revealed that diagnostic peptides, among others, could be useful for the identification and characterization of mastitis-causing Streptococcus spp., particularly peptides that belong to specific functional proteins, such as phage-origin proteins, because of their specificity to bacterial hosts.
Collapse
Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Jose L. R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| |
Collapse
|
16
|
Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Rama JLR, Calo-Mata P, Sánchez-Pérez A, Villa TG. Proteomic Characterization of Antibiotic Resistance, and Production of Antimicrobial and Virulence Factors in Streptococcus Species Associated with Bovine Mastitis. Could Enzybiotics Represent Novel Therapeutic Agents Against These Pathogens? Antibiotics (Basel) 2020; 9:antibiotics9060302. [PMID: 32512932 PMCID: PMC7344566 DOI: 10.3390/antibiotics9060302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 06/03/2020] [Indexed: 01/31/2023] Open
Abstract
Streptococcus spp. are major mastitis pathogens present in dairy products, which produce a variety of virulence factors that are involved in streptococcal pathogenicity. These include neuraminidase, pyrogenic exotoxin, and M protein, and in addition they might produce bacteriocins and antibiotic-resistance proteins. Unjustifiable misuse of antimicrobials has led to an increase in antibiotic-resistant bacteria present in foodstuffs. Identification of the mastitis-causing bacterial strain, as well as determining its antibiotic resistance and sensitivity is crucial for effective therapy. The present work focused on the LC–ESI–MS/MS (liquid chromatography–electrospray ionization tandem mass spectrometry) analysis of tryptic digestion peptides from mastitis-causing Streptococcus spp. isolated from milk. A total of 2706 non-redundant peptides belonging to 2510 proteins was identified and analyzed. Among them, 168 peptides were determined, representing proteins that act as virulence factors, toxins, anti-toxins, provide resistance to antibiotics that are associated with the production of lantibiotic-related compounds, or play a role in the resistance to toxic substances. Protein comparisons with the NCBI database allowed the identification of 134 peptides as specific to Streptococcus spp., while two peptides (EATGNQNISPNLTISNAQLNLEDKNK and DLWC*NM*IIAAK) were found to be species-specific to Streptococcus dysgalactiae. This proteomic repository might be useful for further studies and research work, as well as for the development of new therapeutics for the mastitis-causing Streptococcus strains.
Collapse
Affiliation(s)
- Ana G. Abril
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, 15705 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.)
| | - Mónica Carrera
- Marine Research Institute (IIM), Spanish National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Pontevedra, Spain;
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, Montirón 154, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (J.B.-V.); (P.C.-M.)
| | - José-Luis R. Rama
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, 15705 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.)
| | - Pilar Calo-Mata
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (J.B.-V.); (P.C.-M.)
| | - Angeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Tomás G. Villa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, 15705 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.)
- Correspondence:
| |
Collapse
|
17
|
Kuhring M, Doellinger J, Nitsche A, Muth T, Renard BY. TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples. J Proteome Res 2020; 19:2501-2510. [PMID: 32362126 DOI: 10.1021/acs.jproteome.9b00714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to noniterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted, and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt.
Collapse
Affiliation(s)
- Mathias Kuhring
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health (BIH), 10178 Berlin, Germany.,Berlin Institute of Health Metabolomics Platform, Berlin Institute of Health (BIH), 10178 Berlin, Germany.,Max Delbrück Center (MDC) for Molecular Medicine, 13125 Berlin, Germany
| | - Joerg Doellinger
- Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS 6), Robert Koch Institute, 13353 Berlin, Germany.,Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, 13353 Berlin, Germany
| | - Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.,eScience Division (S.3), Federal Institute for Materials Research and Testing, 12489 Berlin, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany.,Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, 14482 Potsdam, Germany
| |
Collapse
|
18
|
Lee SY, Yun SH, Lee H, Yi YS, Park EC, Kim W, Kim HY, Lee JC, Kim GH, Kim SI. Analysis of the Extracellular Proteome of Colistin-Resistant Korean Acinetobacter baumannii Strains. ACS OMEGA 2020; 5:5713-5720. [PMID: 32226849 PMCID: PMC7097930 DOI: 10.1021/acsomega.9b03723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/27/2020] [Indexed: 05/08/2023]
Abstract
We analyzed the extracellular proteome of colistin-resistant Korean Acinetobacter baumannii (KAB) strains to identify proteome profiles that can be used to characterize extensively drug-resistant KAB strains. Four colistin-resistant KAB strains with colistin resistance associated with point mutations in pmrB and pmrC genes were analyzed. Analysis of the extracellular proteome of these strains revealed the presence of 506 induced common proteins, which were hence considered as the core extracellular proteome. Class C ADC-30 and class D OXA-23 β-lactamases were abundantly induced in these strains. Porins (CarO and CarO-like porin), outer membrane proteins (OmpH and BamABDE), transport protein (AdeK), receptor (TonB), and several proteins of unknown function were among the specifically induced proteins. Based on the sequence homology analysis of proteins from the core proteome and those of other A. baumannii strains and pathogenic bacterial species as well as further in silico screening, we propose that CarO-like porin is an A. baumannii-specific protein and that two tryptic peptides that originate from CarO-like porin detected by tandem mass spectrometry are peptide makers of this protein.
Collapse
Affiliation(s)
- Sang-Yeop Lee
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Sung Ho Yun
- Center
for Research Equipment, Korea Basic Science
Institute, Ochang 28119, Korea
| | - Hayoung Lee
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
| | - Yoon-Sun Yi
- Center
for Research Equipment, Korea Basic Science
Institute, Ochang 28119, Korea
| | - Edmond Changkyun Park
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
| | - Wooyoung Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- Department
of Toxicology, College of Pharmacy, Chungnam
National University, Daejeon 34134, Korea
| | - Hye-Yeon Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | - Je Chul Lee
- Department
of Microbiology, School of Medicine, Kyungpook
National University, Daegu 41944, Korea
| | - Gun-Hwa Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research
Center for Bioconvergence Analysis, Korea
Basic Science Institute, Ochang 28119, Korea
- Center
for Convegent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
- Department
of Bio-Analytical Science, University of
Science and Technology (UST), Daejeon 34113, Korea
- E-mail: . Phone: +82-43-240-5422. Fax: +82-43-240-5416
| |
Collapse
|
19
|
Merkley ED, Burnum-Johnson KE, Anderson LN, Jenson SC, Wahl KL. Uniformly 15N-Labeled Recombinant Ricin A-Chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2019; 91:13372-13376. [PMID: 31596564 DOI: 10.1021/acs.analchem.9b03389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ricin, a toxic protein from the castor plant, is of forensic and biosecurity interest because of its high toxicity and common occurrence in crimes and attempted crimes. Qualitative methods to detect ricin are therefore needed. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics methods are well suited because of their high specificity. Specificity in LC-MS/MS comes from both the LC and MS components. However, modern untargeted proteomics methods often use nanoflow LC, which has less reproducible retention times than standard-flow LC, making it challenging to use retention time as a point of identification in a forensic assay. We address this challenge by using retention times relative to a standard, namely, the uniformly 15N-labeled ricin A-chain produced recombinantly in a bacterial expression system. This material, added as an internal standard prior to trypsin digestion, produces a stable-isotope-labeled standard for every ricin tryptic peptide in the sample. We show that the MS signals for 15N and natural isotopic abundance ricin peptides are distinct, with mass shifts that correspond to the numbers of nitrogen atoms in each peptide or fragment. We also show that, as expected, labeled and unlabeled peptides coelute, with relative retention time differences of less than 0.2%.
Collapse
Affiliation(s)
- Eric D Merkley
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kristin E Burnum-Johnson
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Lindsey N Anderson
- Biological Systems Science Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Sarah C Jenson
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Karen L Wahl
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| |
Collapse
|
20
|
Wei S, Chelliah R, Park BJ, Kim SH, Forghani F, Cho MS, Park DS, Jin YG, Oh DH. Differentiation of Bacillus thuringiensis From Bacillus cereus Group Using a Unique Marker Based on Real-Time PCR. Front Microbiol 2019; 10:883. [PMID: 31114555 PMCID: PMC6503103 DOI: 10.3389/fmicb.2019.00883] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
The efficiency of a novel biomarker (the transcriptional regulator, XRE) was tested and evaluated in differentiating Bacillus thuringiensis from Bacillus cereus group species in environmental and spiked samples based on PCR and real-time PCR. Totally 120 strains, representing two bacterial groups, B. cereus group and non-Bacillus sp., were used to evaluate the performance of XRE and crystal protein (cry2, an existing biomarker). Further, three diverse samples (kimbap, lettuce, and spinach) were inoculated with B. thuringiensis and prominent biomarkers XRE and cry2 were used as targets. Direct analysis of the detection results for the pure cultures of B. cereus group wild-types, references and type strains revealed an accuracy rate of 97.5% targeting XRE, and 83.3% targeting cry2. The real-time PCR was constructed with a R 2-value of 0.993. For the artificially contaminated samples, a concentration of 103 CFU/g of B. thuringiensis in spiked food samples could be detected using real-time PCR targeting XRE. A good performance was obtained with XRE in discriminating B. thuringiensis from B. cereus groups, as well as detecting B. thuringiensis in spiked food samples with PCR or real-time PCR. Therefore, this real-time PCR targeting XRE can be used as a dependable and promising tool to identify B. thuringiensis in foods.
Collapse
Affiliation(s)
- Shuai Wei
- Department of Medical Biomaterials Engineering, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Byung-Jae Park
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Se-Hun Kim
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| | - Fereidoun Forghani
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, United States
| | - Min Seok Cho
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Dong-Suk Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Yong-Guo Jin
- National Research and Development Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon, South Korea
| |
Collapse
|
21
|
Ducrest PJ, Pfammatter S, Stephan D, Vogel G, Thibault P, Schnyder B. Rapid detection of Bacillus ionophore cereulide in food products. Sci Rep 2019; 9:5814. [PMID: 30967595 PMCID: PMC6456620 DOI: 10.1038/s41598-019-42167-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/22/2019] [Indexed: 12/17/2022] Open
Abstract
Cereulide is a toxic cyclic depsipeptide produced by certain strains of Bacillus cereus found in soil and food products. While some harmless strains of Bacillus are used as probiotic, others can cause nausea and vomiting, and represent an important food safety concern. Current detection methods are time consuming and do not necessarily detect toxic cereulide. Here, we developed a rapid protocol using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) mass spectrometry that detects the toxin originating from a colony smear of B. cereus. The distinct molecular feature of the toxin peak at m/z 1,191 was clearly identified from bacterial extracts with a limit of detection (LOD) of 30 ng/mL. Final optimisation of the sample preparation was based on cereulide chelating cations to produce the alkali adduct [M + K]+ without the use of a MALDI matrix, and provided a 1,000-fold improvement of LOD with 30 pg/mL of cereulide. We evaluated the application of this method for the detection of cereulide in rice, milk, and different ready-to-eat meals. The proposed protocol is quick, easy and provides an improvement over conventional methods for the detection of B. cereus toxin.
Collapse
Affiliation(s)
- P J Ducrest
- University of Applied Sciences, HES-SO Valais//Wallis, Institute of Life Technologies, Sion, Switzerland
| | - S Pfammatter
- University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - D Stephan
- University of Applied Sciences, HES-SO Valais//Wallis, Institute of Life Technologies, Sion, Switzerland
| | - G Vogel
- Mabritec AG, Riehen, Switzerland
| | - P Thibault
- University of Montreal, Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada
| | - B Schnyder
- University of Applied Sciences, HES-SO Valais//Wallis, Institute of Life Technologies, Sion, Switzerland.
| |
Collapse
|
22
|
Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
|
23
|
Chelliah R, Wei S, Park BJ, Rubab M, Banan-Mwine Dalirii E, Barathikannan K, Jin YG, Oh DH. Whole genome sequence of Bacillus thuringiensis ATCC 10792 and improved discrimination of Bacillus thuringiensis from Bacillus cereus group based on novel biomarkers. Microb Pathog 2019; 129:284-297. [DOI: 10.1016/j.micpath.2019.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 11/17/2022]
|
24
|
Lüdin P, Roetschi A, Wüthrich D, Bruggmann R, Berthoud H, Shani N. Update on Tetracycline Susceptibility of Pediococcus acidilactici Based on Strains Isolated from Swiss Cheese and Whey. J Food Prot 2018; 81:1582-1589. [PMID: 30169118 DOI: 10.4315/0362-028x.jfp-18-160] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacterial strains used as starter cultures in the production of fermented foods may act as reservoirs for antibiotic resistance (AbR) genes. To avoid the introduction of such genes into the food chain, the presence of acquired AbR in bacterial strains added to food must be tested. Standard protocols and microbiological cut-off values have been defined to provide practitioners with a basis for evaluating whether their bacterial isolates harbor an acquired resistance to a given antibiotic. Here, we tested the AbR of 24 strains of Pediococcus acidilactici by using the standard protocol and microbiological cut-off values recommended by the European Food Safety Authority. Phenotypic data were complemented by searching for known AbR genes using an in silico analysis of whole genomes. The majority (54.2%) of the strains were able to grow at a tetracycline concentration above the defined cut-off, even though only one strain carried a known tetracycline resistance gene, tetM. The same strain also carried the AbR gene of an erythromycin resistance methylase, ermA, and displayed resistance toward clindamycin and erythromycin. Our results bolster the scarce data on the sensitivity of P. acidilactici to tetracycline and suggest that the microbiological cut-off recommended by the European Food Safety Authority for this antibiotic should be amended.
Collapse
Affiliation(s)
- Petra Lüdin
- 1 Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; and
| | | | - Daniel Wüthrich
- 2 Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Rémy Bruggmann
- 2 Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Hélène Berthoud
- 1 Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; and
| | - Noam Shani
- 1 Agroscope, Schwarzenburgstrasse 161, 3003 Bern, Switzerland; and
| |
Collapse
|
25
|
Abhyankar WR, Wen J, Swarge BN, Tu Z, de Boer R, Smelt JPPM, de Koning LJ, Manders E, de Koster CG, Brul S. Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores. Food Microbiol 2018; 81:89-96. [PMID: 30910091 DOI: 10.1016/j.fm.2018.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/21/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
Bacterial spores are ubiquitous in nature and can withstand both chemical and physical stresses. Spores can survive food preservation processes and upon outgrowth cause food spoilage as well as safety risks. The heterogeneous germination and outgrowth behavior of isogenic spore populations exacerbates this risk. A major unknown factor of spores is likely to be the inherently heterogeneous spore protein composition. The proteomics methods discussed here help in broadening the knowledge about spore structure and identification of putative target proteins from spores of different spore formers. Approaches to synchronize Bacillus subtilis spore formation, and to analyze spore proteins as well as the physiology of spore germination and outgrowth are also discussed. Live-imaging and fluorescence microscopy techniques discussed here allow analysis, at single cell level, of the 'germinosome', the process of spore germination itself, spore outgrowth and the spore intracellular pH dynamics. For the latter, a recently published improved pHluorin (IpHluorin) under control of the ptsG promoter is applicable. While the data obtained from such tools offers novel insight in the mechanisms of bacterial spore awakening, it may also be used to probe candidate antimicrobial compounds for inhibitory effects on spore germination and strengthen microbial risk assessment.
Collapse
Affiliation(s)
- W R Abhyankar
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - J Wen
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - B N Swarge
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Z Tu
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - R de Boer
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - J P P M Smelt
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - L J de Koning
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - E Manders
- Van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - C G de Koster
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| |
Collapse
|
26
|
Gdoura-Ben Amor M, Siala M, Zayani M, Grosset N, Smaoui S, Messadi-Akrout F, Baron F, Jan S, Gautier M, Gdoura R. Isolation, Identification, Prevalence, and Genetic Diversity of Bacillus cereus Group Bacteria From Different Foodstuffs in Tunisia. Front Microbiol 2018; 9:447. [PMID: 29593691 PMCID: PMC5858518 DOI: 10.3389/fmicb.2018.00447] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/26/2018] [Indexed: 11/13/2022] Open
Abstract
Bacillus cereus group is widespread in nature and foods. Several members of this group are recognized as causing food spoilage and/or health issues. This study was designed to determine the prevalence and genetic diversity of the B. cereus group strains isolated in Tunisia from different foods (cereals, spices, cooked food, fresh-cut vegetables, raw and cooked poultry meats, seafood, canned, pastry, and dairy products). In total, 687 different samples were collected and searched for the presence of the B. cereus group after selective plating on MYP agar and enumeration of each sample. The typical pink-orange uniform colonies surrounded by a zone of precipitate were assumed to belong to the B. cereus group. One typical colony from each sample was subcultured and preserved as cryoculture. Overall, 191 (27.8%) food samples were found positive, giving rise to a collection of 191 B. cereus-like isolates. The concentration of B. cereus-like bacteria were below 103 cfu/g or ml in 77.5% of the tested samples. Higher counts (>104 cfu/g or ml) were found in 6.8% of samples including fresh-cut vegetables, cooked foods, cereals, and pastry products. To verify whether B. cereus-like isolates belonged to the B. cereus group, a PCR test targeting the sspE gene sequence specific of the group was carried out. Therefore, 174 isolates were found to be positive. Food samples were contaminated as follows: cereals (67.6%), pastry products (46.2%), cooked food (40.8%), cooked poultry meat (32.7%), seafood products (32.3%), spices (28.8%), canned products (16.7%), raw poultry meat (9.4%), fresh-cut vegetables (5.0%), and dairy products (4.8%). The 174 B. cereus isolates were characterized by partial sequencing of the panC gene, using a Sym'Previous software tool to assign them to different phylogenetic groups. Strains were distributed as follows: 61.3, 29.5, 7.5, and 1.7% in the group III, IV, II, and V, respectively. The genetic diversity was further assessed by ERIC-PCR and PFGE typing methods. PFGE and ERIC-PCR patterns analysis allowed discriminating 143 and 99 different profiles, respectivey. These findings, associated to a relatively higher prevalence of B. cereus group in different foods, could be a significant etiological agent of food in Tunisia.
Collapse
Affiliation(s)
- Maroua Gdoura-Ben Amor
- Laboratory Research of Toxicology-Microbiology Environmental and Health, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia.,Equipe Microbiologie, Agrocampus Ouest, Institut National de la Recherche Agronomique, UMR1253 Science et Technologie du Lait et de l'œuf, Rennes, France
| | - Mariam Siala
- Laboratory Research of Toxicology-Microbiology Environmental and Health, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia.,Department of Biology, Preparatory Institute for Engineering Studies, University of Sfax, Sfax, Tunisia
| | - Mariem Zayani
- Laboratory Research of Toxicology-Microbiology Environmental and Health, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia
| | - Noël Grosset
- Equipe Microbiologie, Agrocampus Ouest, Institut National de la Recherche Agronomique, UMR1253 Science et Technologie du Lait et de l'œuf, Rennes, France
| | - Salma Smaoui
- Regional Laboratory of Hygiene, Hedi Chaker University Hospital, Sfax, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Feriele Messadi-Akrout
- Regional Laboratory of Hygiene, Hedi Chaker University Hospital, Sfax, Tunisia.,Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Florence Baron
- Equipe Microbiologie, Agrocampus Ouest, Institut National de la Recherche Agronomique, UMR1253 Science et Technologie du Lait et de l'œuf, Rennes, France
| | - Sophie Jan
- Equipe Microbiologie, Agrocampus Ouest, Institut National de la Recherche Agronomique, UMR1253 Science et Technologie du Lait et de l'œuf, Rennes, France
| | - Michel Gautier
- Equipe Microbiologie, Agrocampus Ouest, Institut National de la Recherche Agronomique, UMR1253 Science et Technologie du Lait et de l'œuf, Rennes, France
| | - Radhouane Gdoura
- Laboratory Research of Toxicology-Microbiology Environmental and Health, Sciences Faculty of Sfax, University of Sfax, Sfax, Tunisia
| |
Collapse
|
27
|
Are injectable illegal polypeptide drugs safe? Case report demonstrating the presence of haemolyticBacillus cereusin 2 illegal peptide drugs. Drug Test Anal 2017; 10:791-795. [DOI: 10.1002/dta.2304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 01/18/2023]
|
28
|
Gekenidis MT, Gossin D, Schmelcher M, Schöner U, Remus-Emsermann MNP, Drissner D. Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment. J Appl Microbiol 2017; 123:916-932. [PMID: 28708321 DOI: 10.1111/jam.13532] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/06/2017] [Accepted: 07/06/2017] [Indexed: 01/06/2023]
Abstract
AIM Investigate dynamics of culturable mesophilic bacteria and selected food-contaminating bacteria from three herbs and their production environment. METHODS AND RESULTS Marjoram, basil and thyme were investigated during one growing season by sampling plants, organic fertilizers, soil, irrigation water and marketed products. Mesophilic bacteria and selected food-contaminating bacteria (Escherichia coli, Enterococcus spp., Bacillus cereus group) were cultured and identified by MALDI biotyping. Culturable mesophilic bacteria on marjoram and basil plants decreased over time by two orders of magnitude starting at above 106 colony forming units per gram (CFU per g), while they remained constant on thyme (~104 CFU per g). Compared to the last field sample, mesophilic bacteria were increased on all market-ready products by one order of magnitude. Marjoram and basil were dominated by B. cereus group, Enterobacter spp. and Pseudomonas spp., thyme by Bacillus spp. and Pseudomonas spp. All selected food-contaminating bacteria were detected in soil and reservoir-sourced irrigation water, whereas in municipal water, only B. cereus group and rarely Enterococcus spp. were found. Escherichia coli was detected only on young marjoram and basil plants (5 × 102 and 5 × 101 CFU per g, respectively), whereas Enterococcus spp. and B. cereus group were consistently detected on these two herbs. Thyme plants only contained B. cereus group consistently (above 103 CFU per g). Marketed marjoram and thyme contained Enterococcus spp. (5 × 102 and 104 CFU per g) and B. cereus group (~5 × 102 CFU per g), while no selected food-contaminating bacteria were found on marketed basil. CONCLUSIONS Overall, culturable mesophilic bacteria were dominated by Pseudomonas spp. and Bacillus spp., with increased numbers on market-ready products. Selected food-contaminating bacteria were readily detectable, however, only the B. cereus group was found throughout in all systems. SIGNIFICANCE AND IMPACT OF THE STUDY Insight into composition and development of mesophilic bacterial communities and selected food-contaminating bacteria of fresh herbs contributes to estimating consumer exposure.
Collapse
Affiliation(s)
- M-T Gekenidis
- Microbiology of Plant Foods, Agroscope, Waedenswil, Switzerland.,Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - D Gossin
- Microbiology of Plant Foods, Agroscope, Waedenswil, Switzerland
| | - M Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - U Schöner
- Mäder Kräuter, Boppelsen, Switzerland
| | - M N P Remus-Emsermann
- Microbiology of Plant Foods, Agroscope, Waedenswil, Switzerland.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - D Drissner
- Microbiology of Plant Foods, Agroscope, Waedenswil, Switzerland
| |
Collapse
|
29
|
Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station. mSystems 2017; 2:mSystems00021-17. [PMID: 28680972 PMCID: PMC5487513 DOI: 10.1128/msystems.00021-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/23/2017] [Indexed: 12/30/2022] Open
Abstract
The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions. In an ongoing Microbial Observatory investigation of the International Space Station (ISS), 11 Bacillus strains (2 from the Kibo Japanese experimental module, 4 from the U.S. segment, and 5 from the Russian module) were isolated and their whole genomes were sequenced. A comparative analysis of the 16S rRNA gene sequences of these isolates showed the highest similarity (>99%) to the Bacillus anthracis-B. cereus-B. thuringiensis group. The fatty acid composition, polar lipid profile, peptidoglycan type, and matrix-assisted laser desorption ionization–time of flight profiles were consistent with the B. cereus sensu lato group. The phenotypic traits such as motile rods, enterotoxin production, lack of capsule, and resistance to gamma phage/penicillin observed in ISS isolates were not characteristics of B. anthracis. Whole-genome sequence characterizations showed that ISS strains had the plcR non-B. anthracis ancestral “C” allele and lacked anthrax toxin-encoding plasmids pXO1 and pXO2, excluding their identification as B. anthracis. The genetic identities of all 11 ISS isolates characterized via gyrB analyses arbitrarily identified them as members of the B. cereus group, but traditional DNA-DNA hybridization (DDH) showed that the ISS isolates are similar to B. anthracis (88% to 90%) but distant from the B. cereus (42%) and B. thuringiensis (48%) type strains. The DDH results were supported by average nucleotide identity (>98.5%) and digital DDH (>86%) analyses. However, the collective phenotypic traits and genomic evidence were the reasons to exclude the ISS isolates from B. anthracis. Nevertheless, multilocus sequence typing and whole-genome single nucleotide polymorphism analyses placed these isolates in a clade that is distinct from previously described members of the B. cereus sensu lato group but closely related to B. anthracis. IMPORTANCE The International Space Station Microbial Observatory (Microbial Tracking-1) study is generating a microbial census of the space station’s surfaces and atmosphere by using advanced molecular microbial community analysis techniques supported by traditional culture-based methods and modern bioinformatic computational modeling. This approach will lead to long-term, multigenerational studies of microbial population dynamics in a closed environment and address key questions, including whether microgravity influences the evolution and genetic modification of microorganisms. The spore-forming Bacillus cereus sensu lato group consists of pathogenic (B. anthracis), food poisoning (B. cereus), and biotechnologically useful (B. thuringiensis) microorganisms; their presence in a closed system such as the ISS might be a concern for the health of crew members. A detailed characterization of these potential pathogens would lead to the development of suitable countermeasures that are needed for long-term future missions and a better understanding of microorganisms associated with space missions.
Collapse
|