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Guard J, Jones DR, Gast RK, Garcia JS, Rothrock MJ. Serotype Screening of Salmonella enterica Subspecies I by Intergenic Sequence Ribotyping (ISR): Critical Updates. Microorganisms 2022; 11:microorganisms11010097. [PMID: 36677389 PMCID: PMC9863722 DOI: 10.3390/microorganisms11010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/03/2023] Open
Abstract
(1) Background: Foodborne illness from Salmonella enterica subspecies I is most associated with approximately 32 out of 1600 serotypes. While whole genome sequencing and other nucleic acid-based methods are preferred for serotyping, they require expertise in bioinformatics and often submission to an external agency. Intergenic Sequence Ribotyping (ISR) assigns serotype to Salmonella in coordination with information freely available at the National Center for Biotechnology Information. ISR requires updating because it was developed from 26 genomes while there are now currently 1804 genomes and 1685 plasmids. (2) Methods: Serotypes available for sequencing were analyzed by ISR to confirm primer efficacy and to identify any issues in application. Differences between the 2012 and 2022 ISR database were tabulated, nomenclature edited, and instances of multiple serotypes aligning to a single ISR were examined. (3) Results: The 2022 ISR database has 268 sequences and 40 of these were assigned new NCBI accession numbers that were not previously available. Extending boundaries of sequences resolved hdfR cross-alignment and reduced multiplicity of alignment for 37 ISRs. Comparison of gene cyaA sequences and some cell surface epitopes provided evidence that homologous recombination was potentially impacting results for this subset. There were 99 sequences that still had no match with an NCBI submission. (4) The 2022 ISR database is available for use as a serotype screening method for Salmonella enterica subspecies I. Finding that 36.9% of the sequences in the ISR database still have no match within the NCBI Salmonella enterica database suggests that there is more genomic heterogeneity yet to characterize.
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Affiliation(s)
- Jean Guard
- Correspondence: ; Tel.: +1-706-546-3131 or +1-706-546-3445
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2
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Metabolomic Profiles of Multidrug-Resistant Salmonella Typhimurium from Humans, Bovine, and Porcine Hosts. Animals (Basel) 2022; 12:ani12121518. [PMID: 35739855 PMCID: PMC9219436 DOI: 10.3390/ani12121518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The global threat that is imposed by the resistance the pathogens develop to antimicrobial drugs is escalating. Tools to detect the resistance (with evidence on molecular and cellular outcomes) would reveal intricate mechanisms through which novel drugs could be developed. Approaches such as metabolomics, which involve metabolite detection, provide scientific evidence of metabolite expression of antimicrobial-resistant pathogens. The current study involved metabolomics of antimicrobial-resistant Salmonella Typhimurium collected from various hosts (human, porcine, bovine) and were exposed to antimicrobial drugs—ampicillin, chloramphenicol, streptomycin, sulfisoxazole, and tetracycline—as one set of the experiment. The same isolates were also cultured with no drug exposure as a comparison. There are certain pathways of metabolite expression that are impacted by drug exposure when compared to no drug exposure, meaning that the expressed metabolites could be potential targets for drug companies for the treatment of antimicrobial-resistant pathogens. Abstract Antimicrobial resistance (AMR) is a global public health threat, yet tools for detecting resistance patterns are limited and require advanced molecular methods. Metabolomic approaches produce metabolite profiles and help provide scientific evidence of differences in metabolite expressions between Salmonella Typhimurium from various hosts. This research aimed to evaluate the metabolomic profiles of S. Typhimurium associated with AMR and it compares profiles across various hosts. Three samples, each from bovine, porcine, and humans (total n = 9), were selectively chosen from an existing library to compare these nine isolates cultured under no drug exposure to the same isolates cultured in the presence of the antimicrobial drug panel ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfisoxazole, tetracycline). This was followed by metabolomic profiling using UPLC and GC–mass spectrometry. The results indicated that the metabolite regulation was affected by antibiotic exposure, irrespective of the host species. When exposed to antibiotics, 59.69% and 40.31% of metabolites had increased and decreased expressions, respectively. The most significantly regulated metabolic pathway was aminoacyl-tRNA biosynthesis, which demonstrated increased expressions of serine, aspartate, alanine, and citric acid. Metabolites that showed decreased expressions included glutamate and pyruvate. This pathway and associated metabolites have known AMR associations and could be targeted for new drug discoveries and diagnostic methods.
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Kariuki F, Getanda P, Nyachieo A, Juma G, Kinyanjui P, Kamau J. Evaluation of the detection of staA, viaB and sopE genes in Salmonella spp. using the polymerase chain reaction (PCR). Arch Microbiol 2021; 204:25. [DOI: 10.1007/s00203-021-02654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022]
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Rivera D, Allel K, Dueñas F, Tardone R, Soza P, Hamilton-West C, Moreno-Switt AI. Screening the Presence of Non-Typhoidal Salmonella in Different Animal Systems and the Assessment of Antimicrobial Resistance. Animals (Basel) 2021; 11:ani11061532. [PMID: 34074040 PMCID: PMC8225015 DOI: 10.3390/ani11061532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 01/14/2023] Open
Abstract
Salmonella is a major bacterial foodborne pathogen that causes the majority of worldwide food-related outbreaks and hospitalizations. Salmonellosis outbreaks can be caused by multidrug-resistant (MDR) strains, emphasizing the importance of maintaining public health and safer food production. Nevertheless, the drivers of MDR Salmonella serovars have remained poorly understood. In this study, we compare the resistance profiles of Salmonella strains isolated from 4047 samples from domestic and wild animals in Chile. A total of 106 Salmonella strains (2.61%) are isolated, and their serogroups are characterized and tested for susceptibility to 16 different antimicrobials. The association between antimicrobial resistance (AMR) and a subset of independent variables is evaluated using multivariate logistic models. Our results show that 47 antimicrobial-resistant strains were found (44.3% of the total strains). Of the 47, 28 correspond to single-drug resistance (SDR = 26.4%) and 19 are MDR (17.9%). S. Enteritidis is highly persistent in animal production systems; however, we report that serogroup D strains are 18 times less likely to be resistant to at least one antimicrobial agent than the most common serogroup (serogroup B). The antimicrobials presenting the greatest contributions to AMR are ampicillin, streptomycin and tetracycline. Additionally, equines and industrial swine are more likely to acquire Salmonella strains with AMR. This study reports antimicrobial-susceptible and resistant Salmonella in Chile by expanding the extant literature on the potential variables affecting antimicrobial-resistant Salmonella.
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Affiliation(s)
- Dácil Rivera
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile;
| | - Kasim Allel
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile;
- Department of Disease Control, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Antimicrobial Resistance Centre, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Fernando Dueñas
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
| | - Rodolfo Tardone
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
| | - Paula Soza
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
| | - Christopher Hamilton-West
- Departamento de Medicina Preventiva, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santa Rosa 11735, La Pintana, Santiago 8820000, Chile;
| | - Andrea I. Moreno-Switt
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Republica 440, Santiago 8320000, Chile; (D.R.); (F.D.); (R.T.); (P.S.)
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile;
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago 7810000, Chile
- Correspondence:
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Prax N, Wagner S, Schardt J, Neuhaus K, Clavel T, Fuchs TM. A diet-specific microbiota drives Salmonella Typhimurium to adapt its in vivo response to plant-derived substrates. Anim Microbiome 2021; 3:24. [PMID: 33731218 PMCID: PMC7972205 DOI: 10.1186/s42523-021-00082-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 02/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background Little is known about the complex interactions between the diet, the gut microbiota, and enteropathogens. Here, the impact of two specific diets on the composition of the mouse gut microbiota and on the transcriptional response of Salmonella Typhimurium (S. Typhimurium) was analyzed in an enteritis model. Results Mice were fed for two weeks a fibre-rich, plant-based diet (PD), or a Westernized diet (WD) rich in animal fat and proteins and in simple sugars, and then infected with an invasin-negative S. Typhimurium strain ST4/74 following streptomycin-treatment. Seventy-two hours post infection, fecal pathogen loads were equal in both diet groups, suggesting that neither of the diets had negatively influenced the ability of this ST4/74 strain to colonize and proliferate in the gut at this time point. To define its diet-dependent gene expression pattern, S. Typhimurium was immunomagnetically isolated from the gut content, and its transcriptome was analyzed. A total of 66 genes were more strongly expressed in mice fed the plant-based diet. The majority of these genes was involved in metabolic functions degrading substrates of fruits and plants. Four of them are part of the gat gene cluster responsible for the uptake and metabolism of galactitol and D-tagatose. In line with this finding, 16S rRNA gene amplicon analysis revealed higher relative abundance of bacterial families able to degrade fiber and nutritive carbohydrates in PD-fed mice in comparison with those nourished with a WD. Competitive mice infection experiments performed with strain ST4/74 and ST4/74 ΔSTM3254 lacking tagatose-1,6-biphosphate aldolase, which is essential for galactitol and tagatose utilization, did not reveal a growth advantage of strain ST4/74 in the gastrointestinal tract of mice fed plant-based diet as compared to the deletion mutant. Conclusion A Westernized diet and a plant-based diet evoke distinct transcriptional responses of S. Typhimurium during infection that allows the pathogen to adapt its metabolic activities to the diet-derived nutrients. This study therefore provides new insights into the dynamic interplay between nutrient availability, indigenous gut microbiota, and proliferation of S. Typhimurium. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00082-8.
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Affiliation(s)
- Nicoletta Prax
- Lehrstuhl für Mikrobielle Ökologie, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany
| | - Stefanie Wagner
- Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743, Jena, Germany
| | - Jakob Schardt
- Lehrstuhl für Mikrobielle Ökologie, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany.,Core Facility Microbiome, ZIEL - Institute für Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Thomas Clavel
- ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany.,Arbeitsgruppe Funktionelle Mikrobiomforschung, Institut für Medizinische Mikrobiologie, Uniklinik der RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Thilo M Fuchs
- Lehrstuhl für Mikrobielle Ökologie, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany. .,ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 1, 85354, Freising, Germany. .,Friedrich-Loeffler-Institut, Institut für Molekulare Pathogenese, Naumburger Str. 96a, 07743, Jena, Germany.
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Fabri RL, Campos LM, Florêncio JR, Oliveira LG, Aragão DMDO, Ferreira ALP, de Aguiar JAK, Apolônio ACM, Alves MS, Scio E. Mitracarpus frigidus (Rubiaceae) inhibits inflammatory and oxidative stress mediators in Salmonella sp. mouse infection. J Pharm Pharmacol 2021; 73:82-92. [PMID: 33791804 DOI: 10.1093/jpp/rgaa001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Evaluation of the in-vivo anti-inflammatory activity of the methanolic extract obtained from the aerial parts of Mitracarpus frigidus (MFM) in the infection caused by two Salmonella strains and its chemical fingerprint by UFLC-quadrupole time of flight-MS. METHODS The efficacy of MFM was investigated in a classical in-vivo Salmonella infection mouse model. A Salmonella reference strain (ATCC 13311) and a clinical isolate were used to infect mice and then MFM was orally administered during 14 days. At the end of the treatment with MFM, the infection and inflammatory levels were assayed. KEY FINDINGS MFM treatment showed a significant reduction in mice mortality by Salmonella infection and, also, did not cause alterations in the liver function. Inhibitions of inflammatory and oxidative stress mediators [malondialdehyde (MDA), catalase, and metalloproteinase] were possibly involved in the observed effects. Chlorogenic acid, clarinoside, quercetin-pentosylhexoside, rutin, kaempferol-3O-rutinoside, kaempferol-rhamnosylhexoside and 2-azaanthraquinone were identified in MFM. CONCLUSIONS MFM was effective in some inflammatory parameters, in the experimental conditions that were used in the study. The results presented in this study and the previous in-vitro anti-Salmonella activity reported by our research group reinforce the importance of MFM studies to considerer it as an alternative treatment for salmonellosis.
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Affiliation(s)
- Rodrigo Luiz Fabri
- Bioactive Natural Products Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Lara Melo Campos
- Bioactive Natural Products Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Jônatas Rodrigues Florêncio
- Bioactive Natural Products Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Luiz Gustavo Oliveira
- Glycoconjugate Analysis Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Danielle Maria de Oliveira Aragão
- Bioactive Natural Products Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Adriana Lúcia Pires Ferreira
- Laboratory of Bacteriology, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Jair Adriano Kopke de Aguiar
- Glycoconjugate Analysis Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Ana Carolina Morais Apolônio
- Center of Microbiology Studies, Institute of Biological Sciences, Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Maria Silvana Alves
- Molecular and Cellular Bioactivity Laboratory, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Elita Scio
- Bioactive Natural Products Laboratory, Department of Biochemistry, Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
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Quantitative LAMP and PCR Detection of Salmonella in Chicken Samples Collected from Local Markets around Pathum Thani Province, Thailand. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2020; 2020:8833173. [PMID: 32695808 PMCID: PMC7368944 DOI: 10.1155/2020/8833173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Salmonella is a bacterium that infects people when they consume contaminated food or liquids. To prevent humans from becoming ill, it is useful to have an efficient method of detecting Salmonella before the disease is passed on through the food chain. In this research, the efficiency of Salmonella detection was compared using the following four methods: conventional loop-mediated isothermal amplification (LAMP), PCR, quantitative LAMP (qLAMP), and qPCR. The artificial infection of chicken samples started with incubating of 10 mL of 108 CFU of S. typhimurium for 6 hr. and enriching for 2 hr. to represent real contamination of the samples. The results show that the sensitivity of Salmonella DNA detection in PCR, qPCR, LAMP, and qLAMP were 50 ng, 5 ng, 50 pg, and and 500 fg, respectively. Thirty samples of 10 g chicken were collected from 10 markets in Pathum Thani, Thailand; then, the infection was detected. The conventional LAMP, qLAMP, and qPCR methods detected Salmonella in all the chicken samples. However, the conventional PCR method detected Salmonella infection in only eight of the samples. Overall, the qLAMP method had the highest sensitivity of Salmonella DNA detection.
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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Wang X, Zhu S, Zhao JH, Bao HX, Liu H, Ding TM, Liu GR, Li YG, Johnston RN, Cao FL, Tang L, Liu SL. Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation. BMC Genomics 2019; 20:930. [PMID: 31801462 PMCID: PMC6894293 DOI: 10.1186/s12864-019-6259-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
Background Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts. Results To inspect the divergence status of S. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequenced S. bongori strains. We found that RKS3044 contained a novel T6SS encoded in a pathogenicity island-like structure, in addition to a T6SS encoded in SPI-22, which is common to all S. bongori strains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among the S. bongori strains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and other S. bongori lineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the other S. bongori lineages/strains analyzed in this study. Conclusions The warm-blooded host-infecting S. bongori strain RKS3044 has diverged with distinct genomic features from other S. bongori strains, including a novel T6SS encoded in a previously not reported pathogenicity island-like structure and a unique genomic sequence degeneration pattern. These findings alert cautions about the emergence of new pathogens originating from non-pathogenic ancestors by acquiring specific pathogenic traits.
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Affiliation(s)
- Xiaoyu Wang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Songling Zhu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Jian-Hua Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hong-Xia Bao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Huidi Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Tie-Min Ding
- Department of Medicine and Food Engineering, Harbin Labor Technician College, Harbin, China
| | - Gui-Rong Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Feng-Lin Cao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China. .,Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China.
| | - Le Tang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China. .,Department of Ecosystems and Public Health, University of Calgary, Calgary, Canada.
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081, China. .,HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China. .,Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China. .,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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Rubira I, Figueras L, De las Heras M, Bueso J, Castells E, Climent M, Lacasta D. Chronic proliferative rhinitis in sheep: An update. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Nontyphoidal Salmonella purulent pericarditis presenting with pericardial tamponade in a patient on infliximab therapy. IDCases 2019; 15:e00500. [PMID: 30788216 PMCID: PMC6370545 DOI: 10.1016/j.idcr.2019.e00500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 12/15/2022] Open
Abstract
Infection with nontyphoidal Salmonella is traditionally characterized by intestinal manifestations. However, extra-intestinal infections are known to occur, with purulent pericarditis associated with cardiac tamponade being rare. This case report is of a 57-year-old male with Crohn’s disease initiated on infliximab therapy two months prior to presentation. He presented with recurrent chest pain and a single occurrence of fever. A Computed Tomography (CT) scan of the chest revealed a pericardial effusion. An echocardiogram confirmed the presence of the fluid with tamponade physiology, requiring immediate surgical decompression. The pericardial fluid culture grew Salmonella enterica, despite the patient having only a single episode of fever, disproportionate to the severity of the infection. Conceivably, the lack of systemic symptoms may be attributed to recent infliximab therapy. Upon conducting a literature review, immunosuppressive factors seem to play a significant role in nontyphoid Salmonella enterica pericardial effusion presenting with cardiac tamponade.
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Tolerance to benzalkonium chloride and antimicrobial activity of Butia odorata Barb. Rodr. extract in Salmonella spp. isolates from food and food environments. Food Res Int 2019; 116:652-659. [DOI: 10.1016/j.foodres.2018.08.092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/21/2018] [Accepted: 08/19/2018] [Indexed: 11/23/2022]
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Draft Genome Sequences of Three Salmonella enterica Serovar 4,[5],12:i:- Strains and One S. enterica Serovar Typhimurium Strain, Isolated in Brazil. GENOME ANNOUNCEMENTS 2018; 6:6/27/e00488-18. [PMID: 29976603 PMCID: PMC6033978 DOI: 10.1128/genomea.00488-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Draft genomes of three Salmonella enterica 4,[5],12:i:− (STi) strains isolated from human infections were obtained using Illumina sequencing. They were negative for the fljBA operon but positive for hin, and k-mer analyses revealed their identity as S. enterica 4,[5],12:i:− 08-1736 and S. Draft genomes of three Salmonella enterica 4,[5],12:i:− (STi) strains isolated from human infections were obtained using Illumina sequencing. They were negative for the fljBA operon but positive for hin, and k-mer analyses revealed their identity as S. enterica 4,[5],12:i:− 08-1736 and S. Typhimurium. A draft S. Typhimurium sequence is described for comparison.
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Chlebicz A, Śliżewska K. Campylobacteriosis, Salmonellosis, Yersiniosis, and Listeriosis as Zoonotic Foodborne Diseases: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E863. [PMID: 29701663 PMCID: PMC5981902 DOI: 10.3390/ijerph15050863] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/16/2022]
Abstract
Zoonoses are diseases transmitted from animals to humans, posing a great threat to the health and life of people all over the world. According to WHO estimations, 600 million cases of diseases caused by contaminated food were noted in 2010, including almost 350 million caused by pathogenic bacteria. Campylobacter, Salmonella, as well as Yersinia enterocolitica and Listeria monocytogenes may dwell in livestock (poultry, cattle, and swine) but are also found in wild animals, pets, fish, and rodents. Animals, often being asymptomatic carriers of pathogens, excrete them with faeces, thus delivering them to the environment. Therefore, pathogens may invade new individuals, as well as reside on vegetables and fruits. Pathogenic bacteria also penetrate food production areas and may remain there in the form of a biofilm covering the surfaces of machines and equipment. A common occurrence of microbes in food products, as well as their improper or careless processing, leads to common poisonings. Symptoms of foodborne infections may be mild, sometimes flu-like, but they also may be accompanied by severe complications, some even fatal. The aim of the paper is to summarize and provide information on campylobacteriosis, salmonellosis, yersiniosis, and listeriosis and the aetiological factors of those diseases, along with the general characteristics of pathogens, virulence factors, and reservoirs.
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Affiliation(s)
- Agnieszka Chlebicz
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland.
| | - Katarzyna Śliżewska
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland.
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Lamas A, Miranda JM, Regal P, Vázquez B, Franco CM, Cepeda A. A comprehensive review of non-enterica subspecies of Salmonella enterica. Microbiol Res 2018; 206:60-73. [DOI: 10.1016/j.micres.2017.09.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
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Aguilar-Montes de Oca S, Talavera-Rojas M, Soriano-Vargas E, Barba-León J, Vázquez-Navarrete J, Acosta-Dibarrat J, Salgado-Miranda C. Phenotypic and genotypic profile of clinical and animal multidrug-resistant Salmonella enterica isolates from Mexico. J Appl Microbiol 2017; 124:67-74. [PMID: 29044980 DOI: 10.1111/jam.13615] [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: 06/12/2017] [Revised: 08/18/2017] [Accepted: 09/09/2017] [Indexed: 11/27/2022]
Abstract
AIMS The objective of this study was to obtain a phenotypic and genotypic profile of Salmonella enterica including multidrug-resistant (MDR) isolates from food-producing animals and clinical isolates, as well as their genetic relatedness in two different States of Mexico (Jalisco and State of Mexico). METHODS AND RESULTS A total of 243 isolates were evaluated in terms of antimicrobial resistance (AMR) and related genes through a disk diffusion method and PCR respectively; we found 16 MDR isolates, all of them harbouring the blaCMY gene but not qnr genes, these isolates represent less than 10% of the collection. The pulsed-field gel electrophoresis revealed a higher genotypic similitude within isolates of State of Mexico than Jalisco. CONCLUSIONS A low percentage of Salmonella isolates were resistant to relevant antibiotics in human health, nevertheless, the AMR and involved genes were similar despite the different serovars and origin of the isolates. SIGNIFICANCE AND IMPACT OF THE STUDY This investigation provided an insight of the current status of AMR of Salmonella isolates in two States of Mexico and pinpoint the genes involved in AMR and their epidemiological relationship, the information could help to determine an adequate therapy in human and veterinary medicine.
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Affiliation(s)
- S Aguilar-Montes de Oca
- Centro de Investigación y Estudios Avanzados en Salud Animal, Universidad Autónoma del Estado de Mexico, Carretera Toluca-Atlacomulco, Estado de Mexico, Mexico
| | - M Talavera-Rojas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Universidad Autónoma del Estado de Mexico, Carretera Toluca-Atlacomulco, Estado de Mexico, Mexico
| | - E Soriano-Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Universidad Autónoma del Estado de Mexico, Carretera Toluca-Atlacomulco, Estado de Mexico, Mexico
| | - J Barba-León
- Departamento de Salud Pública, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Jalisco, Mexico
| | - J Vázquez-Navarrete
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Mexico City, Mexico
| | - J Acosta-Dibarrat
- Centro de Investigación y Estudios Avanzados en Salud Animal, Universidad Autónoma del Estado de Mexico, Carretera Toluca-Atlacomulco, Estado de Mexico, Mexico
| | - C Salgado-Miranda
- Centro de Investigación y Estudios Avanzados en Salud Animal, Universidad Autónoma del Estado de Mexico, Carretera Toluca-Atlacomulco, Estado de Mexico, Mexico
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Genetic Characterization of the Galactitol Utilization Pathway of Salmonella enterica Serovar Typhimurium. J Bacteriol 2017; 199:JB.00595-16. [PMID: 27956522 DOI: 10.1128/jb.00595-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/25/2016] [Indexed: 12/26/2022] Open
Abstract
Galactitol degradation by salmonellae remains underinvestigated, although this metabolic capability contributes to growth in animals (R. R. Chaudhuri et al., PLoS Genet 9:e1003456, 2013, https://doi.org/10.1371/journal.pgen.1003456). The genes responsible for this metabolic capability are part of a 9.6-kb gene cluster that spans from gatY to gatR (STM3253 to STM3262) and encodes a phosphotransferase system, four enzymes, and a transporter of the major facilitator superfamily. Genome comparison revealed the presence of this genetic determinant in nearly all Salmonella strains. The generation time of Salmonella enterica serovar Typhimurium strain ST4/74 was higher in minimal medium with galactitol than with glucose. Knockout of STM3254 and gatC resulted in a growth-deficient phenotype of S Typhimurium, with galactitol as the sole carbon source. Partial deletion of gatR strongly reduced the lag phase of growth with galactitol, whereas strains overproducing GatR exhibited a near-zero growth phenotype. Luciferase reporter assays demonstrated strong induction of the gatY and gatZ promoters, which control all genes of this cluster except gatR, in the presence of galactitol but not glucose. Purified GatR bound to these two main gat gene cluster promoters as well as to its own promoter, demonstrating that this autoregulated repressor controls galactitol degradation. Surface plasmon resonance spectroscopy revealed distinct binding properties of GatR toward the three promoters, resulting in a model of differential gat gene expression. The cyclic AMP receptor protein (CRP) bound these promoters with similarly high affinities, and a mutant lacking crp showed severe growth attenuation, demonstrating that galactitol utilization is subject to catabolite repression. Here, we provide the first genetic characterization of galactitol degradation in Salmonella, revealing novel insights into the regulation of this dissimilatory pathway. IMPORTANCE The knowledge of how pathogens adapt their metabolism to the compartments encountered in hosts is pivotal to our understanding of bacterial infections. Recent research revealed that enteropathogens have adapted specific metabolic pathways that contribute to their virulence properties, for example, by helping to overcome limitations in nutrient availability in the gut due to colonization resistance. The capability of Salmonella enterica serovar Typhimurium to degrade galactitol has already been demonstrated to play a role in vivo, but it has not been investigated so far on the genetic level. To our knowledge, this is the first molecular description of the galactitol degradation pathway of a pathogen.
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Efficient and Specific Detection of Salmonella in Food Samples Using a stn-Based Loop-Mediated Isothermal Amplification Method. BIOMED RESEARCH INTERNATIONAL 2015; 2015:356401. [PMID: 26543859 PMCID: PMC4620276 DOI: 10.1155/2015/356401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/09/2015] [Accepted: 05/01/2015] [Indexed: 11/17/2022]
Abstract
The Salmonella enterotoxin (stn) gene exhibits high homology among S. enterica serovars and S. bongori. A set of 6 specific primers targeting the stn gene were designed for detection of Salmonella spp. using the loop-mediated isothermal amplification (LAMP) method. The primers amplified target sequences in all 102 strains of 87 serovars of Salmonella tested and no products were detected in 57 non-Salmonella strains. The detection limit in pure cultures was 5 fg DNA/reaction when amplified at 65°C for 25 min. The LAMP assay could detect Salmonella in artificially contaminated food samples as low as 220 cells/g of food without a preenrichment step. However, the sensitivity was increased 100-fold (~2 cells/g) following 5 hr preenrichment at 35°C. The LAMP technique, with a preenrichment step for 5 and 16 hr, was shown to give 100% specificity with food samples compared to the reference culture method in which 67 out of 90 food samples gave positive results. Different food matrixes did not interfere with LAMP detection which employed a simple boiling method for DNA template preparation. The results indicate that the LAMP method, targeting the stn gene, has great potential for detection of Salmonella in food samples with both high specificity and high sensitivity.
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Evangelopo G, Kritas S, Govaris A, Burriel AR. A Brief Account of the Rules Applied to the Naming and Epidemiologically
Grouping Salmonella Strains when Isolated from Animals. JOURNAL OF MEDICAL SCIENCES 2014. [DOI: 10.3923/jms.2014.101.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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SHIMIZU S, AOI R, OSANAI Y, KAWAI Y, YAMAZAKI K. Rapid Quantitative Detection of Salmonella enterica Using Fluorescence In Situ Hybridization with Filter-cultivation (FISHFC) Method. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2013. [DOI: 10.3136/fstr.19.59] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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