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Myszka K, Tomaś N, Wolko Ł. Gallic and ferulic acids suppress proteolytic activities and volatile trimethylamine production in the food-borne spoiler Rahnella aquatilis KM05. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:6584-6594. [PMID: 37245214 DOI: 10.1002/jsfa.12753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/20/2023] [Accepted: 05/28/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Rahnella aquatilis is a recognised microbial threat that alters the sensory properties of seafood. The high frequency with which R. aquatilis is isolated from fish has prompted a search for alternative preservatives. In the present study, in vitro and fish-based ecosystem (raw salmon-based medium) approaches were used to validate the antimicrobial effects of gallic (GA) and ferulic (FA) acids against R. aquatilis KM05. The results were compared with data describing the response of KM05 to sodium benzoate. Bioinformatics data of the whole genome were used to analyse the potential for fish spoilage by KM05 in detail, and the results revealed the main physiological characteristics that underlie reduced seafood quality. RESULTS In the KM05 genome, the most abundantly enriched Gene Ontology terms were 'metabolic process', 'organic substance metabolic process' and 'cellular process'. Through an evaluation of the Pfam annotations, 15 annotations were found to be directly involved in the proteolytic activity of KM05. Peptidase_M20 was the most abundantly represented (abundance value of 14060). Proteins representing the CutC family (abundance value of 427) indicated the potential for KM05 degradation of trimethyl-amine-N-oxide. Subinhibitory concentrations of GA and FA suppressed the proteolytic activities of KM05 both in vitro and in RS medium by an average of 33-45%. These results were confirmed by quantitative real-time PCR experiments, which also showed that the expression levels of genes involved in proteolytic activities and volatile trimethylamine production were also decreased. CONCLUSION Phenolic compounds can be used as potential food additives for preventing quality deterioration of fish products. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Kamila Myszka
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Natalia Tomaś
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Poznan, Poland
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Poznan, Poland
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Fang Y, Tran F, Stanford K, Yang X. Stress Resistance and Virulence Gene Profiles Associated with Phylogeny and Phenotypes of Escherichia coli from Cattle. J Food Prot 2023; 86:100122. [PMID: 37355007 DOI: 10.1016/j.jfp.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/26/2023]
Abstract
Seven serogroups of E. coli (Top seven E. coli) are frequently implicated in foodborne outbreaks in North America, largely due to their carriage of Shiga toxin genes (stx). This study aimed to profile resistance genes and virulence factors (VF), and their potential association with phylogeny and phenotypes of Top seven E. coli originating from cattle in Canada. 155 Top seven E. coli isolates previously characterized for heat and acid resistance and biofilm-forming ability were whole-genome sequenced and analyzed for phylogeny, VF, and stress resistance genes. The 155 E. coli strains belonged to six phylogroups: A (n = 32), B1 (n = 93), C (n = 3), D (n = 11), E (n = 15), and G (n = 1). Different phylogroups were clearly separated on the core genome tree, with strains of the same serotype closely clustered. The carriage of stx and the transmissible locus of stress tolerance (tLST), the extreme heat resistance marker, was mutually exclusive, in 33 and 15 genomes, respectively. A novel O84:H2 strain carrying stx1a was also identified. In total, 70, 41, and 32 VF, stress resistance genes and antibiotic resistance genes were identified. The stress resistance genes included those for metal (n = 29), biocides/acid (n = 4), and heat (n = 8) resistance. All heat resistance genes and most metal-resistance genes that were differentially distributed among the phylogroups were exclusively in phylogroup A. VF were least and most present in phylogroups A and D, respectively. No specific genes associated with acid resistance or biofilm formation phenotypes were identified. VF were more abundant (P < 0.05) in the non-biofilm-forming population and acid-resistant population.
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Affiliation(s)
- Yuan Fang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada
| | - Frances Tran
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada
| | - Kim Stanford
- University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada.
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Byarugaba DK, Wokorach G, Alafi S, Erima B, Najjuka F, Mworozi EA, Kibuuka H, Wabwire-Mangen F. Whole Genome Sequencing Reveals High Genetic Diversity, Diverse Repertoire of Virulence-Associated Genes and Limited Antibiotic Resistance Genes among Commensal Escherichia coli from Food Animals in Uganda. Microorganisms 2023; 11:1868. [PMID: 37630428 PMCID: PMC10457813 DOI: 10.3390/microorganisms11081868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 08/27/2023] Open
Abstract
Commensal Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups (A, B1, and E). A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by blaEC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- College of Veterinary Medicine, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- Gulu University Multifunctional Research Laboratories, Gulu P.O. Box 166, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Edison A. Mworozi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
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Joddha HB, Mathakiya RA, Joshi KV, Khant RB, Golaviya AV, Hinsu AT, Desai MR, Jakhesara SJ, Koringa PG. Profiling of Antimicrobial Resistance Genes and Integron from Escherichia coli Isolates Using Whole Genome Sequencing. Genes (Basel) 2023; 14:1212. [PMID: 37372392 DOI: 10.3390/genes14061212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This study is designed to investigate Escherichia coli for the antibiotic resistance genes (ARGs) and integrons from healthy as well as diarrhoeic/diseased animals/birds' faecal samples. A total of eight samples were selected for the study; from each animal, two samples were taken, one from healthy animals/birds and one from diarrhoeic/diseased animals/birds. Antibiotic sensitivity testing (AST) and whole genome sequencing (WGS) was performed for selected isolates. The E. coli isolates showed resistance to moxifloxacin, followed by erythromycin, ciprofloxacin, pefloxacin, tetracycline, levofloxacin, ampicillin, amoxicillin, and sulfadiazine (4/8, 50.00% each). The E. coli isolates were 100% sensitive to amikacin, followed by chloramphenicol, cefixime, cefoperazone, and cephalothin. A total of 47 ARGs from 12 different antibiotic classes were detected among the eight isolates by WGS. The different classes of antibiotics included aminoglycoside, sulphonamide, tetracycline, trimethoprim, quinolone, fosfomycin, phenicol, macrolide, colistin, fosmidomycin, and multidrug efflux. The class 1 integrons were detected in 6/8 (75.00%) isolates with 14 different gene cassettes.
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Affiliation(s)
- Harshrajsinh B Joddha
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Rafiyuddin A Mathakiya
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Kuldip V Joshi
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Ravindra B Khant
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Akash V Golaviya
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Mansi R Desai
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
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Calero-Cáceres W, Rodríguez K, Medina A, Medina J, Ortuño-Gutiérrez N, Sunyoto T, Dias CAG, Bastidas-Caldes C, Ramírez MS, Harries AD. Genomic insights of mcr-1 harboring Escherichia coli by geographical region and a One-Health perspective. Front Microbiol 2023; 13:1032753. [PMID: 36726572 PMCID: PMC9884825 DOI: 10.3389/fmicb.2022.1032753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
The importance of the One Health concept in attempting to deal with the increasing levels of multidrug-resistant bacteria in both human and animal health is a challenge for the scientific community, policymakers, and the industry. The discovery of the plasmid-borne mobile colistin resistance (mcr) in 2015 poses a significant threat because of the ability of these plasmids to move between different bacterial species through horizontal gene transfer. In light of these findings, the World Health Organization (WHO) recommends that countries implement surveillance strategies to detect the presence of plasmid-mediated colistin-resistant microorganisms and take suitable measures to control and prevent their dissemination. Seven years later, ten different variants of the mcr gene (mcr-1 to mcr-10) have been detected worldwide in bacteria isolated from humans, animals, foods, the environment, and farms. However, the possible transmission mechanisms of the mcr gene among isolates from different geographical origins and sources are largely unknown. This article presents an analysis of whole-genome sequences of Escherichia coli that harbor mcr-1 gene from different origins (human, animal, food, or environment) and geographical location, to identify specific patterns related to virulence genes, plasmid content and antibiotic resistance genes, as well as their phylogeny and their distribution with their origin. In general, E. coli isolates that harbor mcr-1 showed a wide plethora of ARGs. Regarding the plasmid content, the highest concentration of plasmids was found in animal samples. In turn, Asia was the continent that led with the largest diversity and occurrence of these plasmids. Finally, about virulence genes, terC, gad, and traT represent the most frequent virulence genes detected. These findings highlight the relevance of analyzing the environmental settings as an integrative part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance.
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Affiliation(s)
- William Calero-Cáceres
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador,Bacteriophage Research Association, Ambato, Ecuador,*Correspondence: William Calero-Cáceres,
| | | | - Anabell Medina
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Jennifer Medina
- UTA RAM One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | | | - Temmy Sunyoto
- MSFOCB Luxembourg Operational Research (LuxOR) Unit, Luxembourg, Luxembourg
| | - Cícero Armídio Gomes Dias
- Department of Basic Health Sciences, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | - Carlos Bastidas-Caldes
- One Health Research Group, Biotecnología, Facultad de Ingeniería y Ciencias Aplicadas (FICA), Universidad de las Américas (UDLA), Quito, Ecuador
| | - Maria Soledad Ramírez
- Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
| | - Anthony David Harries
- International Union Against Tuberculosis and Lung Disease, Paris, France,London School of Hygiene and Tropical Medicine, London, United Kingdom
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Khawaskar D, Anbazhagan S, Balusamy D, Inbaraj S, Verma A, Vinodh Kumar OR, Nagaleekar VK, Sinha DK, Chaudhuri P, Singh BR, Chaturvedi VK, Thomas P. A comparative genomics approach for identifying genetic factors in Escherichia coli isolates associated with bovine diseases. J Appl Microbiol 2022; 133:3490-3501. [PMID: 36648155 DOI: 10.1111/jam.15781] [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: 06/09/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 01/20/2023]
Abstract
AIMS Escherichia coli are ubiquitously present bacterial pathogens that cause septicaemia, diarrhoea and other clinical illness in farm animals. Many pathogen factors can be associated with disease conditions. Currently, studies inferring E. coli genetic factors associated with infection in bovines are limited. Hence, the present study envisaged to determine the pathogen genetic factors associated with bovine disease conditions. METHOD AND RESULTS The comparative genomic analysis involved genome sequence data of 135 diseased and 145 healthy bovine origin E. coli strains. Phylogroups A and C, as well as pathotypes ExPEC and EPEC, were found to have a strong connection with bovine disease strains. STEC strains, including EHEC, seem to play a less important role in bovine disease. Sequence types (STs) predominant among strains from diarrhoeal origin were ST 301 (CC 165) and ST 342. Correlation of core genome phylogeny with accessory gene based clustering, phylogroups and pathotypes indicated lineage specific virulence factors mostly associated with disease conditions. CONCLUSIONS Comparative genomic analysis was applied to infer genetic factors significant in bovine disease origin E. coli strains. Isolates from bovine disease origin were enriched for the phylogroups A and C, and for the pathotypes ExPEC and EPEC. However, there was minimal evidence of STEC involvement. The study also indicated predominant genetic lineages and virulence genes (pap, sfa and afa) associated with disease origin strains. SIGNIFICANCE AND IMPACT OF STUDY;: The study revealed significant pathotypes, phylgroups, serotypes and sequence types associated with bovine disease conditions. These identified genetic factors can be applied for disease diagnosis, implementing vaccine and therapeutic measures. In addition, E. coli isolates from the bovine species revealed a complex pattern of disease epidemiology.
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Affiliation(s)
- Damini Khawaskar
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Subbaiyan Anbazhagan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh.,ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad
| | - Dhayanath Balusamy
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Sophia Inbaraj
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Abhishek Verma
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | | | - Viswas Konasagara Nagaleekar
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Dharmendra K Sinha
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Pallab Chaudhuri
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Bhoj R Singh
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - V K Chaturvedi
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly - 243122, Uttar Pradesh
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Yun J, Mao L, Li J, Hao F, Yang L, Zhang W, Sun M, Liu M, Wang S, Li W. Molecular characterization and antimicrobial resistance profile of pathogenic Escherichia coli from goats with respiratory disease in eastern China. Microb Pathog 2022; 166:105501. [DOI: 10.1016/j.micpath.2022.105501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
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Characterisation of atypical Shiga toxin gene sequences and description of Stx2j, a new subtype. J Clin Microbiol 2022; 60:e0222921. [PMID: 35225693 DOI: 10.1128/jcm.02229-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shiga toxin (Stx) is the definitive virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx variants are currently organised into a taxonomic system of three Stx1 (a,c,d) and seven Stx2 (a,b,c,d,e,f,g) subtypes. In this study, seven STEC isolates from food and clinical samples possessing stx2 sequences that do not fit current Shiga toxin taxonomy were identified. Genome assemblies of the STEC strains was created from Oxford Nanopore and Illumina sequence data. The presence of atypical stx2 sequences were confirmed by Sanger sequencing, as were Stx2 expression and cytotoxicity. A strain of O157:H7 was found to possess stx1a and a truncated stx2a, which were originally misidentified as an atypical stx2. Two strains possessed unreported variants of Stx2a (O8:H28) and Stx2b (O146:H21). In four of the strains we found three Stx-subtypes that are not included in the current taxonomy. Stx2h (O170:H18) was identified in a Canadian sprout isolate; this subtype has only previously been reported in STEC from Tibetan Marmots. Stx2o (O85:H1) was identified in a clinical isolate. Finally, Stx2j (O158:H23 and O33:H14) was found in lettuce and clinical isolates. The results of this study expands the number of known Stx subtypes, the range of STEC serotypes, and isolation sources in which they may be found. The presence of the Stx2j and Stx2o in clinical isolates of STEC indicates that strains carrying these variants are potential human pathogens. Highlights Atypical Shiga toxin (stx) genes in Escherichia coli were sequenced. Two new variants of stx2a and stx2b are described. Two strains carried subtypes Stx2h and Stx2o, which have only one previous report. Two strains carried a previously undescribed subtype, Stx2j.
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