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Sha W, Beshir Ata E, Yan M, Zhang Z, Fan H. Swine Colibacillosis: Analysis of the Gut Bacterial Microbiome. Microorganisms 2024; 12:1233. [PMID: 38930615 PMCID: PMC11205844 DOI: 10.3390/microorganisms12061233] [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: 05/22/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to evaluate the disruption of the swine gut microbiota and histopathological changes caused by infection with enterotoxigenic E. coli. Fecal samples were collected from piglets suffering from diarrhea post-recovery and healthy animals. Intestinal tissues were collected for histopathological changes. The results revealed histopathological changes mainly in the ileum of the infected animals compared to those in the ileum of the control and recovered animals. The operational taxonomic units (OTUs) revealed that the E. coli diarrheal group exhibited the highest bacterial richness. Principal coordinate analysis (PCoA) corroborated the presence of dysbiosis in the gut microbiota following E. coli-induced diarrhea. While the normal control and infected groups displayed slight clustering, the recovery group formed a distinct cluster with a distinct flora. Bacteroidetes, Firmicutes, and Fusobacteria were the dominant phyla in both the healthy and recovered piglets and in the diarrheal group. LEfSe and the associated LDA score analysis revealed that the recovered group exhibited dominance of the phyla Euryarchaeota and Bacteroidota, while groups N and I showed dominance of the phyla Firmicutes and Fusobacteriota, respectively. The LDA scores highlighted a significant expression of the Muribaculacea family in group R. The obtained findings will help in understanding the microbiome during swine colibacillosis, which will support control of the outbreaks.
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Affiliation(s)
- Wanli Sha
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China;
- Technology Innovation Center of Pig Ecological Breeding and Disease Prevention and Control, College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132109, China;
| | - Emad Beshir Ata
- Parasitology and Animal Diseases, Veterinary Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt;
| | - Man Yan
- Technology Innovation Center of Pig Ecological Breeding and Disease Prevention and Control, College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin 132109, China;
| | - Zhijie Zhang
- Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China;
| | - Honggang Fan
- Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China;
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Fernández-Yáñez V, Suazo P, Hormazábal C, Ibaceta V, Arenas-Salinas M, Vidal RM, Silva-Ojeda F, Arellano C, Muñoz I, Del Canto F. Distribution of papA and papG Variants among Escherichia coli Genotypes: Association with Major Extraintestinal Pathogenic Lineages. Int J Mol Sci 2024; 25:6657. [PMID: 38928363 PMCID: PMC11203468 DOI: 10.3390/ijms25126657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The pyelonephritis-associated fimbria (P fimbria) is one of the most recognized adhesion determinants of extraintestinal pathogenic Escherichia coli strains (ExPECs). Twelve variants have been described for the gene encoding the P fimbria major structural subunit PapA and three variants for the gene encoding the adhesin subunit PapG. However, their distribution among the ExPEC diversity has not been comprehensively addressed. A complete landscape of that distribution might be valuable for delineating basic studies about the pathogenicity mechanisms of ExPECs and following up on the evolution of ExPEC lineages, particularly those most epidemiologically relevant. Therefore, we performed a massive descriptive study to detect the papA and papG variants along different E. coli genotypes represented by genomic sequences contained in the NCBI Assembly Refseq database. The most common papA variants were F11, F10, F48, F16, F12, and F7-2, which were found in significant association with the most relevant ExPEC genotypes, the phylogroups B2 and D, and the sequence types ST95, ST131, ST127, ST69, ST12, and ST73. On the other hand, the papGII variant was by far the most common followed by papGIII, and both were also found to have a significant association with common ExPEC genotypes. We noticed the presence of genomes, mainly belonging to the sequence type ST12, harboring two or three papA variants and two papG variants. Furthermore, the most common papA and papG variants were also detected in records representing strains isolated from humans and animals such as poultry, bovine, and dogs, supporting previous hypotheses of potential cross-transmission. Finally, we characterized a set of 17 genomes from Chilean uropathogenic E. coli strains and found that ST12 and ST73 were the predominant sequence types. Variants F7-1, F7-2, F8, F9, F11, F13, F14, F16, and F48 were detected for papA, and papGII and papGIII variants were detected for papG. Significant associations with the sequence types observed in the analysis of genomes contained in the NCBI Assembly Refseq database were also found in this collection in 16 of 19 cases for papA variants and 7 of 9 cases for the papG variants. This comprehensive characterization might support future basic studies about P fimbria-mediated ExPEC adherence and future typing or epidemiological studies to monitor the evolution of ExPECs producing P fimbria.
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Affiliation(s)
- Valentina Fernández-Yáñez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Santiago 9170022, Chile; (V.F.-Y.)
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Patricio Suazo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Claudia Hormazábal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Santiago 9170022, Chile; (V.F.-Y.)
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Valentina Ibaceta
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Mauricio Arenas-Salinas
- Centro de Bioinformática Simulación y Modelado, Facultad de Ingeniería, Universidad de Talca, Av. Lircay s/n, Talca 3460787, Chile
| | - Roberto M. Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Francisco Silva-Ojeda
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Av. Dr. Carlos Lorca Tobar 999, Santiago 8380453, Chile
| | - Carolina Arellano
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Ignacio Muñoz
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Felipe Del Canto
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
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von Mentzer A, Svennerholm AM. Colonization factors of human and animal-specific enterotoxigenic Escherichia coli (ETEC). Trends Microbiol 2024; 32:448-464. [PMID: 38052687 DOI: 10.1016/j.tim.2023.11.001] [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: 07/11/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
Colonization factors (CFs) are major virulence factors of enterotoxigenic Escherichia coli (ETEC). This pathogen is among the most common causes of bacterial diarrhea in children in low- and middle-income countries, travelers, and livestock. CFs are major candidate antigens in vaccines under development as preventive measures against ETEC infections in humans and livestock. Recent molecular studies have indicated that newly identified CFs on human ETEC are closely related to animal ETEC CFs. Increased knowledge of pathogenic mechanisms, immunogenicity, regulation, and expression of ETEC CFs, as well as the possible spread of animal ETEC to humans, may facilitate the future development of ETEC vaccines for humans and animals. Here, we present an updated review of CFs in ETEC.
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Affiliation(s)
- Astrid von Mentzer
- Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Sweden; Wellcome Sanger Institute, Hinxton, UK.
| | - Ann-Mari Svennerholm
- Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Sweden
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Kompes G, Duvnjak S, Reil I, Hendriksen RS, Sørensen LH, Zdelar-Tuk M, Habrun B, Cvetnić L, Bagarić A, Špičić S. First Report and Characterization of the mcr-1 Positive Multidrug-Resistant Escherichia coli Strain Isolated from Pigs in Croatia. Microorganisms 2023; 11:2442. [PMID: 37894098 PMCID: PMC10609023 DOI: 10.3390/microorganisms11102442] [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: 07/31/2023] [Revised: 08/21/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence and rapid spread of the plasmid-mediated colistin-resistant mcr-1 gene introduced a serious threat to public health. In 2021, a multi-drug resistant, mcr-1 positive Escherichia coli EC1945 strain, was isolated from pig caecal content in Croatia. Antimicrobial susceptibility testing and whole genome sequencing were performed. Bioinformatics tools were used to determine the presence of resistance genes, plasmid Inc groups, serotype, sequence type, virulence factors, and plasmid reconstruction. The isolated strain showed phenotypic and genotypic resistance to nine antimicrobial classes. It was resistant to colistin, gentamicin, ampicillin, cefepime, cefotaxime, ceftazidime, sulfamethoxazole, chloramphenicol, nalidixic acid, and ciprofloxacin. Antimicrobial resistance genes included mcr-1, blaTEM-1B, blaCTX-M-1, aac(3)-IId, aph(3')-Ia, aadA5, sul2, catA1, gyrA (S83L, D87N), and parC (A56T, S80I). The mcr-1 gene was located within the conjugative IncX4 plasmid. IncI1, IncFIB, and IncFII plasmids were also detected. The isolate also harbored 14 virulence genes and was classified as ST744 and O101:H10. ST744 is a member of the ST10 group which includes commensal, extraintestinal pathogenic E. coli isolates that play a crucial role as a reservoir of genes. Further efforts are needed to identify mcr-1-carrying E. coli isolates in Croatia, especially in food-producing animals to identify such gene reservoirs.
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Affiliation(s)
- Gordan Kompes
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Sanja Duvnjak
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Irena Reil
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Rene S. Hendriksen
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark; (R.S.H.); (L.H.S.)
| | - Lauge Holm Sørensen
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark; (R.S.H.); (L.H.S.)
| | - Maja Zdelar-Tuk
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Boris Habrun
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Luka Cvetnić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Antonela Bagarić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
| | - Silvio Špičić
- Department for Bacteriology and Parasitology, Croatian Veterinary Institute, 10000 Zagreb, Croatia; (G.K.); (M.Z.-T.); (B.H.); (L.C.); (A.B.); (S.Š.)
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Duarte ME, Garavito-Duarte Y, Kim SW. Impacts of F18 +Escherichia coli on Intestinal Health of Nursery Pigs and Dietary Interventions. Animals (Basel) 2023; 13:2791. [PMID: 37685055 PMCID: PMC10487041 DOI: 10.3390/ani13172791] [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: 08/15/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
This review focused on the impact of F18+E. coli on pig production and explored nutritional interventions to mitigate its deleterious effects. F18+E. coli is a primary cause of PWD in nursery pigs, resulting in substantial economic losses through diminished feed efficiency, morbidity, and mortality. In summary, the F18+E. coli induces intestinal inflammation with elevated IL6 (60%), IL8 (43%), and TNF-α (28%), disrupting the microbiota and resulting in 14% villus height reduction. Besides the mortality, the compromised intestinal health results in a 20% G:F decrease and a 10% ADFI reduction, ultimately culminating in a 28% ADG decrease. Among nutritional interventions to counter F18+E. coli impacts, zinc glycinate lowered TNF-α (26%) and protein carbonyl (45%) in jejunal mucosa, resulting in a 39% ADG increase. Lactic acid bacteria reduced TNF-α (36%), increasing 51% ADG, whereas Bacillus spp. reduced IL6 (27%), increasing BW (12%). Lactobacillus postbiotic increased BW (14%) and the diversity of beneficial bacteria. Phytobiotics reduced TNF-α (23%) and IL6 (21%), enhancing feed efficiency (37%). Additional interventions, including low crude protein formulation, antibacterial minerals, prebiotics, and organic acids, can be effectively used to combat F18+E. coli infection. These findings collectively underscore a range of effective strategies for managing the challenges posed by F18+E. coli in pig production.
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Affiliation(s)
| | | | - Sung Woo Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA; (M.E.D.); (Y.G.-D.)
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Kaleva MD, Ilieva Y, Zaharieva MM, Dimitrova L, Kim TC, Tsvetkova I, Georgiev Y, Orozova P, Nedev K, Najdenski H. Antimicrobial Resistance and Biofilm Formation of Escherichia coli Isolated from Pig Farms and Surroundings in Bulgaria. Microorganisms 2023; 11:1909. [PMID: 37630469 PMCID: PMC10459462 DOI: 10.3390/microorganisms11081909] [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: 04/25/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Escherichia coli (E. coli) is a ubiquitous microorganism with pathogenic and saprophytic clones. The objective of this study was to evaluate the presence, virulence, antibiotic resistance and biofilm formation of E. coli in three industrial farms in Bulgaria, as well as their adjacent sites related to the utilization of manure (feces, wastewater in a separator, lagoons, means of transport, and soils). The isolation of single bacterial cultures was performed via standard procedures with modifications, and E. coli isolates were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and polymerase chain reaction (PCR). The disk diffusion method was used to assess antimicrobial resistance, and PCR was used to detect genes for antibiotic resistance (GAR) (qnr, aac(3), ampC, blaSHV/blaTEM and erm) and virulence genes (stx, stx2all, LT, STa, F4 and eae). The protocol of Stepanović was utilized to measure the biofilm formation of the isolates. A total of 84 isolates from different samples (n = 53) were identified as E. coli. Almost all demonstrated antimicrobial resistance, and most of them demonstrated resistance to multiple antibiotics from different classes. No virulence genes coding the Shiga toxin or enterotoxins or those associated with enteropathogenicity were detected. No GAR from those tested for quinolones, aminoglycosides and macrolides were found. However, all isolates that were resistant to a penicillin-class antibiotic (56) had β-lactamase-producing plasmid genes. All of them had ampC, and 34 of them had blaTEM. A total of 14 isolates formed strongly adherent biofilms. These results in a country where the use of antibiotics for growth promotion and prophylaxis in farms is highly restricted corroborate that the global implemented policy on antibiotics in human medicine and in animal husbandry needs revision.
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Affiliation(s)
- Mila D. Kaleva
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Yana Ilieva
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Maya Margaritova Zaharieva
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Lyudmila Dimitrova
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Tanya Chan Kim
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Iva Tsvetkova
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Yordan Georgiev
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
| | - Petya Orozova
- National Reference Laboratory for Fish, Mollusks and Crustacean Diseases, National Diagnostic Research Veterinary Institute, 1000 Sofia, Bulgaria;
| | - Krasimir Nedev
- Swine Complex (Svinekompleks) Krumovo Gradishte, Boni Holding AD, 1527 Sofia, Bulgaria;
| | - Hristo Najdenski
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.D.K.); (Y.I.); (M.M.Z.); (L.D.); (T.C.K.); (I.T.); (Y.G.)
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