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Zalewska M, Błażejewska A, Gawor J, Adamska D, Goryca K, Szeląg M, Kalinowski P, Popowska M. A newly identified IncY plasmid from multi-drug-resistant Escherichia coli isolated from dairy cattle feces in Poland. Microbiol Spectr 2024:e0087724. [PMID: 39012117 DOI: 10.1128/spectrum.00877-24] [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: 04/09/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
Comprehensive whole-genome sequencing was performed on two multi-drug-resistant Escherichia coli strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene tet(A), aph family aminoglycoside resistance genes aph(3″)-lb and aph (6)-ld, beta-lactam resistance genes blaTEM-1 and blaCTX-M-15, sulfonamide resistance gene sul2, fluoroquinolone resistance gene qnrS1, and the trimethoprim resistance gene dfrA14. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the Enterobacteriaceae. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant E. coli from livestock and food sources to be transmitted to humans and vice versa. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach. IMPORTANCE This study reveals the identification of new strains of antibiotic-resistant Escherichia coli in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Adamska
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michał Szeląg
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Patryk Kalinowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Li X, Hu H, Zhu Y, Wang T, Lu Y, Wang X, Peng Z, Sun M, Chen H, Zheng J, Tan C. Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China. Nat Commun 2024; 15:5811. [PMID: 38987310 PMCID: PMC11237156 DOI: 10.1038/s41467-024-50268-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
Extraintestinal Pathogenic Escherichia coli (ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin E. coli strains. Additionally, 49 strains harbor toxins typical of enteric E. coli pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring fosA3, blaCTX-M-14, and mcr-1 genes between swine ExPEC and human-origin Salmonella enterica is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.
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Affiliation(s)
- Xudong Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huifeng Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yongwei Zhu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Taiquan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Youlan Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Zhong Peng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Ming Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China.
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Ballesteros-Monrreal MG, Mendez-Pfeiffer P, Ortíz B, Bolado-Martínez E, Álvarez-Ainza ML, Enciso-Martínez Y, Arenas-Hernández MMP, Diaz-Murrieta B, Barrios-Villa E, Valencia D. Uropathogenic E. coli and Hybrid Pathotypes in Mexican Women with Urinary Tract Infections: A Comprehensive Molecular and Phenotypic Overview. Curr Issues Mol Biol 2024; 46:5909-5928. [PMID: 38921024 PMCID: PMC11202577 DOI: 10.3390/cimb46060353] [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: 05/01/2024] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 06/27/2024] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the main cause of urinary tract infections (UTIs) and carries virulence and resistance factors often found in mobilizable genetic elements, such as plasmids or pathogenicity islands (PAIs). UPEC is part of the extraintestinal pathogenic E. coli (ExPEC), but hybrid strains possessing both diarrheagenic E. coli (DEC) and ExPEC traits, termed "hypervirulent", present a significant health threat. This study assessed the prevalence of UPEC PAIs, ExPEC sequence types (ST), DEC genes, carbapenemase and extended-spectrum β-lactamase (ESBL) phenotypes, resistance genotypes, and plasmids in 40 clinical isolates of UPEC. Results showed that 72.5% of isolates had PAIs, mainly PAI IV536 (53%). ESBL phenotypes were found in 65% of β-lactam-resistant isolates, with 100% of carbapenem-resistant isolates producing carbapenemase. The predominant ESBL gene was blaCTX-M-2 (60%), and the most common resistance gene in fluoroquinolone and aminoglycoside-resistant isolates was aac(6')Ib (93%). Plasmids were present in 57% of isolates, and 70% belonged to the ST131 clonal group. Molecular markers for DEC pathotypes were detected in 20 isolates, with 60% classified as hybrid pathotypes. These findings indicate significant pathogenic potential and the presence of hybrid pathotypes in E. coli UTI clinical isolates in the Mexican population.
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Affiliation(s)
- Manuel G. Ballesteros-Monrreal
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83621, Sonora, Mexico; (M.G.B.-M.); (P.M.-P.); (Y.E.-M.); (B.D.-M.)
| | - Pablo Mendez-Pfeiffer
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83621, Sonora, Mexico; (M.G.B.-M.); (P.M.-P.); (Y.E.-M.); (B.D.-M.)
| | - Bryan Ortíz
- Instituto de Investigaciones en Microbiología, Facultad de Ciencias, Universidad Nacional Autónoma de Honduras, Tegucigalpa 11101, Honduras;
| | - Enrique Bolado-Martínez
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo CP 83000, Sonora, Mexico; (E.B.-M.); (M.L.Á.-A.)
| | - Maritza Lizeth Álvarez-Ainza
- Departamento de Ciencias Químico-Biológicas, Universidad de Sonora, Hermosillo CP 83000, Sonora, Mexico; (E.B.-M.); (M.L.Á.-A.)
| | - Yessica Enciso-Martínez
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83621, Sonora, Mexico; (M.G.B.-M.); (P.M.-P.); (Y.E.-M.); (B.D.-M.)
| | - Margarita M. P. Arenas-Hernández
- Posgrado en Microbiología, Centro de Investigación en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla CP 72570, Pue, Mexico
| | - Betsaida Diaz-Murrieta
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83621, Sonora, Mexico; (M.G.B.-M.); (P.M.-P.); (Y.E.-M.); (B.D.-M.)
| | - Edwin Barrios-Villa
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83621, Sonora, Mexico; (M.G.B.-M.); (P.M.-P.); (Y.E.-M.); (B.D.-M.)
| | - Dora Valencia
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca CP 83621, Sonora, Mexico; (M.G.B.-M.); (P.M.-P.); (Y.E.-M.); (B.D.-M.)
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Lee W, Ha J, Choi J, Jung Y, Kim E, An ES, Kim SH, Shin H, Ryu S, Kim SH, Kim HY. Genetic and virulence characteristics of hybrid Shiga toxin-producing and atypical enteropathogenic Escherichia coli strains isolated in South Korea. Front Microbiol 2024; 15:1398262. [PMID: 38812694 PMCID: PMC11133561 DOI: 10.3389/fmicb.2024.1398262] [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: 03/09/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Introduction The predominant hybrid pathogenic E. coli, enterohemorrhagic E. coli (EHEC), combines characteristics of Shiga toxin-producing E. coli (STEC) and enteropathogenic E. coli (EPEC), contributing to global outbreaks with severe symptoms including fatal consequences. Since EHEC infection was designated as a notifiable disease in 2000 in South Korea, around 2000 cases have been reported, averaging approximately 90 cases annually. Aim In this work, genome-based characteristic analysis and cell-based assay of hybrid STEC/aEPEC strains isolated from livestock feces, animal source foods, and water in South Korea was performed. Methods To identify the virulence and antimicrobial resistance genes, determining the phylogenetic position of hybrid STEC/aEPEC strains isolated in South Korea, a combination of real-time PCR and whole-genome sequencing (WGS) was used. Additionally, to assess the virulence of the hybrid strains and compare them with genomic characterization, we performed a cell cytotoxicity and invasion assays. Results The hybrid STEC/aEPEC strains harbored stx and eae genes, encoding Shiga toxins and E. coli attachment/effacement related protein of STEC and EPEC, respectively. Furthermore, all hybrid strains harbored plasmid-carried enterohemolysin(ehxCABD), a key virulence factor in prevalent pathogenic E. coli infections, such as diarrheal disease and hemolytic-uremic syndrome (HUS). Genome-wide phylogenetic analysis revealed a close association between all hybrid strains and specific EPEC strains, suggesting the potential acquisition of Stx phages during STEC/aEPEC hybrid formation. Some hybrid strains showed cytotoxic activity against HeLa cells and invasive properties against epithelial cells. Notably, all STEC/aEPEC hybrids with sequence type (ST) 1,034 (n = 11) exhibited higher invasiveness than those with E2348/69. This highlights the importance of investigating potential correlations between STs and virulence characteristics of E. coli hybrid strains. Conclusion Through genome-based characterization, we confirmed that the hybrid STEC/aEPEC strains are likely EPEC strains that have acquired STEC virulence genes via phage. Furthermore, our results emphasize the potential increased danger to humans posed by hybrid STEC/aEPEC strains isolated in South Korea, containing both stx and eaeA, compared to STEC or EPEC alone.
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Jina Ha
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Jaehyun Choi
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Yewon Jung
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
| | - Eun Sook An
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Hakdong Shin
- Department of Biotechnology, and Carbohydrate Bioproduct Research Center, Sejong University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, Republic of Korea
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Naderi Z, Ghanbarpour R, Jajarmi M, Dehdashti S, Bagheri M, Eskandarzade N, Mohseni P, Alizade H. Antibiotic resistance profiling and phylotyping of human-diarrheagenic Escherichia coli pathotypes detected from diarrheic and non-diarrheic calves in Iran. Mol Biol Rep 2024; 51:494. [PMID: 38581525 DOI: 10.1007/s11033-024-09494-6] [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: 02/11/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Escherichia coli (E. coli) serves as a common indicator of gut microbiota and is utilized for monitoring antimicrobial resistance determinants in food-producing animals. This study aimed to investigate antimicrobial resistance patterns in virulence gene-positive E. coli isolates obtained from 340 healthy and diarrheic calves. METHODS AND RESULTS A total of 340 fecal swab samples were obtained from diarrheic (n = 170) and healthy (n = 170) calves for 12 months from different farms in Kerman, Iran. The samples were phenotypically analyzed to detect E. coli isolates and antibiotic resistance. Also, antimicrobial resistance genes, diarrheagenic E. coli pathotypes, and phylogenetic background were screened by PCR. Fifteen percent (51/340) of E. coli isolates were positive for at least one of the examined virulence genes (VGs); the prevalence of VGs in E. coli isolates from healthy calves (36/170; 21.17%) was higher than that in diarrheic cases (15/170; 8.82%). Out of the 51 VG-positive isolates, six pathotypes including Shiga toxin-producing E. coli (STEC; 27.45%), enterotoxigenic E. coli (ETEC; 23.52%), enterohemorrhagic E. coli (EHEC; 19.6%), necrotoxigenic E. coli (NTEC; 19.6%), enteropathogenic E. coli (EPEC; 15.68%), enteroinvasive E. coli (EIEC; 1.96%) and three hybrid pathotypes including ETEC/STEC, ETEC/EHEC, and STEC/EIEC were detected among the strains. Antimicrobial resistance (AR) was observed in 98.03% of the VG-positive isolates, which was the same for both healthy and diarrheic calves. The maximum prevalence rate of AR was found against trimethoprim/sulfamethoxazole (49.01%; 3/51), while the minimum prevalence rate was against gentamycin (5.88%; 25/51). Among the VG-positives, phylotype A was found to be the most prevalent followed by B1 and D phylotypes. CONCLUSIONS The prevalence of VG-positive E. coli isolates was higher in healthy calves compared to diarrheic cases. AR was widespread among VG-positive isolates. These findings suggest that calves may serve as potential reservoirs of antimicrobial-resistant hybrid pathotypes of E. coli.
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Affiliation(s)
- Zahede Naderi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Reza Ghanbarpour
- Molecular Microbiology Research Group, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Maziar Jajarmi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Sanaz Dehdashti
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahboube Bagheri
- Department of Food Science and Technology, Bardsir Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Neda Eskandarzade
- Department of Basic Sciences, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Parvin Mohseni
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hesam Alizade
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Chen C, Hu H, Li Z, Qi M, Qiu Y, Hu Z, Feng F, Tang W, Diao H, Sun W, Tang Z. Dietary tryptophan improves growth and intestinal health by promoting the secretion of intestinal β-defensins against enterotoxigenic E. coli F4 in weaned piglets. J Nutr Biochem 2024:109637. [PMID: 38574828 DOI: 10.1016/j.jnutbio.2024.109637] [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: 11/23/2023] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Adequate dietary L-tryptophan (Trp) governs intestinal homeostasis in piglets. However, the defensive role of Trp in the diet against enterotoxigenic E. coli F4 (K88) in pigs is still poorly understood. Here, sixty (6.15 ± 1.52 kg, 24-day-old, Duroc × Landrace × Yorkshire) weaned piglets were used for an E. coli F4 attack test in a 2 × 2 factorial design. The growth (ADG, ADFI, GH), immune factors (IL-10, IgA, IgG, IgM), Trp metabolite 5-HT, intestinal morphology (jejunal and colonic VH), mRNA expression of β-defensins (jejunal BD-127, BD-119, ileal BD-1, BD-127), and abundance of beneficial microorganisms in the colon (Prevotella 9, Lactobacillus, Phascolarctobacterium, Faecalibacterium) were higher in the piglets in the HT (High Trp) and HTK (High Trp, K88) groups than in the LT (Low Trp) and LTK (Low Trp, K88) groups (P < 0.05), while FCR, diarrhea rate, diarrhea index, serum Trp, Kyn, IDO, D-LA, ET, and abundance of harmful microorganisms in the colon (Spirochaetes, Fusobacteria, Prevotella, Christensenellaceae R7) were lower in the HT and HTK groups than in the LT and LTK groups (P < 0.05). High Trp reduced the expression of virulence genes (K88 and LT) after E. coli F4 attack (P < 0.05). The IL-6, TNF-α was lower in the HTK group than in the LT, LTK group (P < 0.05). In short, a diet containing 0.35% Trp protected piglets from enterotoxigenic E. coli F4 (K88) via Trp metabolism promoting BD expression in the intestinal mucosa, which improved growth and intestinal health.
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Affiliation(s)
- Chen Chen
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Hong Hu
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhangcheng Li
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Min Qi
- Yunnan Animal Husbandry Station, Kunming 650225, China
| | - Yibin Qiu
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhijin Hu
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Fu Feng
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Wenjie Tang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animtche Group Co., Ltd., Chengdu 610066, China
| | - Hui Diao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animtche Group Co., Ltd., Chengdu 610066, China
| | - Weizhong Sun
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhiru Tang
- Animal Nutrition and Bio-feed, Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
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Dunbar A, Drigo B, Djordjevic SP, Donner E, Hoye BJ. Impacts of coprophagic foraging behaviour on the avian gut microbiome. Biol Rev Camb Philos Soc 2024; 99:582-597. [PMID: 38062990 DOI: 10.1111/brv.13036] [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: 08/14/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 03/06/2024]
Abstract
Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.
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Affiliation(s)
- Alice Dunbar
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
- UniSA STEM, University of South Australia, GPO Box 2471, Adelaide, South Australia, 5001, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, PO Box 123, Ultimo, New South Wales, 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Ultimo, New South Wales, 2007, Australia
| | - Erica Donner
- Future Industries Institute (FII), University of South Australia, Mawson Lakes Campus, GPO Box 2471 5095, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), University of South Australia, GPO Box 2471 5095, Adelaide, South Australia, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia
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8
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Yunusbaeva M, Borodina L, Terentyeva D, Bogdanova A, Zakirova A, Bulatov S, Altinbaev R, Bilalov F, Yunusbayev B. Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients. Front Cell Infect Microbiol 2024; 14:1331521. [PMID: 38440790 PMCID: PMC10910113 DOI: 10.3389/fcimb.2024.1331521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction The link between gut microbiota and host immunity motivated numerous studies of the gut microbiome in tuberculosis (TB) patients. However, these studies did not explore the metabolic capacity of the gut community, which is a key axis of impact on the host's immunity. Methods We used deep sequencing of fecal samples from 23 treatment-naive TB patients and 48 healthy donors to reconstruct the gut microbiome's metabolic capacity and strain/species-level content. Results We show that the systematic depletion of the commensal flora of the large intestine, Bacteroidetes, and an increase in Actinobacteria, Firmicutes, and Proteobacteria such as Streptococcaceae, Erysipelotrichaceae, Lachnospiraceae, and Enterobacteriaceae explains the strong taxonomic divergence of the gut community in TB patients. The cumulative expansion of diverse disease-associated pathobionts in patients reached 1/4 of the total gut microbiota, suggesting a heavy toll on host immunity along with MTB infection. Reconstruction of metabolic pathways showed that the microbial community in patients shifted toward rapid growth using glycolysis and excess fermentation to produce acetate and lactate. Higher glucose availability in the intestine likely drives fermentation to lactate and growth, causing acidosis and endotoxemia. Discussion Excessive fermentation and lactic acidosis likely characterize TB patients' disturbed gut microbiomes. Since lactic acidosis strongly suppresses the normal gut flora, directly interferes with macrophage function, and is linked to mortality in TB patients, our findings highlight gut lactate acidosis as a novel research focus. If confirmed, gut acidosis may be a novel potential host-directed treatment target to augment traditional TB treatment.
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Affiliation(s)
- Milyausha Yunusbaeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Liliya Borodina
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Darya Terentyeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, Saint Petersburg Pasteur Institute, Saint Petersburg, Russia
| | - Anna Bogdanova
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
| | - Aigul Zakirova
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Shamil Bulatov
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Radick Altinbaev
- Laboratory of Neurophysiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
| | - Fanil Bilalov
- Laboratory of Molecular Genetics, Republic Medical Genetic Centre, Ufa, Russia
- Department of Public Health and Health Organization with a course of ICPE, Bashkir State Medical University, Ufa, Russia
| | - Bayazit Yunusbayev
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
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9
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Jiang F, Yang Y, Mao Z, Cai W, Li G. ArcA positively regulates the expression of virulence genes and contributes to virulence of porcine Shiga toxin-producing enterotoxigenic Escherichia coli. Microbiol Spectr 2023; 11:e0152523. [PMID: 37916813 PMCID: PMC10714933 DOI: 10.1128/spectrum.01525-23] [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: 04/12/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Enterotoxigenic Escherichia coli (ETEC) cause severe diarrhea in humans and animals, leading to death and huge economic loss worldwide. Thus, elucidation of ETEC's pathogenic mechanisms will provide powerful data for the discovery of drugs serving as prevention or therapeutics against ETEC-caused diarrheal diseases. Here, we report that ArcA plays an essential role in the pathogenicity and virulence regulation in ETEC by positively regulating the expression of several key virulence factors including F18 fimbriae, heat-labile and heat-stable toxins, Shiga toxin 2e, and hemolysin, under microaerobic conditions and in vivo. Moreover, we found that positive regulation of several virulence genes by ArcA requires a global repressor H-NS (histone-like nucleoid structuring), implying that ArcA may exert positive effects by antagonizing H-NS. Collectively, our data established a key role for ArcA in the pathogenicity of porcine ETEC and ETEC strains isolated from human infections. Moreover, our work reveals another layer of regulation in relation to oxygen control of virulence factors in ETEC.
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Affiliation(s)
- Fengwei Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Yan Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhao Mao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wentong Cai
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ganwu Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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10
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Akinlabi OC, Nwoko ESQ, Dada RA, Ekpo S, Omotuyi A, Nwimo CC, Adepoju A, Popoola O, Dougan G, Thomson NR, Okeke IN. Epidemiology and Risk Factors for Diarrheagenic Escherichia coli Carriage among Children in Northern Ibadan, Nigeria. Am J Trop Med Hyg 2023; 109:1223-1232. [PMID: 37903436 PMCID: PMC10793065 DOI: 10.4269/ajtmh.22-0618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/14/2023] [Indexed: 11/01/2023] Open
Abstract
Diarrhea is a leading cause of childhood morbidity in Africa, but few studies, focus on bacterial diarrheal etiology including multicountry studies that typically excluded Nigeria. We collected stool specimens from 477 children under 5 years of age, 120 with diarrhea, who were enrolled in our prospective case-control study between November 2015 and August 2019. All were attending primary health clinics on the northern outskirts of Ibadan. Up to 10 Escherichia coli isolates were obtained per specimen, and at least three of them were sequenced using Illumina whole-genome sequence technology. Genomes were assembled using SPAdes and evaluated for quality using QUAST. VirulenceFinder was used to identify virulence genes. The microbiological quality of water from 14 wells within the study area was assessed using total and coliform counts. Diarrheagenic E. coli (DEC) were isolated from 79 (65.8%) cases and 217 (60.8%) control children. A number of hybrid DEC pathotypes, Salmonella spp., Yersinia spp., and all DEC pathotypes except Shiga toxin-producing E. coli were detected, but no pathogen showed association with disease (P > 0.05). Enterotoxigenic E. coli were more commonly recovered from children without diarrhea aged below 6 months but exclusively detected in children with diarrhea aged over 9 months. Temporally linked, genetically similar enteroaggregative E. coli were isolated from children in different households in eight instances. No well water sample drawn in the study was potable. Children in northern Ibadan were commonly colonized with DEC. Access to water, proper sanitation, and vaccination against the prevailing pathogens may be critical for protecting children from the less overt consequences of enteric pathogen carriage.
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Affiliation(s)
- Olabisi C. Akinlabi
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo, Nigeria
| | - El-shama Q. Nwoko
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo, Nigeria
| | - Rotimi A. Dada
- Medical Laboratory Science Program, College of Health Sciences, Bowen University, Iwo, Nigeria
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Ahmadu Bello University, Zaria, Nigeria
| | - Stella Ekpo
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo, Nigeria
| | - Adeola Omotuyi
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo, Nigeria
| | - Chukwuemeka C. Nwimo
- Department of Clinical Medicine, College of Medicine, University of Ibadan, Oyo, Nigeria
| | - Akinlolu Adepoju
- Department of Pediatrics, College of Medicine, University of Ibadan, Oyo, Nigeria
| | - Oluwafemi Popoola
- Department of Community Medicine, Faculty of Public Health, College of Medicine, University of Ibadan, Oyo, Nigeria
| | - Gordon Dougan
- Wellcome Sanger Institute, Saffron Walden, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | | | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo, Nigeria
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11
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Witsø IL, Basson A, Vinje H, Llarena AK, Bringas CS, Aspholm M, Wasteson Y, Myrmel M. Freshwater plastispheres as a vector for foodborne bacteria and viruses. Environ Microbiol 2023; 25:2864-2881. [PMID: 37964725 DOI: 10.1111/1462-2920.16536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023]
Abstract
There is growing evidence that plastic particles can accumulate microorganisms that are pathogenic to humans or animals. In the current study, the composition of the plastispheres that accumulated on polypropylene (PP), polyvinyl chloride (PVC), and high-density polyethylene (HDPE) pieces submerged in a river in the southeast Norway was characterized by 16S rRNA amplicon sequencing. Seasonal and geographical effects on the bacterial composition of the plastisphere were identified, in addition to the detection of potential foodborne pathogenic bacteria and viruses as part of the plastisphere. The diversity and taxonomic composition of the plastispheres were influenced by the number of weeks in the river, the season, and the location. The bacterial diversity differed significantly in the plastisphere from June and September, with a generally higher diversity in June. Also, the community composition of the plastisphere was significantly influenced by the geographical location, while the type of plastic had less impact. Plastics submerged in river water assembled a variety of microorganisms including potentially pathogenic bacteria and viruses (noro- and adenovirus) detected by qPCR. Cultivation methods detected viable bacteria such as Escherichia coli and Listeria monocytogenes. The results highlight the need for additional research on the risk of contaminating food with plastic particles colonized with human pathogens through irrigation water.
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Affiliation(s)
- Ingun Lund Witsø
- Faculty of Veterinary Medicine, Food Safety Unit, The Norwegian University of Life Sciences, Ås, Norway
| | - Adelle Basson
- Faculty of Veterinary Medicine, Food Safety Unit, The Norwegian University of Life Sciences, Ås, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hilde Vinje
- Faculty of Chemistry, Biotechnology and Food Science, The Norwegian University of Life Sciences, Ås, Norway
| | - Ann-Katrin Llarena
- Faculty of Veterinary Medicine, Food Safety Unit, The Norwegian University of Life Sciences, Ås, Norway
| | - Carlos Salas Bringas
- Institute for Marine Operations and Civil Engineering, Norwegian University of Science and Technology, Ålesund, Norway
| | - Marina Aspholm
- Faculty of Veterinary Medicine, Food Safety Unit, The Norwegian University of Life Sciences, Ås, Norway
| | - Yngvild Wasteson
- Faculty of Veterinary Medicine, Food Safety Unit, The Norwegian University of Life Sciences, Ås, Norway
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, The Norwegian University of Life Sciences, Ås, Norway
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12
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Furlan JPR, Ramos MS, Dos Santos LDR, da Silva Rosa R, Stehling EG. Multidrug-resistant Shiga toxin-producing Escherichia coli and hybrid pathogenic strains of bovine origin. Vet Res Commun 2023; 47:1907-1913. [PMID: 37199834 DOI: 10.1007/s11259-023-10141-x] [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: 08/08/2022] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Antimicrobial-resistant Escherichia coli strains have been circulating in various sectors and can be cross-transferred between them. Among pathogenic E. coli strains, Shiga toxin-producing E. coli (STEC) and hybrid pathogenic E. coli (HyPEC) emerged as responsible for outbreaks worldwide. As bovine are reservoir of STEC strains, these pathogens primarily spread to food products, exposing humans to risk. Therefore, this study aimed to characterize antimicrobial-resistant and potentially pathogenic E. coli strains from fecal samples of dairy cattle. In this regard, most E. coli strains (phylogenetic groups A, B1, B2, and E) were resistant to β-lactams and non-β-lactams and were classified as multidrug-resistant (MDR). Antimicrobial resistance genes (ARGs) related to multidrug resistance profiles were detected. Furthermore, mutations in fluoroquinolone and colistin resistance determinants were also identified, highlighting the deleterious mutation His152Gln in PmrB that may have contributed to the high level (> 64 mg/L) of colistin resistance. Virulence genes of diarrheagenic and extraintestinal pathogenic E. coli (ExPEC) pathotypes were shared among strains and even within the same strain, evidencing the presence of HyPEC (i.e., ExPEC/STEC), which were assigned as unusual B2-ST126-H3 and B1-ST3695-H31. These findings provide phenotypic and molecular data of MDR, ARGs-producing, and potentially pathogenic E. coli strains in dairy cattle, contributing to the monitoring of antimicrobial resistance and pathogens in healthy animals and alerting to potential bovine-associated zoonotic infections.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil.
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13
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Okumu NO, Ngeranwa JJN, Muloi DM, Ochien’g L, Moodley A, Mutisya C, Kiarie A, Wasonga JO, Watson J, Amon-Tanoh MA, Cumming O, Cook EAJ. Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002594. [PMID: 37992040 PMCID: PMC10664883 DOI: 10.1371/journal.pgph.0002594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.
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Affiliation(s)
- Noah O. Okumu
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
- Department of Biochemistry, Biotechnology and Microbiology, Kenyatta University, Nairobi, Kenya
| | - Joseph J. N. Ngeranwa
- Department of Biochemistry, Biotechnology and Microbiology, Kenyatta University, Nairobi, Kenya
| | - Dishon M. Muloi
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Linnet Ochien’g
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Arshnee Moodley
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Christine Mutisya
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Alice Kiarie
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Joseph O. Wasonga
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
| | - Julie Watson
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Maud Akissi Amon-Tanoh
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth A. J. Cook
- Animal and Human Health Department, International Livestock Research Institute, Nairobi, Kenya
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14
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Ogunbiyi TS, Fayemi OE, Akanni GB, Ayolabi CI, Hald T. Molecular Characterization of Hetero-Pathogenic and Diarrheagenic Escherichia coli Pathotypes in Diarrheic Children under Five Years and Exposure Environment in Ogun State, South-West Nigeria. Pathogens 2023; 12:1358. [PMID: 38003822 PMCID: PMC10675616 DOI: 10.3390/pathogens12111358] [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: 10/07/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Diarrheagenic Escherichia coli (DEC) is one of the most common etiological agents of moderate-to-severe diarrhea in Low- and Middle-Income Countries (LMICs). Therefore, determining the source(s) of DEC in index cases and exposure environment is important for developing a prevention strategy. The current study aims to investigate the prevalence of DEC among children under 5 years and their exposure environment in Ogun State, Nigeria. METHODS Samples from 228 diarrheic children and their exposure environment were collected and screened for E. coli. Bio-chemically compatible distinct colonies were molecularly characterized using a 7-virulence-gene multiplex PCR with virulence factors (VFs) indicative of four pathotypes of E. coli: enterotoxigenic (ETEC), verotoxigenic (VTEC), enteropathogenic (EPEC), and enteroinvasive (EIEC). Representative pathotypes were subjected to antimicrobial susceptibility and over-expressed efflux pump assays. RESULTS One or more VFs typical of specific pathotypes were detected in 25.9% (59/228) diarrhea cases consisting of ETEC (21.5%) and EPEC (0.4%), while hetero-pathogenic pathotypes were found in 4.0% of cases. Of the food sources, 27.9% (101/362) were positive for DEC, of which ETEC accounted for 21.0%, VTEC 1.9%, EPEC 0.6%, EIEC 0.6%, and hetero-pathogenic pathotypes were 3.9%. Furthermore, ETEC was the only pathotype detected in the wastewater (4/183). Interestingly, the consumption of street-vended foods was the most significant (p = 0.04) risk factor for DEC infection in the study area. A total of 73.3% of selected DEC pathotypes showed resistance to antimicrobials, while 27.5% demonstrated over-expression of efflux pump activity. CONCLUSION The high prevalence of ETEC across all sources and the occurrence of hetero-pathogenic DEC in diarrheic children and food sources emphasizes the importance of establishing a better strategy for the control and prevention of diarrhea among children in low- and medium-income households.
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Affiliation(s)
- Tosin Segun Ogunbiyi
- Department of Biological Sciences, Mountain Top University, Ibafo, 110106 Ogun State, Nigeria; (G.B.A.); (C.I.A.)
| | - Olanrewaju Emmanuel Fayemi
- Department of Biological Sciences, Mountain Top University, Ibafo, 110106 Ogun State, Nigeria; (G.B.A.); (C.I.A.)
| | - Gabriel Bidemi Akanni
- Department of Biological Sciences, Mountain Top University, Ibafo, 110106 Ogun State, Nigeria; (G.B.A.); (C.I.A.)
| | - Christianah Idowu Ayolabi
- Department of Biological Sciences, Mountain Top University, Ibafo, 110106 Ogun State, Nigeria; (G.B.A.); (C.I.A.)
- Department of Microbiology, University of Lagos, Akoka, 101017 Lagos State, Nigeria
| | - Tine Hald
- National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
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15
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Roy Chowdhury P, Hastak P, DeMaere M, Wyrsch E, Li D, Elankumaran P, Dolejska M, Browning GF, Marenda MS, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP. Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission? mSystems 2023; 8:e0123622. [PMID: 37675998 PMCID: PMC10654095 DOI: 10.1128/msystems.01236-22] [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: 12/10/2022] [Accepted: 07/11/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.
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Affiliation(s)
- Piklu Roy Chowdhury
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Priyanka Hastak
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Matthew DeMaere
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Ethan Wyrsch
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Paarthiphan Elankumaran
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Monika Dolejska
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
- Central European Institute of Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
- Biomedical Center, Charles University, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital, Brno, Czech Republic
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Mark S. Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
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16
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Zelelie TZ, Eguale T, Yitayew B, Abeje D, Alemu A, Seman A, Jass J, Mihret A, Abebe T. Molecular epidemiology and antimicrobial susceptibility of diarrheagenic Escherichia coli isolated from children under age five with and without diarrhea in Central Ethiopia. PLoS One 2023; 18:e0288517. [PMID: 37450423 PMCID: PMC10348587 DOI: 10.1371/journal.pone.0288517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Diarrhea is a serious health problem in children, with the highest mortality rate in sub-Saharan Africa. Diarrheagenic Escherichia coli (DEC) is among the major bacterial causes of diarrhea in children under age five. The present study aims to determine molecular epidemiology and antimicrobial resistance profiles of DEC and identify contributing factors for acquisition among children under age five in Central Ethiopia. METHODS A health facility-centered cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia, from December 2020 to August 2021. A total of 476 specimens, 391 from diarrheic and 85 from non-diarrheic children under age five were collected. Bacterial isolation and identification, antimicrobial susceptibility, and pathotype determination using polymerase chain reaction (PCR) were done. RESULTS Of the 476 specimens analyzed, 89.9% (428/476) were positive for E. coli, of which 183 were positive for one or more genes coding DEC pathotypes. The overall prevalence of the DEC pathotype was 38.2% (183/476). The predominant DEC pathotype was enteroaggregative E. coli (EAEC) (41.5%, 76/183), followed by enterotoxigenic E. coli (21.3%, 39/183), enteropathogenic E. coli (15.3%, 28/183), enteroinvasive E. coli (12.6%, 23/183), hybrid strains (7.1%, 13/183), Shiga toxin-producing E. coli (1.6%, 3/183), and diffusely-adherent E. coli (0.6%, 1/183). DEC was detected in 40.7% (159/391) of diarrheic and 28.2% (24/85) in non-diarrheic children (p = 0.020). The majority of the DEC pathotypes were resistant to ampicillin (95.1%, 174/183) and tetracycline (91.3%, 167/183). A higher rate of resistance to trimethoprim-sulfamethoxazole (58%, 44/76), ciprofloxacin (22%, 17/76), ceftazidime and cefotaxime (20%, 15/76) was seen among EAEC pathotypes. Multidrug resistance (MDR) was detected in 43.2% (79/183) of the pathotypes, whereas extended spectrum ß-lactamase and carbapenemase producers were 16.4% (30/183) and 2.2% (4/183), respectively. CONCLUSION All six common DEC pathotypes that have the potential to cause severe diarrheal outbreaks were found in children in the study area; the dominant one being EAEC with a high rate of MDR.
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Affiliation(s)
- Tizazu Zenebe Zelelie
- Department of Medical Laboratory Science, Debre Berhan University, Debre Birhan, Ethiopia
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- Armeur Hansen Research Institue (AHRI), Addis Ababa, Ethiopia
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ohio State University Global One Health LLC, Addis Ababa, Ethiopia
| | - Berhanu Yitayew
- Department of Medical Laboratory Science, Debre Berhan University, Debre Birhan, Ethiopia
| | - Dessalegn Abeje
- Armeur Hansen Research Institue (AHRI), Addis Ababa, Ethiopia
| | - Ashenafi Alemu
- Armeur Hansen Research Institue (AHRI), Addis Ababa, Ethiopia
| | - Aminu Seman
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jana Jass
- The Life Science Centre—Biology, School of Science and Technology, Orebro University, Örebro, Sweden
| | - Adane Mihret
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- Armeur Hansen Research Institue (AHRI), Addis Ababa, Ethiopia
| | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
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Kartsev NN, Detusheva EV, Kalmantaeva OV, Korobova OV, Gerasimov VN, Kombarova TI, Borzilov AI, Fursova NK, Vereshchagin AN, Svetoch EA. Hetero-Pathogenic O181:H4 EAHEC Strain of Sequence Type ST678 Associated with Hemolytic-Uremic Syndrome in Schoolchildren in Russia. Microorganisms 2023; 11:1771. [PMID: 37512943 PMCID: PMC10383572 DOI: 10.3390/microorganisms11071771] [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: 05/15/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND In the last decade, the importance of hetero-pathogenic enteroaggregative Shiga-toxin-producing E. coli for public health has increased. Recently, we described the genetic background of the EAHEC O181:H4 strain of ST678 carrying the stx2 gene in prophage and five plasmids, including the plasmid-carrying aggR and aaiC genes. Here, we present the morphological and enzymatic characteristics of this strain, as well as susceptibility to antimicrobials, biofilm formation, etc. Methods: Bacterial morphology was studied using an electron microscope. Susceptibility to antimicrobials was determined using the microdilution method. Cytotoxicity was estimated in Vero cells. Virulence was studied on mice. RESULTS The morphological and enzymatic properties of the hetero-pathogenic EAHEC strain were typical for E. coli; electron microscopy revealed the specific flagella. The strain was susceptible to most antibiotics and disinfectants but resistant to ampicillin and ciprofloxacin and showed a high degree of biofilm formation. Cytotoxicity towards Vero cells was estimated as 80%. CONCLUSIONS The emergence of a new O181:H4 EAHEC strain poses a potential threat to humans because of the virulence potential that must be taken into account in the epidemiological analysis of outbreaks and sporadic cases of foodborne infections associated with hemolytic-uremic syndrome.
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Affiliation(s)
- Nikolay N Kartsev
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Elena V Detusheva
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Olga V Kalmantaeva
- Laboratory of Molecular Biology, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Olga V Korobova
- Laboratory of Biological Trials, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Vladimir N Gerasimov
- Department of Disinfectology, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Tatiana I Kombarova
- Laboratory of Biological Trials, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Aleksander I Borzilov
- Laboratory of Biological Trials, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | - Nadezhda K Fursova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
| | | | - Edward A Svetoch
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory "Kvartal A", 142279 Obolensk, Russia
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Jalil A, Masood S, Ain Q, Andleeb S, Dudley EG, Adnan F. High resistance of fluoroquinolone and macrolide reported in avian pathogenic Escherichia coli isolates from the humid subtropical regions of Pakistan. J Glob Antimicrob Resist 2023; 33:5-17. [PMID: 36764657 DOI: 10.1016/j.jgar.2023.01.009] [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: 10/07/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
OBJECTIVES This study aimed to assess the antimicrobial resistance profile, virulence potential, and genetic characterization of avian pathogenic Escherichia coli (APEC) that cause colibacillosis in poultry. METHODS Antibiotic susceptibility testing (AST) was measured via the Kirby-Bauer disc diffusion method against 27 commonly used antibiotics. Phylogrouping, virulence-associated gene detection, and hybrid strain detection via multiplex polymerase chain reaction (PCR) and genetic diversity were analysed via ERIC-PCR fingertyping method. RESULTS AST analysis showed 100% of isolates were multidrug-resistant (MDR) and highest resistance was against penicillin, tetracycline, and macrolide classes of antibiotics. The mcr-1 gene was present in 40% of the isolates, though only 4% of isolates were showing phenotypic resistance. Despite the scarce use of fluoroquinolone, carbapenem, and cephalosporin in the poultry sector, resistance was evident because of the high prevalence of extended-spectrum β-lactamase (ESBL) (53.7%) and other β-lactamases in APEC isolates. β-lactamase genotyping of APEC isolates revealed that 85.7% of isolates contained either blaCTX or blaTEM and around 38% of isolates were complement resistant. Growth in human urine was evident in 67.3% of isolates. Phylogroup B1 (51%) was the most prevalent group followed by phylogroups A (30.6%), D (13.61%), and B2 (4.76%). The most prevalent virulence-associated genes were fimH, iss, and tatT. Results showed that 26 isolates (17.69%) can be termed hybrid strains and APEC/EHEC (enterohemorrhagic E. coli) was the most prevalent hybrid E. coli pathotype. ERIC-PCR fingerprinting genotype analysis clustered APEC isolates in 40 groups (E1-E40). This study provides insights into the antibiotic resistance and virulence profiling of the APEC isolates in Pakistan. CONCLUSIONS The findings of this study provide insights into that the antibiotic resistance and virulence profiling of the APEC isolates in Pakistan. This data can inform future studies designed to better estimate the severity of the colibacillosis in poultry farms.
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Affiliation(s)
- Amna Jalil
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saleha Masood
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Quratul Ain
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Edward G Dudley
- Department of Food Sciences, Pennsylvania State University, University Park, Pennsylvania; Escherichia coli Reference Centre, Pennsylvania State University, University Park, Pennsylvania
| | - Fazal Adnan
- Atta Ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
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Lee W, Kim MH, Sung S, Kim E, An ES, Kim SH, Kim SH, Kim HY. Genome-Based Characterization of Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains Isolated in South Korea, 2016-2020. Microorganisms 2023; 11:1285. [PMID: 37317259 DOI: 10.3390/microorganisms11051285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
The global emergence of hybrid diarrheagenic E. coli strains incorporating genetic markers from different pathotypes is a public health concern. Hybrids of Shiga toxin-producing and enterotoxigenic E. coli (STEC/ETEC) are associated with diarrhea and hemolytic uremic syndrome (HUS) in humans. In this study, we identified and characterized STEC/ETEC hybrid strains isolated from livestock feces (cattle and pigs) and animal food sources (beef, pork, and meat patties) in South Korea between 2016 and 2020. The strains were positive for genes from STEC and ETEC, such as stx (encodes Shiga toxins, Stxs) and est (encodes heat-stable enterotoxins, ST), respectively. The strains belong to diverse serogroups (O100, O168, O8, O155, O2, O141, O148, and O174) and sequence types (ST446, ST1021, ST21, ST74, ST785, ST670, ST1780, ST1782, ST10, and ST726). Genome-wide phylogenetic analysis revealed that these hybrids were closely related to certain ETEC and STEC strains, implying the potential acquisition of Stx-phage and/or ETEC virulence genes during the emergence of STEC/ETEC hybrids. Particularly, STEC/ETEC strains isolated from livestock feces and animal source foods mostly exhibited close relatedness with ETEC strains. These findings allow further exploration of the pathogenicity and virulence of STEC/ETEC hybrid strains and may serve as a data source for future comparative studies in evolutionary biology.
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Min-Hee Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Soohyun Sung
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Sook An
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources, Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
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Rivera FP, Medina A, Riveros M, Ochoa TJ, Pons MJ, Ruiz J. Colonizing and Virulence Factors in Enterotoxigenic Escherichia coli from Peru. Am J Trop Med Hyg 2023; 108:948-953. [PMID: 36972692 PMCID: PMC10160877 DOI: 10.4269/ajtmh.22-0677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/12/2023] [Indexed: 03/29/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) ranks among the most relevant diarrheagenic pathogens. Efforts to design vaccines to fight ETEC have been focused on colonizing factors (CFs) and atypical virulence factors (AVF). An effective vaccine must account for differences in the regional prevalence of these CFs and AVFs to be truly effective in a given area. In the present study, the presence of 16 CFs and 9 AVFs, as well as the heat-stable (ST) variants (STh or STp), was established by polymerase chain reaction in 205 Peruvian ETEC isolates (120 from diarrhea cases and 85 from healthy controls). Ninety-nine (48.3%) isolates were heat-labile, 63 (30.7%) ST, and 43 (21.0%) presented both toxins. Of ST isolates, 59 (28.8%) possessed STh, 30 (14.6%) STp, five (2.4%) both STh and STp, and 12 (5.8%) were not amplified for any variant tested. The presence of CFs was associated with diarrhea (P < 0.0001). The presence of eatA as well as concomitant presence of CSI, CS3, and CS21 and of C5 and C6 was statistically related to diarrhea cases. The present results suggests that, if effective, a vaccine considering CS6, CS20, and CS21, together with EtpA, would provide protection against 64.4% of the isolates analyzed, whereas the addition of CS12 and EAST1 would lead to 83.9% coverage. Large studies are needed to establish both the ideal candidates to be considered to develop a vaccine effective in the area, and continuous surveillance is needed to detect displacement of circulating isolates that may compromise future vaccines.
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Affiliation(s)
- Fulton P. Rivera
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Anicia Medina
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maribel Riveros
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Ciencias Naturales y Matemática, Universidad Nacional Federico Villarreal, Lima, Peru
- Laboratorio de Infectología Pediátrica, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Theresa J. Ochoa
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Infectología Pediátrica, Universidad Peruana Cayetano Heredia, Lima, Peru
- University of Texas School of Public Health, Houston, Texas
| | - Maria J. Pons
- Grupo de Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Joaquim Ruiz
- Grupo de Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
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Bejide OS, Odebode MA, Ogunbosi BO, Adekanmbi O, Akande KO, Ilori T, Ogunleye VO, Nwachukwu VU, Grey-Areben A, Akande ET, Okeke IN. Diarrhoeal pathogens in the stools of children living with HIV in Ibadan, Nigeria. Front Cell Infect Microbiol 2023; 13:1108923. [PMID: 36992685 PMCID: PMC10040677 DOI: 10.3389/fcimb.2023.1108923] [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: 11/26/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Introduction Diarrhoea can be debilitating in young children. Few aetiological investigations in Africans living with human immunodeficiency virus (HIV) have been performed since antiretrovirals became widely available. Methods Stool specimens from children with diarrhoea living with HIV, and HIV-uninfected controls, recruited at two hospitals in Ibadan, Nigeria, were screened for parasites and occult blood, and cultured for bacteria. Following biochemical identification of at least five colonies per specimen, diarrhoeagenic Escherichia coli and Salmonella were confirmed by PCR. Data were line-listed and comparisons were made using Fisher's Exact test. Results Only 10 children living with HIV could be enrolled during the 25-month study period and 55 HIV-uninfected children with diarrhoea were included for comparison. The most common pathogens overall were enteroaggregative E. coli (18/65, 27.7%), enteroinvasive E. coli (10/65, 15.4%), Cryptosporidium parvum (8/65, 12.3%) and Cyclospora cayetanensis (7/65, 10.8%). At least one pathogen was detected from seven of ten children living with HIV and 27 (49.1%) HIV-uninfected children. Parasite detection was associated with HIV positive status (p=0.03) with C. parvum specifically recovered more commonly from children living with HIV (p=0.01). Bacterial-parasite pathogen combinations were detected in specimens from four of ten children living with HIV but only 3(5.5%) HIV-uninfected children (p=0.009). Stools from five of ten children living with HIV and 7(12.7%) HIV-negative children (p = 0.014) contained occult blood. Discussion Even though children living with HIV present infrequently to Ibadan health facilities with diarrhoea, their greater propensity for mixed and potentially invasive infections justifies prioritizing laboratory diagnosis of their stools.
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Affiliation(s)
- Oyeniyi S. Bejide
- Department of Microbiology, Chrisland University, Abeokuta, Ogun State, Nigeria
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Mariam A. Odebode
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Babatunde O. Ogunbosi
- Department of Paediatrics, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Olukemi Adekanmbi
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Kolawole O. Akande
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Temitope Ilori
- Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Victoria U. Nwachukwu
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Aghogho Grey-Areben
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Elizabeth T. Akande
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Iruka N. Okeke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Oyo State, Nigeria
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Rapoo SM, Budeli P, Thaoge ML. Recovery of Potential Starter Cultures and Probiotics from Fermented Sorghum (Ting) Slurries. Microorganisms 2023; 11:microorganisms11030715. [PMID: 36985287 PMCID: PMC10054160 DOI: 10.3390/microorganisms11030715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
Fermented foods are thought to provide a source of probiotics that promote gut health. Consequently, isolation and characterization of fermented food strains and their applications in a controlled fermentation process or as probiotics present a new facet in this area of research. Therefore, the current study sought to identify dominant strains in sorghum-fermented foods (ting) and characterize their probiotic potential in vitro. Recovered isolates were identified as Lactobacillus helveticus, Lactobacillus amylolyticus, Lacticaseibacillus paracasei, Lacticaseibacillus paracasei subsp paracasei, Lactiplantibacillus plantarum, Levilactobacillus brevis, Loigolactobacillus coryniformis and Loigolactobacillus coryniformis subsp torquens based on the their 16S rRNA sequences. Increased biomass was noted in seven out of nine under a low pH of 3 and a high bile concentration of 2% in vitro. Bactericidal activities of isolated LABs presented varying degrees of resistance against selected pathogenic bacteria ranging between (1.57 to 41 mm), (10 to 41 mm), and (11.26 to 42 mm) for Salmonella typhimurium ATTC 14028, Staphylococcus aureus ATTC 6538 and Escherichia coli ATTC8739, respectively. Ampicillin, erythromycin, mupirocin, tetracycline and chloramphenicol were able to inhibit growth of all selected LABs. Thus, isolates recovered from ting partially satisfy the potential candidacy for probiotics by virtue of being more tolerant to acid and bile, antibacterial activity and antibiotic resistance.
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Santos ACM, Santos-Neto JF, Trovão LO, Romano RFT, Silva RM, Gomes TAT. Characterization of unconventional pathogenic Escherichia coli isolated from bloodstream infection: virulence beyond the opportunism. Braz J Microbiol 2023; 54:15-28. [PMID: 36480121 PMCID: PMC9943985 DOI: 10.1007/s42770-022-00884-1] [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: 09/27/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of urinary tract infection worldwide and a critical bloodstream infection agent. There are more than 50 virulence factors (VFs) related to ExPEC pathogenesis; however, many strains isolated from extraintestinal infections are devoid of these factors. Since opportunistic infections may occur in immunocompromised patients, E. coli strains that lack recognized VFs are considered opportunist, and their virulence potential is neglected. We assessed eleven E. coli strains isolated from bloodstream infections and devoid of the most common ExPEC VFs to understand their pathogenic potential. The strains were evaluated according to their capacity to interact in vitro with human eukaryotic cell lineages (Caco-2, T24, HEK293T, and A549 cells), produce type 1 fimbriae and biofilm in diverse media, resist to human sera, and be lethal to Galleria mellonella. One strain displaying all phenotypic traits was sequenced and evaluated. Ten strains adhered to Caco-2 (colon), eight to T24 (bladder), five to HEK-293 T (kidney), and four to A549 (lung) cells. Eight strains produced type 1 fimbriae, ten adhered to abiotic surfaces, nine were serum resistant, and seven were virulent in the G. mellonella model. Six of the eleven E. coli strains displayed traits compatible with pathogens, five of which were isolated from an immune-competent host. The genome of the EC175 strain, isolated from a patient with urosepsis, reveals that the strain belonged to ST504-A, and serotype O11:H11; harbors thirteen VFs genes, including genes encoding UpaG and yersiniabactin as the only ExPEC VFs identified. Together, our results suggest that the ExPEC pathotype includes pathogens from phylogroups A and B1, which harbor VFs that remain to be uncovered.
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Affiliation(s)
- Ana Carolina M Santos
- Laboratório Experimental de Patogenicidade de Enterobactérias, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, Edifício Prof. Dr. Antônio C. Mattos Paiva, 3º Andar. Vila Clementino, São Paulo, SP, 04023-062, Brazil.
| | - José F Santos-Neto
- Laboratório Experimental de Patogenicidade de Enterobactérias, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, Edifício Prof. Dr. Antônio C. Mattos Paiva, 3º Andar. Vila Clementino, São Paulo, SP, 04023-062, Brazil
| | - Liana O Trovão
- Laboratório Experimental de Patogenicidade de Enterobactérias, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, Edifício Prof. Dr. Antônio C. Mattos Paiva, 3º Andar. Vila Clementino, São Paulo, SP, 04023-062, Brazil
| | - Ricardo F T Romano
- Laboratório de Patogênese de Enterobacterales, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
- Departamento de Diagnóstico Por Imagem, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa Maria Silva
- Laboratório de Patogênese de Enterobacterales, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia A T Gomes
- Laboratório Experimental de Patogenicidade de Enterobactérias, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Botucatu 862, Edifício Prof. Dr. Antônio C. Mattos Paiva, 3º Andar. Vila Clementino, São Paulo, SP, 04023-062, Brazil.
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Whole genome sequence-based characterisation of Shiga toxin-producing Escherichia coli isolated from game meat originating from several European countries. Sci Rep 2023; 13:3247. [PMID: 36828872 PMCID: PMC9957979 DOI: 10.1038/s41598-023-30333-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
Game meat is becoming increasingly popular but may be contaminated with pathogenic bacteria such as Shiga toxin-producing Escherichia coli (STEC). STEC cause gastrointestinal illnesses including diarrhoea, haemorrhagic colitis (HC), and the haemolytic uremic syndrome (HUS). The aim of this study was to assess the occurrence of STEC in 92 meat samples from chamois (n = 2), red deer (n = 27), roe deer (n = 38), and wild boar (n = 25), from Switzerland and other European countries. After enrichment, Shiga-toxin encoding genes (stx) were detected by PCR in 78 (84%) of the samples and STEC were isolated from 23 (25%) of the same samples. Nine different serotypes and eight different sequence types (STs) were found, with O146:H28 ST738 (n = 10) and O110:H31 ST812 (n = 5) predominating. None of the STEC belonged to the so-called top-five serogroups O26, O103, O111, O145, and O157. Subtyping of stx identified stx1c (n = 9), stx2a (n = 1), stx2b (n = 19), stx2e (n = 2), and stx2g (n = 1). Additional virulence factors (VFs) comprised ehx (n = 12), iha (n = 21), sta1 (n = 1), and subAB (n = 19). None of the isolates contained the eae gene. Twenty-one STEC contained VFs associated with extra-intestinal pathogenic E. coli (ExPEC). Overall, the pathogenic potential of STEC in game meat is moderate, though the isolation of one STEC strain carrying stx2a, and of STEC/ExPEC hybrids suggests a role of game meat as a potential source of STEC infections in humans. Therefore, detailed knowledge of the safe handling and preparation of game meat is needed to prevent foodborne infections.
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Occurrence of diarrheagenic Escherichia coli pathotypes from raw milk and unpasteurized buttermilk by culture and multiplex polymerase chain reaction in southwest Iran. Mol Biol Rep 2023; 50:3661-3667. [PMID: 36808583 DOI: 10.1007/s11033-023-08261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND In developing countries including Iran, there are limited data on diarrheagenic Escherichia coli (DEC) contamination in milk and unpasteurized buttermilks. This study aimed to determine the occurrence of DEC pathotypes by culture and multiplex polymerase chain reaction (M-PCR) in some dairy products from southwest Iran. METHODS AND RESULTS In this cross-sectional study (September to October 2021), 197 samples (87 unpasteurized buttermilk and 110 raw cow milk) were collected from dairy stores of Ahvaz, southwest Iran. The presumptive E. coli isolates were primarily identified using biochemical tests and then confirmed by PCR of uidA gene. The occurrence of 5 DEC pathotypes: enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and enteroinvasive E. coli (EIEC) were investigated using M-PCR. Overall, 76 (76/197, 38.6%) presumptive E. coli isolates were identified by biochemical tests. Using uidA gene, only 50 isolates (50/76, 65.8%) were confirmed as E. coli. DEC pathotypes were detected in 27 of 50 (54.0%) E. coli isolates (74.1%, 20/27 from raw cow milk and 25.9%, 7/27 from unpasteurized buttermilk). The frequency of DEC pathotypes was as follows: 1 (3.7%) EAEC, 2 (7.4%) EHEC, 4 (14.8%) EPEC, 6 (22.2%) ETEC, and 14 (51.9%) EIEC. However, 23 (46.0%) E. coli isolates had only the uidA gene and were not considered DEC pathotypes. CONCLUSION Possible health risks for Iranian consumers can be attributed to the presence of DEC pathotypes in dairy products. Hence, serious control and prevention efforts are needed to stop the spread of these pathogens.
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Yousefipour M, Rezatofighi SE, Ardakani MR. Detection and characterization of hybrid uropathogenic Escherichia coli strains among E. coli isolates causing community-acquired urinary tract infection. J Med Microbiol 2023; 72. [PMID: 36753429 DOI: 10.1099/jmm.0.001660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Introduction. The main aetiological agent of urinary tract infection (UTI) is Escherichia coli, categorized as uropathogenic E. coli (UPEC). The genome of UPEC shows a high degree of plasticity, which leads to the emergence of 'intermediary strains' with different traits from the parental pathotypes.Gap Statement/Aim. We aimed to assess the frequency and types of the hybrid UPEC among isolates causing UTI and characterize virulence properties of these hybrid isolates molecularly and phenotypically.Methodology. After detection of intestinal pathogenic E. coli (IPEC) virulence markers among 200 UPEC isolates, they were assessed for the presence of 40 virulence genes (VGs) of extraintestinal, uropathogenic and diarrhoeagenic E. coli, phylogenetic group typing, phenotypic traits including biofilm formation, adherence and invasion to HeLa cells, haemolysis activity and antimicrobial resistance.Results. The analysis showed 21 (10.5 %) UPEC isolates carried enteroaggregative E. coli (EAEC) and enteropathogenic E. coli (EPEC) virulence markers. Twenty isolates carried the aggR (EAEC) and one the eae and escV genes (EPEC), which were classified as hybrid strains. The most commonly identified genes were fimH (71.5 %), fyuA (66.7 %), iutA (62 %), chuA (57.1) and traT (47.6 %). Biofilm production, adhesion and invasion were found among 17 (81), 18 (85.7) and 11 (52.4 %) hybrids, respectively. Investigation of the genetic characteristics, phylogenetic group and virulence profile of the detected hybrids revealed that they have genetic diversity and do not belong to a particular clonal lineage.Conclusion. The present study reveals that some UPEC may carry virulence markers of IPEC pathotypes. EAEC and EPEC seem to have a greater tendency to form hybrids and cause UTI. Further studies are needed to elucidate what factors contributed to survival in the urinary tract system and facilitate infection and whether these combinations lead to an increase in pathogenicity or not.
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Affiliation(s)
- Mahta Yousefipour
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Pokharel P, Dhakal S, Dozois CM. The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen. Microorganisms 2023; 11:344. [PMID: 36838308 PMCID: PMC9965155 DOI: 10.3390/microorganisms11020344] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes.
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Affiliation(s)
- Pravil Pokharel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Sabin Dhakal
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
- Pasteur Network, Laval, QC H7V 1B7, Canada
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Munhoz DD, Richards AC, Santos FF, Mulvey MA, Piazza RMF. E. coli Common pili promote the fitness and virulence of a hybrid aEPEC/ExPEC strain within diverse host environments. Gut Microbes 2023; 15:2190308. [PMID: 36949030 PMCID: PMC10038029 DOI: 10.1080/19490976.2023.2190308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 03/07/2023] [Indexed: 03/24/2023] Open
Abstract
Pathogenic subsets of Escherichia coli include diarrheagenic (DEC) strains that cause disease within the gut and extraintestinal pathogenic E. coli (ExPEC) strains that are linked with urinary tract infections, bacteremia, and other infections outside of intestinal tract. Among DEC strains is an emergent pathotype known as atypical enteropathogenic E. coli (aEPEC), which can cause severe diarrhea. Recent sequencing efforts revealed that some E. coli strains possess genetic features that are characteristic of both DEC and ExPEC isolates. BA1250 is a newly reclassified hybrid strain with characteristics of aEPEC and ExPEC. This strain was isolated from a child with diarrhea, but its genetic features indicate that it might have the capacity to cause disease at extraintestinal sites. The spectrum of adhesins encoded by hybrid strains like BA1250 are expected to be especially important in facilitating colonization of diverse niches. E. coli common pilus (ECP) is an adhesin expressed by many E. coli pathogens, but how it impacts hybrid strains has not been ascertained. Here, using zebrafish larvae as surrogate hosts to model both gut colonization and extraintestinal infections, we found that ECP can act as a multi-niche colonization and virulence factor for BA1250. Furthermore, our results indicate that ECP-related changes in activation of envelope stress response pathways may alter the fitness of BA1250. Using an in silico approach, we also delineated the broader repertoire of adhesins that are encoded by BA1250, and provide evidence that the expression of at least a few of these varies in the absence of functional ECP.
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Affiliation(s)
| | - Amanda C. Richards
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake, UT, USA
| | - Fernanda F. Santos
- Laboratório Alerta, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Matthew A. Mulvey
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake, UT, USA
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Prendergast DM, Slowey R, Burgess CM, Murphy D, Johnston D, Morris D, O’ Doherty Á, Moriarty J, Gutierrez M. Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing. Front Microbiol 2023; 14:1118264. [PMID: 37032887 PMCID: PMC10073600 DOI: 10.3389/fmicb.2023.1118264] [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: 12/07/2022] [Accepted: 03/01/2023] [Indexed: 04/11/2023] Open
Abstract
Background The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate. Methods To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n = 72) and after (n = 10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission. Results A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n = 24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified. Conclusion Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.
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Affiliation(s)
- Deirdre M. Prendergast
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
- *Correspondence: Deirdre M. Prendergast,
| | - Rosemarie Slowey
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
| | | | - Declan Murphy
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
| | - Dayle Johnston
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, University of Galway, Galway, Ireland
| | - Áine O’ Doherty
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
| | - John Moriarty
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
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30
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Occurrence of Escherichia coli Pathotypes in Diarrheic Calves in a Low-Income Setting. Pathogens 2022; 12:pathogens12010042. [PMID: 36678390 PMCID: PMC9861035 DOI: 10.3390/pathogens12010042] [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: 11/23/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Different E. coli pathotypes are common zoonotic agents. Some of these pathotypes cause recurrent and widespread calf diarrhea and contribute to significant economic losses in the livestock sector worldwide in addition to putting humans at risk. Here, we investigated the occurrence of E. coli pathotypes in diarrheic calves in Ethiopia kept under various calf management practices. One hundred fecal samples were collected from diarrheic calves in 98 different farms. E. coli was isolated in the samples from 99 of the diarrheic calves, and virulence genes were detected in 80% of the samples. The occurrence of E. coli pathotypes in the samples was 32% ETEC, 23% STEC, 18% STEC/ETEC, 3% EPEC, 2% EAEC, and 1% EHEC. No diarrheic calves were positive for the EIEC and DAEC pathotypes. The occurrence of pathotypes was positively associated with female calves (EPEC, p = 0.006), aged less than 2 weeks (STEC, p = 0.059), and calves fed colostrum via the hand method (STEC, p = 0.008 and EAEC, p = 0.003). This study revealed that several E. coli pathotypes occurred among calves affected with diarrhea. Moreover, the presence of a mixed STEC/ETEC pathotypes infection was present in the studied low-income setting. These findings indicate a considerable risk for the zoonotic transmission from calves to humans and the options to provide the better management for younger calves in order to reduce the economic loss.
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Chen H, Lu Q, An H, Li J, Shen S, Zheng X, Chen W, Wang L, Li J, Du Y, Wang Y, Liu X, Baumann M, Tacke M, Zou L, Wang J. The synergistic activity of SBC3 in combination with Ebselen against Escherichia coli infection. Front Pharmacol 2022; 13:1080281. [PMID: 36588729 PMCID: PMC9797518 DOI: 10.3389/fphar.2022.1080281] [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: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli ranks as the number one clinical isolate in the past years in China according to The China Antimicrobial Surveillance Network (CHINET), and its multidrug-resistant (MDR) pathogenic strains account for over 160 million cases of dysentery and one million deaths per year. Here, our work demonstrates that E. coli is highly sensitive to the synergistic combination of SBC3 [1,3-Dibenzyl-4,5-diphenyl-imidazol-2-ylidene silver (I) acetate] and Ebselen, which shows no synergistic toxicity on mammalian cells. The proposed mechanism for the synergistic antibacterial effect of SBC3 in combination with Ebselen is based on directly inhibiting E. coli thioredoxin reductase and rapidly depleting glutathione, resulting in the increase of reactive oxygen species that cause bacterial cell death. Furthermore, the bactericidal efficacy of SBC3 in combination with Ebselen has been confirmed in mild and acute peritonitis mice. In addition, the five most difficult to treat Gram-negative bacteria (including E. coli, Acinetobacter baumannii, Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa) are also highly sensitive to a synergistic combination of SBC3 and Ebselen. Thus, SBC3 in combination with Ebselen has potential as a treatment for clinically important Gram-negative bacterial infections.
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Affiliation(s)
- Hao Chen
- The Second People’s Hospital of China Three Gorges University, Yichang, Hubei, China,The Second People’s Hospital of Yichang, Yichang, Hubei, China
| | - Qianqian Lu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Haoyue An
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Juntong Li
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Shuchu Shen
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Xi Zheng
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Wei Chen
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Lu Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Jihong Li
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Youqin Du
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yueqing Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Xiaowen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Marcus Baumann
- The School of Chemistry, University College Dublin, Belfield, Dublin, Ireland
| | - Matthias Tacke
- The School of Chemistry, University College Dublin, Belfield, Dublin, Ireland,*Correspondence: Lili Zou, ; Jun Wang, ; Matthias Tacke,
| | - Lili Zou
- The Second People’s Hospital of China Three Gorges University, Yichang, Hubei, China,The Second People’s Hospital of Yichang, Yichang, Hubei, China,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China,*Correspondence: Lili Zou, ; Jun Wang, ; Matthias Tacke,
| | - Jun Wang
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China,*Correspondence: Lili Zou, ; Jun Wang, ; Matthias Tacke,
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Schüroff PA, Abe CM, Silva JW, de Paula Coelho C, Andrade FB, Hernandes RT, Dobrindt U, Gomes TAT, Elias WP. Role of aggregate-forming pilus (AFP) in adherence and colonization of both intestinal and urinary tracts. Virulence 2022; 13:1423-1433. [PMID: 35982607 PMCID: PMC9397481 DOI: 10.1080/21505594.2022.2112818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hybrid-pathogenic Escherichia coli represent an important group of strains associated with intestinal and extraintestinal infections. Recently, we described strain UPEC-46, a uropathogenic/enteroaggregative E. coli (UPEC/EAEC) strain presenting the aggregative adherence (AA) pattern on bladder and colorectal epithelial cells mediated by aggregate-forming pili (AFP). However, the role of AFP and other uninvestigated putative fimbriae operons in UPEC-46 pathogenesis remains unclear. Thus, this study evaluated the involvement of AFP and other adhesins in uropathogenicity and intestinal colonization using different in vitro and in vivo models. The strain UPEC-46 was able to adhere and invade intestinal and urinary cell lines. A library of transposon mutants also identified the involvement of type I fimbriae (TIF) in the adherence to HeLa cells, in addition to colorectal and bladder cell lines. The streptomycin-treated mouse in vivo model also showed an increased number of bacterial counts in the colon in the presence of AFP and TIF. In the mouse model of ascending urinary tract infection (UTI), AFP was more associated with kidney colonization, while TIF appears to mediate bladder colonization. Results observed in in vivo experiments were also confirmed by electron microscopy (EM) analyses. In summary, the in vitro and in vivo analyses show a synergistic role of AFP and TIF in the adherence and colonization of intestinal and urinary epithelia. Therefore, we propose that hybrid E. coli strains carrying AFP and TIF could potentially cause intestinal and urinary tract infections in the same patient.
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Affiliation(s)
- Paulo A Schüroff
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil.,Institute of Hygiene, University of Münster, Münster, Germany
| | - Cecilia M Abe
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Jonatas W Silva
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Cidéli de Paula Coelho
- Departamento de Pós-graduação, Faculdade de Medicina Veterinária, Universidade Santo Amaro, São Paulo, Brazil
| | | | - Rodrigo T Hernandes
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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Kislichkina AA, Kartsev NN, Skryabin YP, Sizova AA, Kanashenko ME, Teymurazov MG, Kuzina ES, Bogun AG, Fursova NK, Svetoch EA, Dyatlov IA. Genomic Analysis of a Hybrid Enteroaggregative Hemorrhagic Escherichia coli O181:H4 Strain Causing Colitis with Hemolytic-Uremic Syndrome. Antibiotics (Basel) 2022; 11:antibiotics11101416. [PMID: 36290074 PMCID: PMC9598891 DOI: 10.3390/antibiotics11101416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Hybrid diarrheagenic E. coli strains combining genetic markers belonging to different pathotypes have emerged worldwide and have been reported as a public health concern. The most well-known hybrid strain of enteroaggregative hemorrhagic E. coli is E. coli O104:H4 strain, which was an agent of a serious outbreak of acute gastroenteritis and hemolytic uremic syndrome (HUS) in Germany in 2011. A case of intestinal infection with HUS in St. Petersburg (Russian Federation) occurred in July 2018. E. coli strain SCPM-O-B-9427 was obtained from the rectal swab of the patient with HUS. It was determined as O181:H4-, stx2-, and aggR-positive and belonged to the phylogenetic group B2. The complete genome assembly of the strain SCPM-O-B-9427 contained one chromosome and five plasmids, including the plasmid coding an aggregative adherence fimbriae I. MLST analysis showed that the strain SCPM-O-B-9427 belonged to ST678, and like E. coli O104:H4 strains, 2011C-3493 caused the German outbreak in 2011, and 2009EL-2050 was isolated in the Republic of Georgia in 2009. Comparison of three strains showed almost the same structure of their chromosomes: the plasmids pAA and the stx2a phages are very similar, but they have distinct sets of the plasmids and some unique regions in the chromosomes.
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Affiliation(s)
- Angelina A. Kislichkina
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Correspondence:
| | - Nikolay N. Kartsev
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Yury P. Skryabin
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Angelika A. Sizova
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Maria E. Kanashenko
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Marat G. Teymurazov
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Ekaterina S. Kuzina
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Alexander G. Bogun
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Nadezhda K. Fursova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Edward A. Svetoch
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Ivan A. Dyatlov
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
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Multi-Drug Resistant Pathogenic Escherichia coli Isolated from Wild Birds, Chicken, and the Environment in Malaysia. Antibiotics (Basel) 2022; 11:antibiotics11101275. [PMID: 36289933 PMCID: PMC9598899 DOI: 10.3390/antibiotics11101275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 12/26/2022] Open
Abstract
Transmission of pathogenic microorganisms in the last decades has been considered a significant health hazard and pathogenic E. coli, particularly antibiotic-resistant strains, have long been identified as a zoonotic problem. This study aimed to investigate multidrug resistant pathogenic E. coli isolates from wild birds, chickens, and environment in selected Orang Asli and Malay villages in Peninsular Malaysia. The bacteriological culture-based technique, disc diffusion method, and multiplex Polymerase Chain Reaction (mPCR) assay was used to determine the occurrence of pathogenic E. coli strains in the several samples in the study. E. coli isolates showed a variety of multi-drug resistant (MDR) antibiotypes and Enteropathogenic E. coli (EPEC) and Enteroinvasive E. coli (EIEC) were the most predominantly identified pathogenic E. coli strains. The findings of this study demonstrated the significance of animal reservoirs and the environment as sources of pathogenic E. coli, resistant bacteria, and resistance genes. Hence, there is a need for adoption of a practical surveillance approach on MDR pathogens to control foodborne contamination.
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Mihailovskaya VS, Remezovskaya NB, Zhdanova IN, Starčič Erjavec M, Kuznetsova MV. Virulence potential of faecal <i>Escherichia coli</i> strains isolated from healthy cows and calves on farms in Perm Krai. Vavilovskii Zhurnal Genet Selektsii 2022; 26:486-494. [PMID: 36128572 PMCID: PMC9450034 DOI: 10.18699/vjgb-22-59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
Cattle are a reservoir of pathogenic and potentially pathogenic Escherichia coli (E. coli) strains, which can pose a threat to human and animal health. The aim of the study was to evaluate the occurrence of 22 virulence-associated genes (VAGs), as well as the prevalence of antimicrobial drug resistance and three different bla-genes among 49 E. coli strains isolated from healthy cattle. The presence of VAGs that are common among diarrheagenic E. coli (DEC) strains and/or extraintestinal pathogenic E. coli (ExPEC) strains was determined by amplifying specific gene sequences by PCR. The following VAGs associated with DEC were found: east1 in 24.5 % of the studied E. coli strains, estI in 10.2 %, ehxA in 8.2 %, stx2 in 6.1 %, eltA in 4.1 %, estII and stx1 in 2.0 % of the studied strains. The prevalence of ExPEC VAGs was: fimH – 91.8 %, afa/draBC – 61.2 %, iutA – 44.9 %, flu – 32.7 %, sfaDE and hlyF – 30.6 %, iroN – 22.4 %, ompT and papC – 20.4 %, kpsMTII and hlyA – 18.4 %, iss – 14.3 %, usp – 2.0 %, cnf1 and iha were not detected among the studied strains. Based on the found co-occurrence of VAGs “classical”, hetero-pathogenic and hybrid-pathogenic E. coli strains were found. E. coli strains isolated from cows had a higher diarrheagenic potential, whereas E. coli strains isolated from calves more frequently contained genes associated with the ExPEC pathotype. Among the studied E. coli strains, 77.6 % were resistant to ampicillin, 49.0 % to tetracycline, 20.4 % to chloramphenicol, 16.3 % to cefoperazone, 16.3 % to ceftriaxone, 16.3 % to aztreonam, 14.3 % to cefepime, 10.2 % to norfloxacin, 10.2 % to ciprofloxacin, 6.1 % to levofloxacin and 2.0 % to gentamicin. All strains were sensitive to meropenem and amikacin. 32.7 % of the studied E. coli strains were found to be multidrug resistant, as they were resistant to at least three groups of antibiotics. With PCR, the blaTEM, blaSHV, and blaCTX-M genes were detected in 100, 31.6, and 26.3 %, respectively, of strains resistant to at least one of the beta-lactam antibiotics. Thus, it was shown that the studied faecal E. coli of healthy cows and calves had a high hetero-pathogenic potential, therefore in the future molecular genetic characterization of these bacteria shall be an important part of the epizootic monitoring.
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Affiliation(s)
- V. S. Mihailovskaya
- Institute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences
| | - N. B. Remezovskaya
- Institute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences
| | | | | | - M. V. Kuznetsova
- Institute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences
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Balbuena-Alonso MG, Cortés-Cortés G, Kim JW, Lozano-Zarain P, Camps M, Del Carmen Rocha-Gracia R. Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid 2022; 123-124:102650. [PMID: 36130651 PMCID: PMC10896638 DOI: 10.1016/j.plasmid.2022.102650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.
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Affiliation(s)
- María G Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico; Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico.
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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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Asadi Z, Ghanbarpour R, Kalantar-Neyestanaki D, Alizade H. Determination of extended-spectrum β-lactamase producing and hybrid pathotypes of Escherichia coli isolates from diarrheic samples. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nunes PHS, Valiatti TB, Santos ACDM, Nascimento JADS, Santos-Neto JF, Rocchetti TT, Yu MCZ, Hofling-Lima AL, Gomes TAT. Evaluation of the Pathogenic Potential of Escherichia coli Strains Isolated from Eye Infections. Microorganisms 2022; 10:microorganisms10061084. [PMID: 35744602 PMCID: PMC9229993 DOI: 10.3390/microorganisms10061084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/13/2022] [Accepted: 05/21/2022] [Indexed: 11/29/2022] Open
Abstract
While primarily Gram-positive bacteria cause bacterial eye infections, several Gram-negative species also pose eye health risks. Currently, few studies have tried to understand the pathogenic mechanisms involved in E. coli eye infections. Therefore, this study aimed to establish the pathogenic potential of E. coli strains isolated from eye infections. Twenty-two strains isolated between 2005 and 2019 from patients with keratitis or conjunctivitis were included and submitted to traditional polymerase chain reactions (PCR) to define their virulence profile, phylogeny, clonal relationship, and sequence type (ST). Phenotypic assays were employed to determine hemolytic activity, antimicrobial susceptibility, and adhesion to human primary corneal epithelial cells (PCS-700-010). The phylogenetic results indicated that groups B2 and ST131 were the most frequent. Twenty-five virulence genes were found among our strains, with ecp, sitA, fimA, and fyuA being the most prevalent. Two strains presented a hemolytic phenotype, and resistance to ciprofloxacin and ertapenem was found in six strains and one strain, respectively. Regarding adherence, all but one strains adhered in vitro to corneal cells. Our results indicate significant genetic and virulence variation among ocular strains and point to an ocular pathogenic potential related to multiple virulence mechanisms.
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Affiliation(s)
- Pedro Henrique Soares Nunes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Tiago Barcelos Valiatti
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04039-032, Brazil
| | - Ana Carolina de Mello Santos
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
| | - Júllia Assis da Silva Nascimento
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
| | - José Francisco Santos-Neto
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
| | - Talita Trevizani Rocchetti
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Maria Cecilia Zorat Yu
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Ana Luisa Hofling-Lima
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Tânia Aparecida Tardelli Gomes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
- Correspondence: ; Tel.: +55-11-5576-4848
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Genomic characterization of ESBL/AmpC-producing and high-risk clonal lineages of Escherichia coli and Klebsiella pneumoniae in imported dogs with shelter and stray background. J Glob Antimicrob Resist 2022; 30:183-190. [DOI: 10.1016/j.jgar.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/17/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
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Tanabe RHS, Dias RCB, Orsi H, de Lira DRP, Vieira MA, dos Santos LF, Ferreira AM, Rall VLM, Mondelli AL, Gomes TAT, Camargo CH, Hernandes RT. Characterization of Uropathogenic Escherichia coli Reveals Hybrid Isolates of Uropathogenic and Diarrheagenic (UPEC/DEC) E. coli. Microorganisms 2022; 10:microorganisms10030645. [PMID: 35336220 PMCID: PMC8950336 DOI: 10.3390/microorganisms10030645] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
(1) Background: Pathogenic Escherichia coli are divided into two groups: diarrheagenic (DEC) and extraintestinal pathogenic (ExPEC) E. coli. ExPEC causing urinary tract infections (UTIs) are termed uropathogenic E. coli (UPEC) and are the most common cause of UTIs worldwide. (2) Methods: Here, we characterized 112 UPEC in terms of phylogroup, serotype, the presence of virulence factor-encoding genes, and antimicrobial resistance. (3) Results: The majority of the isolates were assigned into the phylogroup B2 (41.07%), and the serogroups O6 (12.5%) and O25 (8.9%) were the most frequent. Five hybrid UPEC (4.5%), with markers from two DEC pathotypes, i.e., atypical enteropathogenic (aEPEC) and enteroaggregative (EAEC) E. coli, were identified, and designated UPEC/aEPEC (one isolate) and UPEC/EAEC (four isolates), respectively. Three UPEC/EAEC harbored genes from the pap operon, and the UPEC/aEPEC carried ibeA. The highest resistance rates were observed for ampicillin (46.4%) and trimethoprim/sulfamethoxazole (34.8%), while 99.1% of the isolates were susceptible to nitrofurantoin and/or fosfomycin. Moreover, 9.8% of the isolates were identified as Extended Spectrum β-Lactamase producers, including one hybrid UPEC/EAEC. (4) Conclusion: Our data reinforce that hybrid UPEC/DEC are circulating in the city of Botucatu, Brazil, as uropathogens. However, how and whether these combinations of genes influence their pathogenicity is a question that remains to be elucidated.
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Affiliation(s)
- Rodrigo H. S. Tanabe
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
| | - Regiane C. B. Dias
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
| | - Henrique Orsi
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
| | - Daiany R. P. de Lira
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
| | - Melissa A. Vieira
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
| | - Luís F. dos Santos
- Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo 01246-902, SP, Brazil; (L.F.d.S.); (C.H.C.)
| | - Adriano M. Ferreira
- Hospital das Clínicas da Faculdade de Medicina de Botucatu, Botucatu 18607-741, SP, Brazil;
| | - Vera L. M. Rall
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
| | - Alessandro L. Mondelli
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Estadual Paulista (UNESP), Botucatu 18618-970, SP, Brazil;
| | - Tânia A. T. Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina (UNIFESP-EPM), São Paulo 04023-062, SP, Brazil;
| | - Carlos H. Camargo
- Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo 01246-902, SP, Brazil; (L.F.d.S.); (C.H.C.)
| | - Rodrigo T. Hernandes
- Departamento de Ciências Químicas e Biológicas (Setor de Microbiologia e Imunologia), Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu 18618-689, SP, Brazil; (R.H.S.T.); (R.C.B.D.); (H.O.); (D.R.P.d.L.); (M.A.V.); (V.L.M.R.)
- Correspondence: ; Tel.: +55-14-3880-0446
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Escherichia coli Strains Responsible for Cystitis in Female Pediatric Patients with Normal and Abnormal Urinary Tracts Have Different Virulence Profiles. Pathogens 2022; 11:pathogens11020231. [PMID: 35215173 PMCID: PMC8876236 DOI: 10.3390/pathogens11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The role of uropathogenic Escherichia coli (UPEC) in colonization and infection of female patients with anatomical and functional abnormalities of the urinary system is elusive. In this study, the phenotype, genotype and the phylogeny of UPEC strains isolated from the urine of pediatric female patients with cystitis of normal and abnormal urinary tract were determined. Multiplex PCR results demonstrated that 86% of the strains isolated from female patients with normal urinary tract (NUT), belonged to the phylo-groups B2 and D. Their prevalence decreased to 23% in strains isolated from patients with abnormal urinary tract (AUT). More of the isolates from AUT patients produced a biofilm on polystyrene and polyvinyl chloride (PVC), adhered to epithelial cells, and encoded pap and sfa genes than strains isolated from female patients with NUT. In contrast, a higher number of hemolysin-producing strains with serogroups associated with UPEC were isolated from patients with NUT. In summary, the results suggest that cystitis in female patients with NUT is associated with ExPEC, whereas cystitis in female patients with AUT is associated with pathogenic intestinal E. coli strains that have acquired the ability to colonize the bladder.
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Nascimento JAS, Santos FF, Santos-Neto JF, Trovão LO, Valiatti TB, Pinaffi IC, Vieira MAM, Silva RM, Falsetti IN, Santos ACM, Gomes TAT. Molecular Epidemiology and Presence of Hybrid Pathogenic Escherichia coli among Isolates from Community-Acquired Urinary Tract Infection. Microorganisms 2022; 10:microorganisms10020302. [PMID: 35208757 PMCID: PMC8874565 DOI: 10.3390/microorganisms10020302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Urinary tract infections (UTI) affect community and healthcare patients worldwide and may have different clinical outcomes. We assessed the phylogenetic origin, the presence of 43 virulence factors (VFs) of diarrheagenic and extraintestinal pathogenic Escherichia coli, and the occurrence of hybrid strains among E. coli isolates from 172 outpatients with different types of UTI. Isolates from phylogroup B2 (46%) prevailed, followed by phylogroups A (15.7%) and B1 (12.2%), with similar phylogenetic distribution in symptomatic and asymptomatic patients. The most frequent VFs according to their functional category were fimA (94.8%), ompA (83.1%), ompT (63.3%), chuA (57.6%), and vat (22%). Using published molecular criteria, 34.3% and 18.0% of the isolates showed intrinsic virulence and uropathogenic potential, respectively. Two strains carried the eae and escV genes and one the aggR gene, which classified them as hybrid strains. These hybrid strains interacted with renal and bladder cells, reinforcing their uropathogenic potential. The frequency of UPEC strains bearing a more pathogenic potential in the outpatients studied was smaller than reported in other regions. Our data contribute to deepening current knowledge about the mechanisms involved in UTI pathogenesis, especially among hybrid UPEC strains, as these could colonize the host’s intestine, leading to intestinal infections followed by UTI.
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Affiliation(s)
- Júllia A. S. Nascimento
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Fernanda F. Santos
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04039-032, Brazil; (F.F.S.); (T.B.V.)
| | - José F. Santos-Neto
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Liana O. Trovão
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Tiago B. Valiatti
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04039-032, Brazil; (F.F.S.); (T.B.V.)
| | - Isabel C. Pinaffi
- Laboratório Santa Cruz Medicina Diagnóstica, Mogi Guaçu 13840-052, Brazil; (I.C.P.); (I.N.F.)
| | - Mônica A. M. Vieira
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Rosa M. Silva
- Laboratório de Enterobactérias, Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil;
| | - Ivan N. Falsetti
- Laboratório Santa Cruz Medicina Diagnóstica, Mogi Guaçu 13840-052, Brazil; (I.C.P.); (I.N.F.)
| | - Ana C. M. Santos
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
| | - Tânia A. T. Gomes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, Brazil; (J.A.S.N.); (J.F.S.-N.); (L.O.T.); (M.A.M.V.); (A.C.M.S.)
- Correspondence: ; Tel.: +55-11-5576-4848
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Characterization of Escherichia coli from Water and Food Sold on the Streets of Maputo: Molecular Typing, Virulence Genes, and Antibiotic Resistance. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2010008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The aim of this study was to investigate the pathogenic potential and antibiotic resistance of 59 Escherichia coli isolates from ready-to-eat (RTE) street food (n = 31) and drinking water (n = 28) sold in the city of Maputo, Mozambique. The isolates were characterized by XbaI subtyping analysis via pulsed field gel electrophoresis. Multiplex PCRs were performed targeting five virulence genes (stx, lt, st, astA, and eae) and three groups of antibiotic-resistant genes, namely ß-lactamases (extended-spectrum ß-lactamase and AmpC), tetracycline (tetA, tetB, and tetM) and sulfamethoxazole/trimethoprim (sul1, sul2, and sul3). The stx virulence gene, encoding the Shiga/Vero (VT) toxin produced by the verotoxin-producing E. coli (VTEC), was identified with similar frequency in isolates from food (5/31) and water (6/28). The highest percentages of resistant isolates from food and water were found for ß-lactams imipenem (35.5 and 39.3%, respectively) and ampicillin (39.3 and 46.4%, respectively). Multidrug resistance was observed in 31.3% of the isolates, being higher in E. coli isolates from water (45.5%) compared to RTE street food isolates (19.2%). Virulence genes were detected in 73% of the multidrug-resistant isolates. Concerning antibiotic-resistant genes, ESBL was the most frequent (57.7%) among β-lactamases while tetA was the most frequent (50%) among non-β-lactamases.
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Al-Marri T, Al-Marri A, Al-Zanbaqi R, Ajmi AA, Fayez M. Multidrug resistance, biofilm formation, and virulence genes of Escherichia coli from backyard poultry farms. Vet World 2022; 14:2869-2877. [PMID: 35017833 PMCID: PMC8743762 DOI: 10.14202/vetworld.2021.2869-2877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Background and Aim: Backyard chicken flocks have traditionally been regarded as an essential food source in developed countries; however, they may act as reservoirs and spread various zoonotic bacterial pathogens. This study was designed to investigate the prevalence, phenotypic resistance, biofilm formation (BF), and pathotypes of Escherichia coli isolates from backyard poultry farms. Materials and Methods: Cloacal swabs (n=150) and internal organs (n=150) were collected from 30 backyard chicken flocks; 20 of them were experiencing systemic infection, and the other ten were apparently healthy. Samples were bacteriologically examined for E. coli isolation. Isolates were identified biochemically by the VITEK® 2 COMPACT system (BioMérieux, France). For molecular identification, 16S rRNA was amplified and sequenced. Ten antimicrobials were selected for E. coli antimicrobial susceptibility testing. The minimum inhibitory concentration for each antimicrobial was determined. The extended-spectrum β-lactamase activity in isolates was investigated using cephalosporin/clavulanate combination disks. The ability of isolates for BF was determined by the microtiter plate method. Thirteen virulence genes linked to different E. coli pathotypes and two serotype-related genes were investigated by real-time polymerase chain reaction. Results: Eighty-six E. coli strains were isolated from 30 backyard chicken flocks. The isolates were biochemically identified to the species level. Genetically, sequences of the 16S rRNA gene showed >98% identity with E. coli in the National Center for Biological Information database. The frequency of isolation from diseased flocks was significantly higher (p<0.05) than apparently healthy flocks; 63.9% of the isolates were recovered from cloacal swabs and 36.04% were recovered from internal organs. E. coli isolates showed high resistance to ampicillin (AMP; 75.6%), gentamicin (39.5%), and tetracycline (29.1%). However, none of the isolates were resistant to imipenem. A variable drug resistance profile for E. coli isolates was reported. Twenty-one (24.4%) isolates were sensitive to all ten antimicrobials. Seven (8.1%) isolates were resistant only to AMP, and 28 (32.6%) were resistant to two antimicrobials, whereas the remaining 30 (34.9%) isolates showed multidrug resistance (MDR). Of the 86 isolates, 8 (9.3%) were confirmed as extended-spectrum β-lactamase (ESBL)-producing E. coli by the combination disk diffusion method. All ESBL isolates were MDR with an MDR index of 0.5-0.6. Fifty-seven (66.3%) isolates were capable of forming biofilms; 22 (25.6%) of them were strong biofilm producers, 24 (27.9%) moderate producers, and 11 (12.8%) weak producers. A statistically significant pairwise correlation was obtained for MDR versus BF (r=0.512) and MDR index versus BF (r=0.556). Based on virulence gene profiles, five pathotypes were identified, including enteropathogenic E. coli (39.5%), avian pathogenic E. coli (32.53%), enterohemorrhagic E. coli (EHEC; 9.3%), enterotoxigenic E. coli (ETEC; 5.8%), and enteroaggregative E. coli (EAEC; 1.2%). The lower frequency of EAEC and ETEC was statistically significant than other pathotypes. Three isolates were identified as O157 based on the detection of the rbfO157 gene. Conclusion: This study reported a high prevalence of MDR, suggesting the misuse of antimicrobials in backyard chicken farms. The emergence of ESBL and EHEC isolates in backyard chickens is a public health concern. Furthermore, the backyard flocks environment may harbor different pathogenic bacteria that may enhance the persistence of infection and the transmission to in-contact humans. Regular monitoring for the occurrence of MDR and the zoonotic pathotypes among E. coli in backyard chicken flocks is recommended, as these bacteria can transmit to humans through food products or contaminated environments.
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Affiliation(s)
- Theeb Al-Marri
- Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Ahsa 31982, Saudi Arabia
| | - Abdulla Al-Marri
- Veterinary Diagnostic Laboratory, Department of Animal Resources, Doha, Qatar
| | - Reham Al-Zanbaqi
- Veterinary Diagnostic Laboratory , Ministry of Environment, Water and Agriculture, Riyadh, Saudi Arabia
| | - Ahmad Al Ajmi
- The Central Laboratories for Veterinary, Agriculture, and Fisheries, East Amghara 21422, State of Kuwait, Kuwait
| | - Mahmoud Fayez
- Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Environment, Water and Agriculture, Al-Ahsa 31982, Saudi Arabia.,Department of Bacteriology, Veterinary Serum and Vaccine Research Institute, Ministry of Agriculture, Cairo 11381, Egypt
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Schüroff PA, Salvador FA, Abe CM, Wami HT, Carvalho E, Hernandes RT, Dobrindt U, Gomes TAT, Elias WP. The aggregate-forming pili (AFP) mediates the aggregative adherence of a hybrid-pathogenic Escherichia coli (UPEC/EAEC) isolated from a urinary tract infection. Virulence 2021; 12:3073-3093. [PMID: 34923895 PMCID: PMC8923075 DOI: 10.1080/21505594.2021.2007645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) comprises an important diarrheagenic pathotype, while uropathogenic E. coli (UPEC) is the most important agent of urinary tract infection (UTI). Recently, EAEC virulence factors have been detected in E. coli strains causing UTI, showing the importance of these hybrid-pathogenic strains. Previously, we detected an E. coli strain isolated from UTI (UPEC-46) presenting characteristics of EAEC, e.g., the aggregative adherence (AA) pattern and EAEC-associated genes (aatA, aap, and pet). In this current study, we analyzed the whole genomic sequence of UPEC-46 and characterized some phenotypic traits. The AA phenotype was observed in cell lineages of urinary and intestinal origin. The production of curli, cellulose, bacteriocins, and Pet toxin was detected. Additionally, UPEC-46 was not capable of forming biofilm using different culture media and human urine. The genome sequence analysis showed that this strain belongs to serotype O166:H12, ST10, and phylogroup A, harbors the tet, aadA, and dfrA/sul resistance genes, and is phylogenetically more related to EAEC strains isolated from human feces. UPEC-46 harbors three plasmids. Plasmid p46-1 (~135 kb) carries some EAEC marker genes and those encoding the aggregate-forming pili (AFP) and its regulator (afpR). A mutation in afpA (encoding the AFP major pilin) led to the loss of pilin production and assembly, and notably, a strongly reduced adhesion to epithelial cells. In summary, the genetic background and phenotypic traits analyzed suggest that UPEC-46 is a hybrid strain (UPEC/EAEC) and highlights the importance of AFP adhesin in the adherence to colorectal and bladder cell lines.
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Affiliation(s)
- Paulo A Schüroff
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil.,Institute of Hygiene, University of Münster, Münster, Germany
| | - Fábia A Salvador
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cecilia M Abe
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Haleluya T Wami
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Eneas Carvalho
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Rodrigo T Hernandes
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
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48
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Alfinete N, Bolukaoto JY, Heine L, Potgieter N, Barnard TG. Virulence and phylogenetic analysis of enteric pathogenic Escherichia coli isolated from children with diarrhoea in South Africa. Int J Infect Dis 2021; 114:226-232. [PMID: 34775113 DOI: 10.1016/j.ijid.2021.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/22/2021] [Accepted: 11/06/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Diarrhoeagenic E. coli pose a significant risk to human health. As such, determining the source(s) of these bacteria when isolated from patients with diarrhoea is an important step in disease prevention. OBJECTIVES This study aimed to identify the presence of genes coding for virulence and phylogroups among E. coli isolated from children hospitalised due to diarrhoea in Limpopo, South Africa. METHODS E. coli isolates were identified by VITEK®-2 automated system. An 11-gene multiplex PCR was used to differentiate five pathogenic types of E. coli: enteroaggregative (EAEC), enteroinvasive (EIEC), enterohaemorrhagic (EHEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). Clermont quadruplex PCR method was used to identify phylogroups of isolates. RESULTS From the 133 isolates tested, 79 were confirmed as E. coli of which (19.0%, 15/79) were commensals and 81.0% (64/79) isolates were positive for at least one pathotype of which ETEC was predominant (16.5%, 13/79), followed by EAEC (10.1%, 8/79), EPEC (7.6%, 6/79) and EHEC (2.5%, 2/79). Hybrid pathotypes were also detected and EAEC/ETEC was predominant (25.3%, 20/79). Phylogroup B2 was predominant (30.4%, 24/79), followed by group B1 (22.8%, 18/79), phylogroup C and E both had (12.7%, 10/79) each. Just over six percent (5/79) of isolates were non-typable. CONCLUSION There was a high distribution of diarrhoeagenic E. coli associated with different phylogroups among children living in Limpopo province, South Africa. This emphasises the importance of future monitoring of virulence and phylogroup distribution of E. coli isolates in this province in particular and South Africa as a whole.
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Affiliation(s)
- Ntando Alfinete
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - John Y Bolukaoto
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - Lee Heine
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa
| | - Natasha Potgieter
- School of Mathematical and Natural Sciences, University of Venda, Limpopo Province, South Africa
| | - Tobias G Barnard
- Water and Health Research Centre, University of Johannesburg, Doornfontein, South Africa.
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Distribution of virulence factors, antimicrobial resistance genes and phylogenetic relatedness among Shiga toxin-producing Escherichia coli serogroup O91 from human infections. Int J Med Microbiol 2021; 311:151541. [PMID: 34757276 DOI: 10.1016/j.ijmm.2021.151541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 10/10/2021] [Accepted: 10/25/2021] [Indexed: 12/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) belonging to the serogroup O91 are among the most common non-O157 STEC serogroups associated with human illness in Europe. This study aimed to analyse the virulence factors, antimicrobial resistance genes and phylogenetic relatedness among 48 clinical STEC O91 isolates collected during 2003-2019 in Switzerland. The isolates were subjected to whole genome sequencing using short-read sequencing technologies and a subset of isolates additionally to long-read sequencing. They belonged to O91:H10 (n=6), O91:H14 (n=40), and O91:H21 (n=2). Multilocus sequence typing showed that the O91:H10 isolates all belonged to sequence type (ST)641, while the O91:H14 isolates were assigned to ST33, ST9700, or were non-typeable. Both O91:H21 isolates belonged to ST442. Shiga toxin gene stx1a was the most common Shiga toxin gene subtype among the isolates, followed by stx2b, stx2d and stx2a. All isolates were LEE-negative and carried one or two copies of the IrgA adhesin gene iha. In a subset of long-read sequenced isolates, modules of the Locus of Adhesion and Autoaggregation pathogenicity island (LAA-PAI) carrying iha and other genes such as hes, lesP or agn43 were identified. A large proportion of STEC O91:H14 carried the subtilase cytotoxin gene subA, colicin genes (cba, cea, cib and cma) or microcin genes (mcmA, mchB, mchC and mchF). STEC O91:H14 were further distinguished from STEC O91:H10/H21 by one or more virulence factors found in extraintestinal pathogenic E. coli (ExPEC), including hlyF, iucC/iutA, kpsE and traT. The hlyF gene was identified on a novel mosaic plasmid that was unrelated to hlyF+ plasmids described previously in STEC. Core genome phylogenetic analysis revealed that STEC O91:H10 and STEC O91:H21 were clonally conserved, whereas STEC O91:H14 were clonally diverse. Among three STEC O91:H14 isolates, a number of resistance genes were identified, including genes that mediate resistance to aminoglycosides (aadA, aadA2, aadA9, aadA23, aph(3'')-Ib and aph(6)-Id), chloramphenicol (cmlA), sulphonamides (sul2 and sul3), and trimethoprim (drfA12). Our data contribute to understanding the genetic diversity and differing levels of virulence potential within the STEC O91 serogroup.
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50
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Bolukaoto JY, Singh A, Alfinete N, Barnard TG. Occurrence of Hybrid Diarrhoeagenic Escherichia coli Associated with Multidrug Resistance in Environmental Water, Johannesburg, South Africa. Microorganisms 2021; 9:2163. [PMID: 34683484 PMCID: PMC8538365 DOI: 10.3390/microorganisms9102163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
This study was undertaken to determine the virulence and antibiotic resistance profiles of diarrhoeagenic Escherichia coli (DEC) in environmental waters of Johannesburg, South Africa. Samples were collected and cultured on selective media. An 11-plex PCR assay was used to differentiate five DEC, namely: enteroaggregative (EAEC), enterohaemorrhagic (EHEC), enteroinvasive (EIEC), enteropathogenic (EPEC) and enterotoxigenic (ETEC). The antibiotic resistance profile of isolates was determined using the VITEK®-2 automated system. The virulence profiles of 170 E. coli tested showed that 40% (68/170) were commensals and 60% (102/170) were pathogenic. EPEC had a prevalence of 19.2% (32/170), followed by ETEC 11.4% (19/170), EAEC 6% (10/170) and EHEC 3% (5/170). Hybrid DEC carrying a combination of simultaneously two and three pathogenic types was detected in twenty-eight and nine isolates, respectively. The antibiotic susceptibility testing showed isolates with multidrug resistance, including cefuroxime (100%), ceftazidime (86%), cefotaxime (81%) and cefepime (79%). This study highlighted the widespread occurrence of DEC and antibiotic resistance strains in the aquatic ecosystem of Johannesburg. The presence of hybrid pathotypes detected in this study is alarming and might lead to more severe diseases. There is a necessity to enhance surveillance in reducing the propagation of pathogenic and antibiotic-resistant strains in this area.
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Affiliation(s)
| | | | | | - Tobias G. Barnard
- Water and Health Research Centre, University of Johannesburg, Doornfontein 2092, South Africa; (J.Y.B.); (A.S.); (N.A.)
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