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Shi Z, Lan Y, Wang Y, Yan X, Ma X, Hassan FU, Rushdi HE, Xu Z, Wang W, Deng T. Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli. mSystems 2024; 9:e0134823. [PMID: 38742910 PMCID: PMC11237395 DOI: 10.1128/msystems.01348-23] [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: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.
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Affiliation(s)
- Zhihai Shi
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yali Lan
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yazhou Wang
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiangzhou Yan
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaoya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenjia Wang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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Kholik K, Sukri A, Riwu KHP, Kurniawan SC, Khairullah AR. Detection of the chuA gene encoding the invasive enterohemorrhagic species Escherichia coli 0157:H7 using qPCR in horse feces samples on Sumbawa Island, Indonesia. Open Vet J 2024; 14:1051-1058. [PMID: 38808295 PMCID: PMC11128647 DOI: 10.5455/ovj.2024.v14.i4.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/30/2024] [Indexed: 05/30/2024] Open
Abstract
Background Bacterial identification can be done using various testing techniques. Molecular techniques are often used to research dangerous diseases, an approach using genetic information on the pathogenic agent. The enterohemorrhagic invasive species Escherichia coli 0157:H7 was identified from the feces of working horses on the island of Sumbawa. Another advance in molecular technology is genome amplification with qPCR which is the gold standard for detecting E. coli. Aim This study aims to detect and identify the invasive species E. coli 0157:H7 using the gene encoding chuA with the qPCR method sourced from horse feces. Methods Fresh fecal samples from horses on Sumbawa Island were isolated and identified, then continued with molecular examination using the gene encoding chuA using the qPCR method. Results qPCR testing in this study showed that six sample isolates that were positive for E. coli 0157:H7 were detected for the presence of the chuA gene, which is a gene coding for an invasive species of E. coli bacteria. The highest to lowest Cq values and Tm from the qPCR results of the sample isolates were 15.98 (4KJ), 14.90 (19KG), 14.6 (3KJ), 13.77 (20KG), 12.56 (5KGB), and 12.20 (6KJ). Tm values are 86.7 (4KJ), 86.69 (3KJ), 86.56 (5KGB), 85.88 (20KGB), 85.81 (19KG), and 85.74 (6KJ). Conclusion Validation, standardization of the development, and modification of qPCR technology must be carried out to harmonize testing throughout to avoid wrong interpretation of the test results so that the determination of actions to eradicate and control diseases originating from animals in the field does not occur.
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Affiliation(s)
- Kholik Kholik
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Pendidikan Mandalika, Mataram, Indonesia
| | - Akhmad Sukri
- Departement of Biology Education, Universitas Pendidikan Mandalika, Mataram, Indonesia
| | - Katty Hendriana Priscilia Riwu
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Pendidikan Mandalika, Mataram, Indonesia
| | - Shendy Canadya Kurniawan
- Master Program of Animal Sciences, Department of Animal Sciences, Specialisation in Molecule, Cell and Organ Functioning, Wageningen University and Research, Wageningen, The Netherlands
| | - Aswin Rafif Khairullah
- Research Center for Veterinary Science, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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Qiu L, Chirman D, Clark JR, Xing Y, Hernandez Santos H, Vaughan EE, Maresso AW. Vaccines against extraintestinal pathogenic Escherichia coli (ExPEC): progress and challenges. Gut Microbes 2024; 16:2359691. [PMID: 38825856 PMCID: PMC11152113 DOI: 10.1080/19490976.2024.2359691] [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: 01/29/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a principal global health crisis projected to cause 10 million deaths annually worldwide by 2050. While the Gram-negative bacteria Escherichia coli is commonly found as a commensal microbe in the human gut, some strains are dangerously pathogenic, contributing to the highest AMR-associated mortality. Strains of E. coli that can translocate from the gastrointestinal tract to distal sites, called extraintestinal E. coli (ExPEC), are particularly problematic and predominantly afflict women, the elderly, and immunocompromised populations. Despite nearly 40 years of clinical trials, there is still no vaccine against ExPEC. One reason for this is the remarkable diversity in the ExPEC pangenome across pathotypes, clades, and strains, with hundreds of genes associated with pathogenesis including toxins, adhesins, and nutrient acquisition systems. Further, ExPEC is intimately associated with human mucosal surfaces and has evolved creative strategies to avoid the immune system. This review summarizes previous and ongoing preclinical and clinical ExPEC vaccine research efforts to help identify key gaps in knowledge and remaining challenges.
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Affiliation(s)
- Ling Qiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dylan Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Haroldo Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Ellen E. Vaughan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
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Luo S, Liao C, Peng J, Tao S, Zhang T, Dai Y, Ding Y, Ma Y. Resistance and virulence gene analysis and molecular typing of Escherichia coli from duck farms in Zhanjiang, China. Front Cell Infect Microbiol 2023; 13:1202013. [PMID: 37396302 PMCID: PMC10308044 DOI: 10.3389/fcimb.2023.1202013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The widespread use of antibiotics in animal agriculture has increased the resistance of Escherichia coli, and pathogenic E. coli often harbor complex virulence factors. Antimicrobial resistance in pathogenic bacteria can cause public health problems. Correlation analyses of the resistance, virulence, and serotype data from the pathogenic bacteria found on farms and in the surrounding environment can thus provide extremely valuable data to help improve public health management. Methods In this investigation, we have assessed the drug resistance and virulence genes as well as the molecular typing characteristics of 30 E. coli strains isolated from duck farms in the Zhanjiang area of China. Polymerase chain reaction was used to detect the drug resistance and virulence genes as well as serotypes, and whole-genome sequencing was used to analyze the multilocus sequence typing. Results The detection rates for the oqxA resistance gene and fimC virulence gene were highest (93.3%, respectively). There were no correlations between the drug resistance and virulence gene numbers in the same strain. The epidemic serotype was O81 (5/24), ST3856 was an epidemic sequence type, and strains I-9 and III-6 carried 11 virulence genes. The E. coli strains from the duck farms in the Zhanjiang area were thus found to have a broad drug resistance spectrum, various virulence genes, complex serotypes, and certain pathogenicity and genetic relationship. Discussion Monitoring the spread of pathogenic bacteria and the provision of guidance regarding the use of antibiotics in the livestock and poultry industries will be required in the future in the Zhanjiang area.
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Affiliation(s)
- Shuaishuai Luo
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Cuiyi Liao
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- College of Traditional Chinese Medicine, Zhanjiang University of Science and Technology, Zhanjiang, China
| | - Jinju Peng
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Songruo Tao
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Tengyue Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yue Dai
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yuexia Ding
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yi Ma
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
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Vitt AR, Sørensen MCH, Bortolaia V, Brøndsted L. A Representative Collection of Commensal Extended-Spectrum- and AmpC-β-Lactamase-Producing Escherichia coli of Animal Origin for Phage Sensitivity Studies. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:35-45. [PMID: 37214655 PMCID: PMC10196081 DOI: 10.1089/phage.2023.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Introduction Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing Escherichia coli from livestock and meat represent a zoonotic risk and biocontrol solutions are needed to prevent transmission to humans. Methods In this study, we established a representative collection of animal-origin ESBL/AmpC E. coli as target to test the antimicrobial potential of bacteriophages. Results Bioinformatic analysis of whole-genome sequence data of 198 ESBL/AmpC E. coli from pigs, broilers, and broiler meat identified strains belonging to all known E. coli phylogroups and 65 multilocus sequence types. Various ESBL/AmpC genes and plasmid types were detected with expected source-specific patterns. Plaque assay using 15 phages previously isolated using the E. coli reference collection demonstrated that Warwickvirus phages showed the broadest host range, killing up to 26 strains. Conclusions 154/198 strains were resistant to infection by all phages tested, suggesting a need for isolating phages specific for ESBL/AmpC E. coli. The strain collection described in this study is a useful resource fulfilling such need.
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Affiliation(s)
- Amira R. Vitt
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Valeria Bortolaia
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Escherichia coli virulence genes and clonality in strains from diarrhoea in goat kids. Small Rumin Res 2023. [DOI: 10.1016/j.smallrumres.2023.106906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Duangurai T, Rungruengkitkul A, Kong-Ngoen T, Tunyong W, Kosoltanapiwat N, Adisakwattana P, Vanaporn M, Indrawattana N, Pumirat P. Phylogenetic analysis and antibiotic resistance of Escherichia coli isolated from wild and domestic animals at an agricultural land interface area of Salaphra wildlife sanctuary, Thailand. Vet World 2022; 15:2800-2809. [PMID: 36718336 PMCID: PMC9880845 DOI: 10.14202/vetworld.2022.2800-2809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022] Open
Abstract
Background and Aim Domestic and wild animals are important reservoirs for antibiotic-resistant bacteria. This study aimed to isolate Escherichia coli from feces of domestic and wild animals at an agricultural land interface area of Salaphra Wildlife Sanctuary, Thailand, and study the phylogenic characteristics and antibiotic resistance in these isolates. Materials and Methods In this cross-sectional, descriptive study, we randomly collected ground feces from free-ranging wild animals (deer and elephants) and domestic animals (cattle and goats). All fecal samples were inoculated onto MacConkey agar plates, and lactose-fermenting colonies were identified as E. coli. Antibiotic susceptibility of the E. coli isolates was determined using the disc diffusion method. Polymerase chain reaction assays were used to detect antibiotic resistance and virulence genes. Results We obtained 362 E. coli isolates from the collected fecal samples. The E. coli isolates were categorized into four phylogenetic groups according to the virulence genes (chuA, vjaA, and TspE4C2). Phylogenetic Group D was predominant in the deer (41.67%) and elephants (63.29%), whereas phylogenetic Group B1 was predominant in the cattle (62.31%), and phylogenetic Groups A (36.36%) and B2 (33.33%) were predominant in the goats. Antibiotic susceptibility testing revealed that most antibiotic-resistant E. coli were isolated from domestic goats (96.96%). Among the 362 E. coli isolates, 38 (10.5%) were resistant to at least one antibiotic, 21 (5.8%) were resistant to two antibiotics, and 6 (1.66%) were resistant to three or more antibiotics. Ampicillin (AMP) was the most common antibiotic (48.48%) to which the E. coli were resistant, followed by tetracycline (TET) (45.45%) and trimethoprim-sulfamethoxazole (3.03%). One isolate from an elephant was resistant to five antibiotics: AMP, amoxicillin, sulfisoxazole, TET, and ciprofloxacin. Determination of antibiotic resistance genes confirmed that E. coli isolates carried antibiotic resistance genes associated with phenotypic resistance to antibiotics. Most antibiotic-resistant E. coli belonged to phylogenic Groups A and B1, and most non-resistant E. coli belonged to phylogenic Groups B2 and D. Conclusion Monitoring E. coli isolates from wild and domestic animals showed that all four phylogenic groups of E. coli have developed antibiotic resistance and are potential sources of multidrug resistance. High levels of antibiotic resistance have been linked to domestic animals. Our results support strengthening surveillance to monitor the emergence and effects of antibiotic-resistant microorganisms in animals.
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Affiliation(s)
- Taksaon Duangurai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Amporn Rungruengkitkul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thida Kong-Ngoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Witawat Tunyong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand,Corresponding author: Pornpan Pumirat, e-mail: Co-authors: TD: , AR: , TK: , WT: , NK: , PA: , MV: , NI:
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Fang Y, Stanford K, Yang X. Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment. Microbiol Spectr 2022; 10:e0135222. [PMID: 36194136 PMCID: PMC9602453 DOI: 10.1128/spectrum.01352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/09/2022] [Indexed: 12/30/2022] Open
Abstract
To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.
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Affiliation(s)
- Yuan Fang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, Lacombe, Alberta, Canada
| | - Kim Stanford
- University of Lethbridge, Lethbridge, Alberta, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, Lacombe, Alberta, Canada
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Pérez-Etayo L, González D, Vitas AI. Clonal Complexes 23, 10, 131 and 38 as Genetic Markers of the Environmental Spread of Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli. Antibiotics (Basel) 2022; 11:1465. [PMID: 36358120 PMCID: PMC9686695 DOI: 10.3390/antibiotics11111465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
In accordance with the global action plan on antimicrobial resistance adopted by the World Health Assembly in 2015, there is a need to develop surveillance programs for antimicrobial resistant bacteria. In this context, we have analyzed the clonal diversity of Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from aquatic environments and human and food samples in Spain, with the aim of determining possible clonal complexes (CCs) that act as markers of the potential risk of transmission of these resistant bacteria. The phylogenetic groups, sequence types (STs) and CCs were determined by different Polymerase Chain Reaction (PCR) and Multilocus Sequence Typing (MLST) techniques. Phylogroup A was prevalent and was mainly present in food and water strains, while human strains were mostly associated with phylogroup B2. According to the observed prevalence in the different niches, CC23 and CC10 are proposed as markers of phylogroups A and C, related with the spread of blaCTX-M1 and blaCTX-M15 genes. Similarly, CC131 and CC38 could be associated to the dissemination of pathogenic strains (phylogroups B2 and D) carrying mainly blaCTX-M14 and blaCTX-M15 genes. Some strains isolated from wastewater treatment plants (WWTPs) showed identical profiles to those isolated from other environments, highlighting the importance that water acquires in the dissemination of bacterial resistance. In conclusion, the detection of these genetic markers in different environments could be considered as an alert in the spread of ESBL.
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Affiliation(s)
- Lara Pérez-Etayo
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - David González
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Ana Isabel Vitas
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
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Prevalence of virulence genes among Escherichia coli strains isolated from food and carcass swabs of different animal origins in Croatia. J Vet Res 2022; 66:395-402. [PMID: 36349139 PMCID: PMC9597930 DOI: 10.2478/jvetres-2022-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022] Open
Abstract
Abstract
Introduction
Escherichia coli is present in the normal intestinal flora but some strains can cause intestinal and extraintestinal diseases, and research on its presence in food of animal origin is in the interests of public health. This study was designed to characterise E. coli strains according to their origin, their carriage of virulence genes specific for certain pathogroups, and phylogenetic group affiliation.
Material and Methods
The study was carried out on 100 E. coli strains isolated from food samples of various animal origin as well as pig and cattle carcass swabs. Isolation of the strains was performed using two methods. One method included colony count and the other an overnight enrichment of the samples. Isolation was followed by DNA extraction and detection of virulence genes and phylogenetic group with conventional and multiplex PCRs.
Results
In this study, the most prevalent gene was EAST1 (20%) and strains which carried it were identified as enteroadherent E. coli. Other pathogroups were represented in lower incidences. Phylogenetic group analysis revealed the prevalence of the A and B1 groups, with B1 mainly present in game and cattle strains, while the majority of pig and poultry strains were assigned to group A.
Conclusion
This study provides an overview of the presence of potentially pathogenic strains and E. coli phylogenetic groups in Croatia, for which the data are limited. Further microbiological and molecular research is required to examine the epidemiological situation in the country.
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Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru. Antibiotics (Basel) 2022; 11:antibiotics11050692. [DOI: 10.3390/antibiotics11050692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
E. coli that produce extended-spectrum β-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.
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Ramos CP, Kamei CYI, Viegas FM, de Melo Barbieri J, Cunha JLR, Hounmanou YMG, Coura FM, Santana JA, Lobato FCF, Bojesen AM, Silva ROS. Fecal Shedding of Multidrug Resistant Escherichia coli Isolates in Dogs Fed with Raw Meat-Based Diets in Brazil. Antibiotics (Basel) 2022; 11:antibiotics11040534. [PMID: 35453285 PMCID: PMC9029118 DOI: 10.3390/antibiotics11040534] [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: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 11/29/2022] Open
Abstract
The practice of feeding dogs raw meat-based diets (RMBDs) is growing in several countries, and the risks associated with the ingestion of pathogenic and antimicrobial-resistant Escherichia coli in dogs fed these diets are largely unknown. We characterized E. coli strains isolated from dogs fed either an RMBD or a conventional dry feed, according to the phylogroup, virulence genes, and antimicrobial susceptibility profiles of the bacteria. Two hundred and sixteen E. coli strains were isolated. Dogs fed RMBDs shed E. coli strains from the phylogroup E more frequently and were positive for the E. coli heat-stable enterotoxin 1-encoding gene. Isolates from RMBD-fed dogs were also frequently positive for multidrug-resistant E. coli isolates including extended-spectrum beta-lactamase (ESBL) producers. Whole-genome sequencing of seven ESBL-producing E. coli strains revealed that they predominantly harbored blaCTX-M-55, and two strains were also positive for the colistin-resistant gene mcr-1. These results suggest that feeding an RMBD can affect the dog’s microbiota, change the frequency of certain phylogroups, and increase the shedding of diarrheagenic E. coli. Also, feeding an RMBD seemed to be linked with the fecal shedding of multidrug-resistant E. coli, including the spread of strains harboring mobilizable colistin resistance and ESBL genes. This finding is of concern for both animal and human health.
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Affiliation(s)
- Carolina Pantuzza Ramos
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - Carolina Yumi Iceri Kamei
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - Flávia Mello Viegas
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - Jonata de Melo Barbieri
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - João Luís Reis Cunha
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark; (Y.M.G.H.); (A.M.B.)
| | - Fernanda Morcatti Coura
- Departamento de Ciências Agrárias, Instituto Federal de Minas Gerais (IFMG), Bambuí 38900-000, Brazil;
| | - Jordana Almeida Santana
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - Francisco Carlos Faria Lobato
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark; (Y.M.G.H.); (A.M.B.)
| | - Rodrigo Otávio Silveira Silva
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30123-970, Brazil; (C.P.R.); (C.Y.I.K.); (F.M.V.); (J.d.M.B.); (J.L.R.C.); (J.A.S.); (F.C.F.L.)
- Correspondence:
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Bacteriophage-Mediated Modulation of Bacterial Competition during Selective Enrichment of Campylobacter. Microbiol Spectr 2021; 9:e0170321. [PMID: 34908437 PMCID: PMC8672905 DOI: 10.1128/spectrum.01703-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Selective media using antimicrobial supplements generate unique microbial ecology to facilitate bacterial isolation. However, antibiotic-resistant bacteria indigenous to samples can interfere with the isolation process using selective media. Recent studies showed that extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highly prevalent on retail raw chicken and compromises the efficacy of Campylobacter isolation because ESBL-producing E. coli are resistant to antimicrobial supplements in Campylobacter-selective media and outgrows Campylobacter. The objective of this study was to improve Campylobacter isolation by inhibiting the growth of ESBL-producing E. coli using bacteriophages (phages). The supplementation of Campylobacter-selective media with E. coli phages reduced the level of ESBL-producing E. coli during the enrichment step. When E. coli phages were combined with the antimicrobial supplements of Campylobacter-selective media, antimicrobial synergy was observed, particularly with rifampicin, an antibiotic used in Preston medium. Although the same materials (i.e., phages and selective media) were used, the sequence of combining the materials markedly influenced the inhibition of ESBL-producing E. coli and the isolation of Campylobacter. These findings indicated that the modulation of microbial competition at the enrichment step was critical to the successful isolation of fastidious bacteria and that phages can be utilized to facilitate the selective enrichment of target bacteria by inhibiting their competitive bacteria. IMPORTANCE Phages are promising antimicrobial alternatives. In this study, we first demonstrated that phages can be used to facilitate selective isolation of fastidious bacteria that are prone to be outgrown by bacterial competitors during isolation. The effectiveness of a phage-based isolation method was primarily dependent on the antimicrobial synergy between phages and antibiotics used in selective media. The same approach could be applied to the development of isolation methods for other fastidious bacteria.
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Kim J, Park H, Ryu S, Jeon B. Inhibition of Antimicrobial-Resistant Escherichia coli Using a Broad Host Range Phage Cocktail Targeting Various Bacterial Phylogenetic Groups. Front Microbiol 2021; 12:699630. [PMID: 34512575 PMCID: PMC8425383 DOI: 10.3389/fmicb.2021.699630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/02/2021] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial-resistant (AMR) commensal Escherichia coli is a major reservoir that disseminates antimicrobial resistance to humans through the consumption of contaminated foods, such as retail poultry products. This study aimed to control AMR E. coli on retail chicken using a broad host range phage cocktail. Five phages (JEP1, 4, 6, 7, and 8) were isolated and used to construct a phage cocktail after testing infectivity on 67 AMR E. coli strains isolated from retail chicken. Transmission electron microscopic analysis revealed that the five phages belong to the Myoviridae family. The phage genomes had various sizes ranging from 39 to 170 kb and did not possess any genes associated with antimicrobial resistance and virulence. Interestingly, each phage exhibited different levels of infection against AMR E. coli strains depending on the bacterial phylogenetic group. A phage cocktail consisting of the five phages was able to infect AMR E. coli in various phylogenetic groups and inhibited 91.0% (61/67) of AMR E. coli strains used in this study. Furthermore, the phage cocktail was effective in inhibiting E. coli on chicken at refrigeration temperatures. The treatment of artificially contaminated raw chicken skin with the phage cocktail rapidly reduced the viable counts of AMR E. coli by approximately 3 log units within 3 h, and the reduction was maintained throughout the experiment without developing resistance to phage infection. These results suggest that phages can be used as a biocontrol agent to inhibit AMR commensal E. coli on raw chicken.
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Affiliation(s)
- Jinshil Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food Bioconvergence, Seoul National University, Seoul, South Korea
| | - Haejoon Park
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food Bioconvergence, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food Bioconvergence, Seoul National University, Seoul, South Korea
| | - Byeonghwa Jeon
- Divison of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, United States
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15
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Leão C, Clemente L, Moura L, Seyfarth AM, Hansen IM, Hendriksen RS, Amaro A. Emergence and Clonal Spread of CTX-M-65-Producing Escherichia coli From Retail Meat in Portugal. Front Microbiol 2021; 12:653595. [PMID: 34354678 PMCID: PMC8329498 DOI: 10.3389/fmicb.2021.653595] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022] Open
Abstract
The emergence and dissemination of resistance to third- and fourth-generation cephalosporins among Enterobacteriaceae from different sources impose a global public health threat. Here, we characterized by whole-genome sequencing four Escherichia coli strains harboring the blaCTX–M–65 gene identified among 49 isolates from beef and pork collected at retail. The genomic content was determined using the Center for Genomic Epidemiology web tools. Additionally, the prediction and reconstruction of plasmids were conducted, the genetic platform of the blaCTX–M–65 genes was investigated, and phylogenetic analysis was carried out using 17 other genomes with the same sequence type and harboring the blaCTX–M–65 gene. All strains harbored blaCTX–M–65, blaOXA–1, and blaTEM–1B, and one also carried the blaSHV–12 gene. Other resistance genes, namely, qnrS2, aac(6′)-Ib-c, dfrA14, sul2, tetA, and mphA, were present in all the genomes; the mcr-1.1 gene was identified in the colistin-resistant strains. They belong to sequence type 2179, phylogenetic group B1, and serotype O9:H9 and carried plasmids IncI, IncFIC(FII), and IncFIB. All strains share an identical genetic environment with IS903 and ISEcp1 flanking the blaCTX–M–65 gene. It seems likely that the blaCTX–M–65 gene is located in the chromosome in all isolates based on deep in silico analysis. Our findings showed that the strains are clonally related and belong to two sub-lineages. This study reports the emergence of CTX-M-65-producing E. coli in Portugal in food products of animal origin. The chromosomal location of the blaCTX–M–65 gene may ensure a stable spread of resistance in the absence of selective pressure.
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Affiliation(s)
- Célia Leão
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.,MED - Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.,Faculty of Veterinary Science, CIISA- Centre for Interdisciplinary Research in Animal Health, Lisbon, Portugal
| | - Laura Moura
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal.,Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Anne Mette Seyfarth
- EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark
| | - Inge M Hansen
- EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark
| | - Rene S Hendriksen
- EURL-AR, European Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark (DTU), National Food Institute, Lyngby, Denmark
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
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Abboud Z, Galuppo L, Tolone M, Vitale M, Puleio R, Osman M, Loria GR, Hamze M. Molecular Characterization of Antimicrobial Resistance and Virulence Genes of Bacterial Pathogens from Bovine and Caprine Mastitis in Northern Lebanon. Microorganisms 2021; 9:1148. [PMID: 34071800 PMCID: PMC8228836 DOI: 10.3390/microorganisms9061148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Mastitis is an infectious disease encountered in dairy animals worldwide that is currently a growing concern in Lebanon. This study aimed at investigating the etiology of the main mastitis-causing pathogens in Northern Lebanon, determining their antimicrobial susceptibility profiles, and identifying their antimicrobial resistance (AMR) genes. A total of 101 quarter milk samples were collected from 77 cows and 11 goats presenting symptoms of mastitis on 45 dairy farms. Bacterial identification was carried out through matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibility was tested by disc diffusion and broth microdilution methods. Molecular characterization included polymerase chain reaction (PCR) screening for genes encoding extended-spectrum beta-lactamases (ESBLs) and plasmid-mediated AmpC among Enterobacterales isolates, and virulence factors among Staphylococcus isolates. Escherichia coli isolates were subjected to phylogenetic typing by a quadruplex PCR method. The most frequently identified species were Streptococcus uberis (19.2%), Streptococcus agalactiae (15.1%), E. coli (12.3%), and Staphylococcus aureus (10.96%). Gram-positive bacteria were resistant to macrolides and tetracycline, whereas gram-negative bacteria displayed resistance to ampicillin and tetracycline. Two ESBL genes, blaTEM (83.3%) and blaOXA (16.7%), and one AmpC beta-lactamase gene, blaCMY-II (16.7%), were detected among six E. coli isolates, which mainly belonged to phylogenetic group B1. Among Staphylococcus spp., the mecA gene was present in three isolates. Furthermore, four isolates contained at least one toxin gene, and all S. aureus isolates carried the ica operon. These findings revealed the alarming risk of AMR in the Lebanese dairy chain and the importance of monitoring antimicrobial usage.
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Affiliation(s)
- Zahie Abboud
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli P.O. Box 146404, Lebanon;
| | - Lucia Galuppo
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Marco Tolone
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy;
| | - Maria Vitale
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Roberto Puleio
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli P.O. Box 146404, Lebanon;
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Guido Ruggero Loria
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli P.O. Box 146404, Lebanon;
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Bakhtiari S, Mahmoudi H, Seftjani SK, Amirzargar MA, Ghiasvand S, Ghaffari ME, Adabi M. Antibiotic resistance pattern and phylogenetic groups of the uropathogenic Escherichia coli isolates from urinary tract infections in Hamedan, west of Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 12:388-394. [PMID: 33603992 PMCID: PMC7867701 DOI: 10.18502/ijm.v12i5.4598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Background and Objectives: Escherichia coli is the most common causative agent of urinary tract infections (UTIs) in 90-80% of patients in all age groups. Phylogenetic groups of these bacteria are variable and the most known groups are A, B1, B2 and D. The present study aimed to evaluate the phylogenetic groups of E. coli samples obtained from UTIs and their relation with antibiotic resistance patterns of isolates. Materials and Methods: In this study 113 E. coli isolates were isolated from distinct patients with UTIs referred to Hamadan hospitals. After biochemical and molecular identification of the isolates, typing and phylogenetic grouping of E. coli strains were performed using multiplex PCR targeting chu, yjaA and TSPE4.C2 genes. The anti-microbial susceptibility of the isolates to amikacin, ampicillin, trimethoprim-sulfamethoxazole, amoxicillin/clavulanic acid, ciprofloxacin, cefotaxime, imipenem, aztreonam, gentamicin, meropenem, nitrofurantoin, nalidixic acid and cefazolin was determined using disk diffusion method. Results: Of 113 isolates, 50 (44.2%), 35 (31%), 23 (20.4%) and 5 (4.4%) of samples belonged to group B2, group D, group A and group B1 phylogenetic groups respectively. All isolates were susceptible to meropenem, imipenem (100%), followed by amikacin (99.1%). The highest resistance rates were observed against ampicillin (74.3%) and nalidixic acid (70.8%). Correlation between phylogenetic groups and antibiotic susceptibilities was significant only with co-amoxiclav (P = 0.006), which had the highest resistance in phylogenetic group A. Conclusion: Prevalence of different phylogroup and resistance associated with them in E. coli samples could be variable in each region. Therefore, investigating of these items in E. coli infections, could be more helpful in selecting the appropriate antibiotic treatment and epidemiological studies.
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Affiliation(s)
- Somayeh Bakhtiari
- Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hassan Mahmoudi
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sara Khosravi Seftjani
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Ali Amirzargar
- Urology and Nephrology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sima Ghiasvand
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Ebrahim Ghaffari
- Department of Biostatistics and Epidemiology, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Maryam Adabi
- Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Foster-Nyarko E, Alikhan NF, Ravi A, Thomson NM, Jarju S, Kwambana-Adams BA, Secka A, O’Grady J, Antonio M, Pallen MJ. Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia. Microb Genom 2021; 7:mgen000484. [PMID: 33253086 PMCID: PMC8115903 DOI: 10.1099/mgen.0.000484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/09/2020] [Indexed: 01/21/2023] Open
Abstract
Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38-39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa - suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
| | | | - Anuradha Ravi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | | | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
| | - Brenda A. Kwambana-Adams
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Arss Secka
- West Africa Livestock Innovation Centre (WALIC), MB 14, Banjul, Gambia
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard Road, Fajara, Gambia
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark John Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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Comparison of virulence genes and phylogenetic groups of Escherichia coli isolates from urinary tract infections and normal fecal flora. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ndegwa E, Alahmde A, Kim C, Kaseloo P, O'Brien D. Age related differences in phylogenetic diversity, prevalence of Shiga toxins, Intimin, Hemolysin genes and select serogroups of Escherichia. coli from pastured meat goats detected in a longitudinal cohort study. BMC Vet Res 2020; 16:266. [PMID: 32731899 PMCID: PMC7391229 DOI: 10.1186/s12917-020-02479-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
Background Little is known on significance, diversity and characteristics of gut E. coli in goats despite their importance as food animals globally. We characterized the temporal dynamics in diversity of E. coli in fecal samples from a cohort of goat kids and adult meat goats on pasture over a one-year period. Isolates were characterized based on phylogenetic grouping, virulence genes; shiga toxins 1 and 2 (Stx1&Stx2) (STEC), intimin (eaeA), hemolysin (hly) and select important sero-groups (026, 045, 0103, 0126 and 0146) using molecular methods. Results A total of 516 E. coli isolates were screened. Prevalence of virulence genes and STEC was 65 and 56% respectively. Prevalence of virulence genes and STEC was significantly higher in goat kids less than six months (76% /66%) than adults (48% /28%). Isolates with virulence profiles of two or more genes were also higher in young goat kids (50%) than adults (20%). Entero-pathogenic E. coli (EPEC-eaeA gene only) were mostly from pre-weaned goat kids while hly gene only isolates were significantly higher in adults. The stx1, stx2 and hly genes peaked around weaning (60, 63 and 52%) respectively. Goats kids were mostly hosts to group D (59%) while adults older than one year had B1 (75%) isolates. Group D isolates were most abundant at weaning (64%) and diarrhea samples (74%). Group B2 isolates overall (6%) were mostly detected around weaning (63%) while A isolates were 4% overall. Twenty-four isolates belonged to sero-groups 026, 0103 and 0146 with 70% of the isolates detected around weaning. Nineteen of these isolates were STEC with most harboring the stx1/stx2/hly/eae (25%) profile. Most belonged to O26 sero-group (75%) and phylogroup D (75%). Conclusion To our knowledge this is the first study to highlight longitudinal age related differences in E. coli phylogenetic diversity, abundance of virulence genes and select important sero-groups in goats. Differences detected suggest a possible role of age and weaning stress in influencing E. coli diversity in the gut of goats. The findings are relevant to both animal and public health to advise on further studies on caprine E. coli isolates as animal and human pathogens.
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Affiliation(s)
- Eunice Ndegwa
- Agricultural Research Station, Virginia State University, Petersburg, VA, 23806, USA.
| | - Aber Alahmde
- Department of Biology, Virginia State University, Petersburg, VA, 23806, USA
| | - Chyer Kim
- Agricultural Research Station, Virginia State University, Petersburg, VA, 23806, USA
| | - Paul Kaseloo
- Department of Biology, Virginia State University, Petersburg, VA, 23806, USA
| | - Dahlia O'Brien
- College of Agriculture, Virginia Cooperative Extension, Virginia State University, Petersburg, VA, 23806, USA
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21
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Identification and Characterization of Escherichia coli, Salmonella Spp., Clostridium perfringens, and C. difficile Isolates from Reptiles in Brazil. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9530732. [PMID: 31263711 PMCID: PMC6556801 DOI: 10.1155/2019/9530732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/09/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022]
Abstract
Considering the increasing popularity of reptiles as pets and their possible role as reservoirs of pathogenic microorganisms, the aim of this study was to isolate Escherichia coli, Salmonella spp., Clostridium perfringens, and C. difficile strains from reptiles in Brazil and to characterize the isolated strains. The characterization was based on phylogenetic typing of E. coli, identification of virulence genes of E. coli, C. perfringens, and C. difficile, serotyping of Salmonella spp., ribotyping and MLST of C. difficile and antimicrobial susceptibility test of pathogenic strains. Cloacal swabs were collected from 76 reptiles, of which 15 were lizards, 16 chelonians, and 45 snakes, either living in captivity, in the wild, or as companion animals. E. coli was isolated from 52 (68.4%) reptiles, of which 46 (88.4%) were characterized as phylogroup B1. The virulence factor CNF1 of E. coli was found in seven (9.2%) sampled animals, whereas the gene of EAST1 was found in isolates from two (2.6%) reptiles. Three isolates positive for CNF1 were resistant to cephalothin, one of which was also resistant to ciprofloxacin, trimethoprim/sulfamethoxazole, and chloramphenicol, being then classified as multidrug resistant strain (MDR). Salmonella enterica was identified in 26 (34.2%) reptiles, of which 13 belonged to the subspecies enterica. Serotypes such as S. Mbandaka, S. Panama, S. Infantis, S. Heidelberg, and S. Anatum were identified. One isolate of S. enterica subsp. houtenae was resistant to cephalothin and ciprofloxacin. C. perfringens type A was isolated from six (7.8%) animals. C. difficile was isolated from three (3.9%) reptiles. Two of these isolates were toxigenic and classified into ribotypes/MLST 081/ST9 and 106/ST42, which have been previously reported to infect humans. In conclusion, reptiles in Brazil can harbor toxigenic C. difficile and potentially pathogenic E. coli and Salmonella enterica subsp. enterica, thus representing a risk to human and animal health.
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Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ. Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study. Front Microbiol 2018; 9:2040. [PMID: 30233526 PMCID: PMC6127291 DOI: 10.3389/fmicb.2018.02040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023] Open
Abstract
In this study, fecal samples were collected from a closed beef herd in Alberta, Canada from 2012 to 2015. To limit serotype bias, which was observed in enrichment broth cultures, Verotoxigenic Escherichia coli (VTEC) were isolated directly from samples using a hydrophobic grid-membrane filter verotoxin immunoblot assay. Overall VTEC isolation rates were similar for three different cohorts of yearling heifers on both an annual (68.5 to 71.8%) and seasonal basis (67.3 to 76.0%). Across all three cohorts, O139:H19 (37.1% of VTEC-positive samples), O22:H8 (15.8%) and O?(O108):H8 (15.4%) were among the most prevalent serotypes. However, isolation rates for serotypes O139:H19, O130:H38, O6:H34, O91:H21, and O113:H21 differed significantly between cohort-years, as did isolation rates for some serotypes within a single heifer cohort. There was a high level of VTEC serotype diversity with an average of 4.3 serotypes isolated per heifer and 65.8% of the heifers classified as "persistent shedders" of VTEC based on the criteria of >50% of samples positive and ≥4 consecutive samples positive. Only 26.8% (90/336) of the VTEC isolates from yearling heifers belonged to the human disease-associated seropathotypes A (O157:H7), B (O26:H11, O111:NM), and C (O22:H8, O91:H21, O113:H21, O137:H41, O2:H6). Conversely, seropathotypes B (O26:NM, O111:NM) and C (O91:H21, O2:H29) strains were dominant (76.0%, 19/25) among VTEC isolates from month-old calves from this herd. Among VTEC from heifers, carriage rates of vt1, vt2, vt1+vt2, eae, and hlyA were 10.7, 20.8, 68.5, 3.9, and 88.7%, respectively. The adhesin gene saa was present in 82.7% of heifer strains but absent from all of 13 eae+ve strains (from serotypes/intimin types O157:H7/γ1, O26:H11/β1, O111:NM/θ, O84:H2/ζ, and O182:H25/ζ). Phylogenetic relationships inferred from wgMLST and pan genome-derived core SNP analysis showed that strains clustered by phylotype and serotype. Further, VTEC strains of the same serotype usually shared the same suite of antibiotic resistance and virulence genes, suggesting the circulation of dominant clones within this distinct herd. This study provides insight into the diverse and dynamic nature of VTEC populations within groups of cattle and points to a broad spectrum of human health risks associated with these E. coli strains.
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Affiliation(s)
- Lu Ya Ruth Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada
| | | | - Chad R Laing
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Victor P J Gannon
- National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, AB, Canada
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Phylogenetic Group of Escherichia coli Isolates from Broilers in Brazilian Poultry Slaughterhouse. ScientificWorldJournal 2017; 2017:5898701. [PMID: 29130064 PMCID: PMC5654288 DOI: 10.1155/2017/5898701] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/25/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023] Open
Abstract
The aim of the study was to determine the phylogenetic groups of E. coli strains isolated from seemingly healthy broiler and broiler condemned suspected of colibacillosis in a Brazilian slaughterhouse. Samples from respiratory tract and edible giblets (liver and heart) of broilers with and without macroscopic lesions of colibacillosis were collected at slaughter. There were 84 strains isolated from broilers condemned of which 11 were obtained from swabs of the heart, 7 from the liver, and 66 from the respiratory tract. Of the 53 E. coli strains isolated from broilers not condemned, 5 were isolated from the heart, 4 from the liver, and 44 from the respiratory tract. E coli strains were tested via PCR for phylogenetic groups A, B1, B2, C, D, E, and F. Phylogroups A and B1 were the most common phylogroups of E. coli obtained from healthy and sick-appearing broiler carcasses. The results of the study showed that phylogroups B2 and E were associated with the heart samples and phylogroup A was associated with respiratory tract samples, phylogroup B1 with not condemned carcass, and phylogroup D with liver samples.
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Hussain HI, Iqbal Z, Seleem MN, Huang D, Sattar A, Hao H, Yuan Z. Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken. Sci Rep 2017; 7:8335. [PMID: 28827616 PMCID: PMC5567091 DOI: 10.1038/s41598-017-07798-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/03/2017] [Indexed: 02/01/2023] Open
Abstract
Numerous studies have examined the prevalence of pathogenic Escherichia coli in poultry and poultry products; however, limited data are available regarding their resistance- and virulence-associated gene expression profiles. This study was designed to examine the resistance and virulence of poultry E. coli strains in vitro and in vivo via antibiotic susceptibility, biofilm formation and adhesion, and invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines as well as the determination of the median lethal dose in two-day old chickens. A clinical pathogenic multidrug-resistant isolate, E. coli 381, isolated from broilers, was found to be highly virulent in cell culture and 1000-fold more virulent in a chicken model than other strains; accordingly, the isolate was subsequently selected for transcriptome analysis. The comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was completed with Illumina HiSeq. 2500 transcriptome analysis. Differential gene expression analysis indicates that there are multiple pathways involved in the resistance and virulence of this highly virulent strain. The results garnered from this study provide critical information about the highly virulent MDR E. coli strain of poultry origin and warrant further investigation due to its significant threat to public health.
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Affiliation(s)
- Hafiz I Hussain
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Zahid Iqbal
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
- University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Deyu Huang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Adeel Sattar
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.
| | - Zonghui Yuan
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China.
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Tymensen L, Booker CW, Hannon SJ, Cook SR, Zaheer R, Read R, McAllister TA. Environmental Growth of Enterococci and Escherichia coli in Feedlot Catch Basins and a Constructed Wetland in the Absence of Fecal Input. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5386-5395. [PMID: 28430425 DOI: 10.1021/acs.est.6b06274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population structures of fecal indicator bacteria (FIB) isolated from catch basins, a constructed wetland, and feces from a beef cattle feedlot were compared over a two-year period. Enterococcus hirae accounted for 92% of the fecal isolates, whereas secondary environments were characterized by greater relative abundance of environmentally adapted species including Enterococcus casseliflavus. While enterococci densities in the catch basins and wetland were similar under wet and drought conditions, E. hirae predominated during rainy periods, while E. casseliflavus predominated during drought conditions. Environmentally adapted species accounted for almost half of the erythromycin resistant enterococci isolated from the wetland. Densities of Escherichia coli were also comparable during wet versus drought conditions, and the relative abundance of strains from environmentally adapted clades was greater in secondary environments compared to feces. Unlike enterococci, fewer environmentally adapted E. coli strains were isolated on selective media containing ceftriaxone from the wetland compared to feces, suggesting resistance to this antibiotic may not be well maintained in the absence of selective pressure. Overall, these findings suggest that secondary environments select for environmentally adapted FIB. While these species and clades tend to be of limited clinical relevance, they could potentially serve as reservoirs of antimicrobial resistance.
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Affiliation(s)
- Lisa Tymensen
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry , 100, 5401 1st Avenue South, Lethbridge, Alberta, Canada , T1J 4 V6
| | - Calvin W Booker
- Feedlot Health Management Services, Ltd. , Okotoks, Alberta, Canada , T1S 2A2
| | - Sherry J Hannon
- Feedlot Health Management Services, Ltd. , Okotoks, Alberta, Canada , T1S 2A2
| | - Shaun R Cook
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry , 100, 5401 1st Avenue South, Lethbridge, Alberta, Canada , T1J 4 V6
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| | - Ron Read
- Microbiology, Immunology and Infectious Diseases, University of Calgary , Calgary, Alberta, Canada , T1Y 6J4
| | - Tim A McAllister
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
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Souto MSM, Coura FM, Dorneles EMS, Stynen APR, Alves TM, Santana JA, Pauletti RB, Guedes RMC, Viott AM, Heinemann MB, Lage AP. Antimicrobial susceptibility and phylotyping profile of pathogenic Escherichia coli and Salmonella enterica isolates from calves and pigs in Minas Gerais, Brazil. Trop Anim Health Prod 2017; 49:13-23. [PMID: 27709395 PMCID: PMC7089450 DOI: 10.1007/s11250-016-1152-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/07/2016] [Indexed: 01/01/2023]
Abstract
The aims of the present study were to determine (i) the profiles of phylogroup and (ii) the antimicrobial susceptibility of pathogenic Escherichia coli strains isolated from calves, and of Salmonella spp. strains isolated from calves and pigs in Minas Gerais State, Brazil. Sixty-one pathogenic E. coli strains and Salmonella spp. (n = 24) strains isolated from fecal samples of calves and Salmonella spp. (n = 39) strains previously isolated from fecal samples of growing/finishing pigs were tested. The minimum inhibitory concentration (MIC) using the agar dilution method was determined for nalidixic acid, amikacin, amoxicillin, ampicillin, cefoxitin, norfloxacin, gentamicin, tetracycline, and trimethoprim-sulfamethoxazole. All E. coli isolates were susceptible to amikacin. Tetracycline was the antimicrobial that presented the higher frequency of resistance among E. coli strains, followed by ampicillin, trimethoprim-sulfamethoxazole, amoxicillin, nalidixic acid, norfloxacin, gentamicin, and cefoxitin. E. coli (n = 61) strains isolated from calves belonged to different phylogroup namely, phylogroup A (n = 26), phylogroup B1 (n = 31), phylogroup E (n = 3), and phylogroup F (n = 1). Phylogroups B2, C, and D were not identified among the E. coli in the present study. All Salmonella spp. (n = 24) strains isolated from fecal samples of calves were susceptible to amikacin, amoxicillin, ampicillin, norfloxacin, gentamicin, tetracycline, and trimethoprim-sulfamethoxazole. Resistance to nalidixic acid and cefoxitin was detected in 16.66 and 8.33 % of the Salmonella spp. strains, respectively. Among the Salmonella spp. (n = 39) strains isolated from fecal samples of pigs, the higher frequency of resistance was observed to tetracycline, followed by amoxicillin, gentamicin, ampicillin, trimethoprim-sulfamethoxazole, nalidixic acid, cefoxitin, and norfloxacin. All strains were susceptible to amikacin. Forty-eight (78.68 %) of the E. coli strains were classified as multidrug-resistant, whereas among Salmonella spp. strains, the percentage of multidrug resistance was 57.14 %, being all multidrug-resistant strains isolated from pigs (92.30 %). The results from the present study indicate a high frequency of antimicrobial resistance among pathogenic E. coli strains isolated from calves and Salmonella spp. strains isolated from pigs and a high rate of susceptibility to most antimicrobials tested among Salmonella spp. strains isolated from calves. Our study highlights the presence of multidrug-resistant strains of E. coli and Salmonella spp. isolated from food-producing animals in Minas Gerais, Brazil.
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Affiliation(s)
- Monalisa S M Souto
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Fernanda M Coura
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Elaine M S Dorneles
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Minas Gerais, Brazil
| | - Ana Paula R Stynen
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Telma M Alves
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Jordana Almeida Santana
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Rebeca B Pauletti
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Roberto M C Guedes
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Aline M Viott
- Laboratório de Patologia Veterinária, Universidade Federal do Paraná, Campus Palotina, Paraná, Brazil
| | - Marcos B Heinemann
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Andrey P Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Minas Gerais, Brazil.
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Coura FM, de Araújo Diniz S, Mussi JMS, Silva MX, Lage AP, Heinemann MB. Characterization of virulence factors and phylogenetic group determination of Escherichia coli isolated from diarrheic and non-diarrheic calves from Brazil. Folia Microbiol (Praha) 2016; 62:139-144. [PMID: 27787756 DOI: 10.1007/s12223-016-0480-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
Abstract
This study aimed to detect virulence factors, pathovars, and phylogenetic groups of Escherichia coli strains obtained from feces of calves with and without diarrhea up to 70 days old and to determine the association between occurrence of diarrhea, phylogenetic groups, and pathovars. Phylo-typing analysis of the 336 E. coli strains isolated from calves with Clermont method showed that 21 (6.25 %) belong to phylogroup A, 228 (67.85 %) to phylogroup B1, 2 (0.6 %) to phylogroup B2, 5 (1.49 %) to phylogroup C, 57 (16.96 %) to phylogroup E, and 3 (0.9 %) to phylogroup F. Phylogroup D was not identified and 20 strains (5.95 %) were assigned as "unknown." The distribution of phylogenetic groups among pathovars showed that NTEC belong to phylogroups B1 (17) and C (4); EPEC to phylogroups B1 (6) and E (8); STEC to phylogroups A (5), B1 (56), B2 (2), C (1), and E (15); EHEC to phylogroups B1 (95) and E (5); and ETEC to phylogroups A (3), B1 (7), and E (10). The EAST-1 strains were phylogroups A (13), B1 (47), E (19), and F (3); E. coli strains of "unknown" phylogroups belonged to pathovars EPEC (1), EHEC (2), STEC (7), and EAST-1 strains (6). ETEC was associated with diarrhea (P = 0.002). Our study did not find association between the phylogenetic background and occurrence of diarrhea (P = 0.164) but did find some relationship in phylogenetic group and pathovar. The study showed that EHEC and STEC are classified as phylogroup B1, EAST-1 phylogroup A, ETEC, and EPEC phylogroup E.
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Affiliation(s)
- Fernanda Morcatti Coura
- Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, UFMG, Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, CEP30123-970, Brazil
| | - Soraia de Araújo Diniz
- Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, UFMG, Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, CEP30123-970, Brazil
| | - Jamili Maria Suhet Mussi
- Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, UFMG, Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, CEP30123-970, Brazil
| | - Marcos Xavier Silva
- Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, UFMG, Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, CEP30123-970, Brazil
| | - Andrey Pereira Lage
- Escola de Veterinária, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, UFMG, Av. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, CEP30123-970, Brazil
| | - Marcos Bryan Heinemann
- Departamento de Medicina Veterinária Preventiva, Faculdade de Medicina Veterinária e Saúde Animal, Universidade de São Paulo, Av. Prof Orlando Marques de Paiva, 87, São Paulo, São Paulo, CEP 05508-270, Brazil.
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