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Ketkhao P, Utrarachkij F, Parikumsil N, Poonchareon K, Kerdsin A, Ekchariyawat P, Narongpun P, Nakajima C, Suzuki Y, Suthienkul O. Phylogenetic diversity and virulence gene characteristics of Escherichia coli from pork and patients with urinary tract infections in Thailand. PLoS One 2024; 19:e0307544. [PMID: 39052658 PMCID: PMC11271939 DOI: 10.1371/journal.pone.0307544] [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: 01/06/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC), especially uropathogenic E. coli (UPEC) are responsible for urinary tract infections (UTIs), while diarrheagenic E. coli (DEC) cause foodborne illnesses. These pathogenic E. coli are a serious threat to human health and a public concern worldwide. However, the evidence on pork E. coli (PEC) harboring UPEC virulence-associated genes is currently limited. Therefore, this study aimed to determine the phylogroups, virulence genes, and their association between PEC and UPEC from UTI patients. In this study, 330 E. coli were obtained from archived stock culture isolated from pork (PEC; n = 165) and urine of patients with UTIs (UPEC; n = 165) during 2014-2022. Phylogroups, UPEC- and diarrheagenic E. coli (DEC) associated virulence genes were assessed using PCR assays. The results showed that phylogroups A (50.3%), and B1 (32.1%) were commonly found among PEC whereas phylogroups B2 (41.8%), and C (25.5%) were commonly detected in the UPEC. PEC and UPEC carried similar virulence-associated genes with different percentages. The most frequent UPEC virulence-associated gene among UPEC, and PEC strains was fimH, (93.3%, and 92.1%), followed by iucC (55.2%, and 12.7%), papC (21.8%, and 4.2%), afaC (22.4%, and 0%), hlyCA (17%, and 0.6%), cnf (16.4%, and 0.6%), and sfa/focDE (8.5%, and 4.8%). Additionally, 6 of 27 UPEC virulence-associated gene patterns were found in both PEC and UPEC strains regardless of phylogroups. Furthermore, the DEC virulence-associated genes were found in only 3 strains, one from PEC harboring eae, and two from UPEC carried fimH-bfpA or afaC-CVD432 indicating hybrid strains. Cluster analysis showed a relationship between PEC and UPEC strains and demonstrated that PEC harboring UPEC virulence-associated genes in pork may be associated with UPEC in humans. Food safety and hygiene practices during pork production chain are important procedures for minimizing cross-contamination of these strains that could be transmitted to the consumers.
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Affiliation(s)
- Pramualchai Ketkhao
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Fuangfa Utrarachkij
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | | | - Kritchai Poonchareon
- Division of Biochemistry, School of Medical Sciences, University of Phayao, Phayao, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermprakiat Sakon Nakhon Province Campus, Sakhon Nakhon, Thailand
| | - Peeraya Ekchariyawat
- Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Pawarut Narongpun
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
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Li D, Elankumaran P, Kudinha T, Kidsley AK, Trott DJ, Jarocki VM, Djordjevic SP. Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids. Microb Genom 2023; 9:mgen001068. [PMID: 37471138 PMCID: PMC10438821 DOI: 10.1099/mgen.0.001068] [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: 12/12/2022] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrABC+ plasmids were split into two categories: pUTI89-like (F29:A-:B10 and/or >95 % identity to pUTI89) (n=73) and non-pUTI89-like (n=53). Compared to all other plasmid replicons, isolates with pUTI89-like plasmids carried fewer antibiotic resistance genes (ARGs), whilst isolates with senB-cjrABC+/non-pUTI89 plasmids had a significantly higher load of ARGs and class 1 integrons. F plasmids were not detected in 89 genomes, predominantly ST73. Our phylogenomic analyses identified closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals.
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Affiliation(s)
- Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Paarthiphan Elankumaran
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, Australia
| | - Amanda K. Kidsley
- School of Animal and Veterinary Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Darren J. Trott
- School of Animal and Veterinary Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Veronica Maria Jarocki
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Steven Philip Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
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García V, Lestón L, Parga A, García-Meniño I, Fernández J, Otero A, Olsen JE, Herrero-Fresno A, Mora A. Genomics, biofilm formation and infection of bladder epithelial cells in potentially uropathogenic Escherichia coli (UPEC) from animal sources and human urinary tract infections (UTIs) further support food-borne transmission. One Health 2023; 16:100558. [PMID: 37363240 PMCID: PMC10288081 DOI: 10.1016/j.onehlt.2023.100558] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 06/28/2023] Open
Abstract
Escherichia coli is the main cause of urinary tract infections (UTI). While genomic comparison of specific clones recovered from animals, and human extraintestinal infections show high identity, studies demonstrating the uropathogenicity are lacking. In this study, comparative genomics combined with bladder-cell and biofilm formation assays, were performed for 31 E. coli of different origins: 7 from meat (poultry, beef, and pork); 2 from avian-farm environment; 12 from human uncomplicated UTI, uUTI; and 10 from human complicated UTI, cUTI. These isolates were selected based on their genetic uropathogenic (UPEC) status and phylogenetic background. In silico analysis revealed similar virulence-gene profiles, with flagella, type 1 and curli fimbriae, outer-membrane proteins (agn43, ompT, iha), and iron-uptake (iutA, entA, and fyuA) associated-traits as the most prevalent (>65%). In bladder-cell assays, moderate to strong values of association (83%, 60%, 77.8%) and invasion (0%, 70%, 55.5%) were exhibited by uUTI, cUTI, and animal-derived isolates, respectively. Of interest, uUTI isolates exhibited a significantly lower invasive capacity than cUTI isolates (p < 0.05). All isolates but one produced measurable biofilm. Notably, 1 turkey meat isolate O11:H6-F-ST457, and 2 cUTI isolates of the pandemic lineages O83:H42-F-ST1485-CC648 and O25b:H4-B2-ST131, showed strong association, invasion and biofilm formation. These isolates showed common carriage of type 1 fimbriae and csg operons, toxins (hlyF, tsh), iron uptake systems (iutA, entA, iroN), colicins, protectins (cvaC, iss, kpsM, traT), ompT, and malX. In summary, the similar in vitro behaviour found here for certain E. coli clones of animal origin would further reinforce the role of food-producing animals as a potential source of UPEC. Bladder-cell infection assays, combined with genomics, might be an alternative to in vivo virulence models to assess uropathogenicity.
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Affiliation(s)
- Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago 15706, Spain
| | - Luz Lestón
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
| | - Ana Parga
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago 15706, Spain
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo 33011, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo 33011, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo 33011, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Otero
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg 1870, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg 1870, Denmark
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago 15706, Spain
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Lenchenko E, Sachivkina N, Lobaeva T, Zhabo N, Avdonina M. Bird immunobiological parameters in the dissemination of the biofilm-forming bacteria Escherichia coli. Vet World 2023; 16:1052-1060. [PMID: 37576771 PMCID: PMC10420717 DOI: 10.14202/vetworld.2023.1052-1060] [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: 02/05/2023] [Accepted: 04/10/2023] [Indexed: 08/15/2023] Open
Abstract
Background and Aim With the development of industrial maintenance technology, a group of pathogens called avian pathogenic Escherichia coli (APEC) became very common. The initiation, development, and outcome of the infectious process mediated by virulent APEC strains occur through a decrease in the colonization resistance of the intestine, an immunobiological marker of homeostasis stability in susceptible species. This study focused on the pathogenetic features of colibacillosis and the morphological features of E. coli. Materials and Methods Clinical, immunological, bacteriological, and histological studies were conducted on 15-day-old white Leghorn birds (n = 20). The birds were divided into two groups: Control group (Group I; n = 10) with birds intranasally inoculated with 0.5 mL of 0.9% NaCl solution and experimental group (Group II; n = 10) with birds intranasally inoculated with 0.5 mL of an E. coli suspension at 1 billion/mL. Results During the biofilm formation, clusters of microcolonies were formed as a gel-like intercellular matrix that accumulated due to cell coagulation. The intercellular matrix "glues" heteromorphic cells together and forms a structure of densely packed heteromorphic cells arranged in an orderly manner and growing in different directions. During the experimental reproduction of E. coli, excessive growth was observed in material isolated from poultry. Pathogenic E. coli strains implementing virulence factors adhered to the receptors of erythrocytes, alveolocytes, and enterocytes. Multicellular heterogeneous biofilms, united by an intercellular matrix, were located at the apical poles of the respiratory tract alveolocytes and enterocytes of the terminal ileum villi. Many bacteria exudate containing desquamated epithelial cells with an admixture of mucus, and polymorphonuclear leukocytes were detected in the lumen of the birds' abdominal organs. Invasive bacteria damaged the epithelial layer, violated the endothelial layer of blood vessels, and developed inflammatory hyperemia of the lamina propria of the respiratory and digestive systems' mucous membrane. A correlative dependence of changes developed by the type of delayed hypersensitivity reaction was established. Signs of accidental transformation of the thymus, atrophy of the bursa of Fabricius, disseminated thrombosis, and septic spleen developed. Moreover, toxic cardiomyocyte dystrophy, signs of congestive vascular hyperemia, massive disintegration of lymphocytes, macrophage reactions, perivascular edema resulting from the release of plasma, and shaped blood elements were detected. Conclusion The development and outcome of the infectious process in escherichiosis primarily depend on the homeostasis stability of susceptible species and virulence factors of the pathogenic microorganisms. One of the selected strains, E. coli O78:K80 displayed the highest ability to form biofilms. Its strong adhesion ability to bird erythrocytes was demonstrated. Deepening the scientific knowledge of the interaction between eukaryotes and prokaryotes will contribute to a better understanding of the pathogenetic aspects of avian escherichiosis and eventually find promising anti-adhesive drugs that could reduce primary bacterial contamination in vivo and in vitro.
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Affiliation(s)
- Ekaterina Lenchenko
- Department of Veterinary Medicine, Russian Biotechnological University (BIOTECH University), 125080, Moscow, Russia
| | - Nadezhda Sachivkina
- Department of Microbiology V.S. Kiktenko, Institute of Medicine, Peoples’ Friendship University of Russia named after Patrice Lumumba (RUDN University), 117198, Moscow, Russia
| | - Tatiana Lobaeva
- Department of Biochemistry T.T. Berezov, Institute of Medicine, Peoples’ Friendship University of Russia named after Patrice Lumumba (RUDN University), 117198 Moscow, Russia
| | - Natallia Zhabo
- Department of Foreign Languages, Institute of Medicine, Peoples’ Friendship University of Russia named after Patrice Lumumba (RUDN University), 117198, Moscow, Russia
| | - Marina Avdonina
- Department of Linguistics and Intercultural Communication, Moscow State Linguistic University, 119034, Moscow, Russia
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Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Baldinelli F, Broglia A, Kohnle L, Alvarez J. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial‐resistant Escherichia coli in dogs and cats, horses, swine, poultry, cattle, sheep and goats. EFSA J 2022; 20:e07311. [PMID: 35582363 PMCID: PMC9087955 DOI: 10.2903/j.efsa.2022.7311] [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] [Indexed: 11/11/2022] Open
Abstract
Escherichia coli (E. coli) was identified among the most relevant antimicrobial‐resistant (AMR) bacteria in the EU for dogs and cats, horses, swine, poultry, cattle, sheep and goats in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. coli can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33–66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2, 3 and 4 (Categories A, B, C and D; 0–5%, 5–10%, 10–33% and 10–33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Section 5 (Category E, 33–66% probability of meeting the criteria). The animal species to be listed for AMR E. coli according to Article 8 criteria include mammals, birds, reptiles and fish.
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Distribution of CRISPR in Escherichia coli Isolated from Bulk Tank Milk and Its Potential Relationship with Virulence. Animals (Basel) 2022; 12:ani12040503. [PMID: 35203211 PMCID: PMC8868466 DOI: 10.3390/ani12040503] [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: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary In the dairy farms of many different countries, E. coli is one of the most common causes of mastitis. It is defined as mammary pathogenic E. coli, and is known to cause opportunistic infections by possessing diverse virulence factors. Therefore, the purpose of this study was to investigate the virulence potential of E. coli isolates from bulk tank milk in Korea, and observe its association with clustered regularly interspaced short palindromic repeat (CRISPR) arrays. The results showed that out of 183 isolates, 164 (89.6%) possessed one or more of 18 virulence genes, and belonged to phylogenetic groups B1 (64.0%), A (20.1%), D (8.5%), and C (7.3%). CRISPR arrays of E. coli are classified as either CRISPR I-E (CRISPR 1 and 2) or CRISPR I-F (CRISPR 3 and 4). In this study, only CRISPR 1 (95.7%) and 2 (74.4%) were detected. Among the eight protospacers matching plasmids and phages, three were associated with gene regulation, and one was associated with virulence. Moreover, the different virulence genes showed significantly different patterns of CRISPR distribution and CRISPR sequence-types. This result implies that CRISPR loci may be associated with gene regulation and pathogenicity in E. coli, and that the CRISPR sequence-typing approach can help to clarify and trace virulence potential, even though the E. coli isolates were from normal bulk tank milk. Abstract Escherichia coli is one of the most common causes of mastitis on dairy farms around the world, but its clinical severity is determined by a combination of virulence factors. Recently, clustered regularly interspaced short palindromic repeat (CRISPR) arrays have been reported as a novel typing method because of their usefulness in discriminating pathogenic bacterial isolates. Therefore, this study aimed to investigate the virulence potential of E. coli isolated from bulk tank milk, not from mastitis, and to analyze its pathogenic characterization using the CRISPR typing method. In total, 164 (89.6%) out of 183 E. coli isolated from the bulk tank milk of 290 farms carried one or more of eighteen virulence genes. The most prevalent virulence gene was fimH (80.9%), followed by iss (38.3%), traT (26.8%), ompT (25.7%), afa/draBC (24.0%), and univcnf (21.9%). Moreover, the phylogenetic group with the highest prevalence was B1 (64.0%), followed by A (20.1%), D (8.5%), and C (7.3%) (p < 0.05). Among the four CRISPR loci, only two, CRISPR 1 and CRISPR 2, were found. Interestingly, the distribution of CRISPR 1 was significantly higher in groups A and B1 compared to that of CRISPR 2 (p < 0.05), but there were no significant differences in groups C and D. The prevalence of CRISPR 1 by virulence gene ranged from 91.8% to 100%, whereas that of CRISPR 2 ranged from 57.5% to 93.9%. The distribution of CRISPR 1 was significantly higher in fimH, ompT, afa/draBC, and univcnf genes than that of CRISPR 2 (p < 0.05). The most prevalent E. coli sequence types (EST) among 26 ESTs was EST 22 (45.1%), followed by EST 4 (23.2%), EST 16 (20.1%), EST 25 (19.5%), and EST 24 (18.3%). Interestingly, four genes, fimH, ompT, afa/draBC, and univcnf, had a significantly higher prevalence in both EST 4 and EST 22 (p < 0.05). Among the seven protospacers derived from CRISPR 1, protospacer 163 had the highest prevalence (20.4%), and it only existed in EST 4 and EST 22. This study suggests that the CRISPR sequence-typing approach can help to clarify and trace virulence potential, although the E. coli isolates were from normal bulk tank milk and not from mastitis.
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Onlen Guneri C, Koksal F, Kizilyildirim S, Bedir B, Nagiyev T. The Distribution of Cytotoxic Necrotizing Factors (CNF-1, CNF-2, CNF-3) and Cytolethal Distending Toxins (CDT-1, CDT-2, CDT-3, CDT-4) in Escherichia coli Isolates Isolated from Extraintestinal Infections and the Determination of their Phylogenetic Relationship by PFGE. Int J Clin Pract 2022; 2022:7200635. [PMID: 36474550 PMCID: PMC9683945 DOI: 10.1155/2022/7200635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/22/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUNDS Diagnostic markers of extraintestinal infection in Escherichia coli (E. coli) remain unclear in the literature. Extraintestinal pathogenic E. coli (ExPEC) is differentiated from other E. coli isolates in terms of virulence factors, such as host cell adhesion, invasion, cytotoxic necrotizing factor (CNF (cnf1-cnf3)) and cytolethal distending toxin (CDT (cdt1-cdt4) that are responsible for cell death. We aimed to investigate the frequency of CNF-CDT and the relationship between the clinical diagnosis and genotypes in E. coli isolates with different clinical origins. METHODS A total of 646 E. coli isolates (obtained from 645 patients) isolated from different infection sites other than the intestine were evaluated in aspects of the CNF, CDT virulence genes, phylogenetic grouping, and phylogenetic relationship by using PCR and PFGE. RESULTS At least one virulence gene was present in 156 (24%) of the 646 ExPEC isolates. We detected cnf1, cnf2, and cnf3, in 78, 12, and 20 ExPEC isolates, respectively. Also, cdt1, cdt2, cdt3, and cdt4 genes were present in 20, 4, 4, and 4 isolates, respectively. Some isolates harbored more than one gene, being cnf1-cnf3 (n = 6), cnf1-cdt1 (n = 4), and cdt1-cdt4 (n = 4). These 156 isolates were distributed into 106 large clusters by PFGE. Virulent ExPEC is primarily related to groups B2 (60%) and D (32%). CONCLUSION To our knowledge, this study demonstrated the presence of cnf2, cnf3, cdt1, cdt2, cdt3, and cdt4 genes for the first time in the literature for Turkey. The widespread presence of the CNF gene in E. coli helps distinguish ExPEC from commensal isolates.
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Affiliation(s)
- Cansu Onlen Guneri
- Department of Medical Laboratory Techniques, Medical Microbiology, Gulhane Vocational School of Health Services, University of Health Sciences, 06018 Ankara, Turkey
| | - Fatih Koksal
- Department of Medical Microbiology, Medical Faculty, Cukurova University, 01380 Adana, Turkey
| | - Suna Kizilyildirim
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Suleyman Demirel University, 32260 Isparta, Turkey
| | - Basak Bedir
- Department of Medical Microbiology, Medical Faculty, Cukurova University, 01380 Adana, Turkey
| | - Togrul Nagiyev
- Department of Medical Microbiology, Medical Faculty, Cukurova University, 01380 Adana, Turkey
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Santos ACDM, Fuga B, Esposito F, Cardoso B, Santos FF, Valiatti TB, Santos-Neto JF, Gales AC, Lincopan N, Silva RM, Gomes TAT. Unveiling the Virulent Genotype and Unusual Biochemical Behavior of Escherichia coli ST59. Appl Environ Microbiol 2021; 87:e0074321. [PMID: 34085857 PMCID: PMC8315172 DOI: 10.1128/aem.00743-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/26/2021] [Indexed: 12/19/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of human and animal infections worldwide. The utilization of selective and differential media to facilitate the isolation and identification of E. coli from complex samples, such as water, food, sediment, and gut tissue, is common in epidemiological studies. During a surveillance study, we identified an E. coli strain isolated from human blood culture that displayed atypical light cream-colored colonies in chromogenic agar and was unable to produce β-glucuronidase and β-galactosidase in biochemical tests. Genomic analysis showed that the strain belongs to sequence type 59 (ST59) and phylogroup F. The evaluation in silico of 104 available sequenced lineages of ST59 complex showed that most of them belong to serotype O1:K1:H7, are β-glucuronidase negative, and harbor a virulent genotype associated with the presence of important virulence markers such as pap, kpsE, chuA, fyuA, and yfcV. Most of them were isolated from extraintestinal human infections in diverse countries worldwide and could be clustered/subgrouped based on papAF allele analysis. Considering that all analyzed strains harbor a virulent genotype and most do not exhibit biochemical behavior typical of E. coli, we report that they could be misclassified or underestimated, especially in epidemiological studies where the screening criteria rely only on typical biochemical phenotypes, as happens when chromogenic media are used. IMPORTANCE The use of selective and differential media guides presumptive bacterial identification based on specific metabolic traits that are specific to each bacterial species. When a bacterial specimen displays an unusual phenotype in these media, this characteristic may lead to bacterial misidentification or a significant delay in its identification, putting a patient at risk depending on the infection type. In the present work, we describe a virulent E. coli sequence type (ST59) that does not produce beta-glucuronidase (GUS negative), production of which is the metabolic trait widely used for E. coli presumptive identification in diverse differential media. The recognition of this unusual metabolic trait may help in the proper identification of ST59 isolates, the identification of their reservoir, and the evaluation of the frequency of these pathogens in places where automatic identification methods are not available.
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Affiliation(s)
- Ana Carolina de Mello Santos
- Disciplina de Microbiologia, Departamento de Microbiologia Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Laboratório ALERTA, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tiago Barcelos Valiatti
- Laboratório ALERTA, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - José Francisco Santos-Neto
- Disciplina de Microbiologia, Departamento de Microbiologia Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Cristina Gales
- Laboratório ALERTA, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Rosa Maria Silva
- Disciplina de Microbiologia, Departamento de Microbiologia Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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9
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Hoseinzadeh F, Ghaemi M, Sharifiyazdi H, Hachesoo BA. Class 1 integron causes vulnerability to formaldehyde in Escherichia coli. Arch Microbiol 2021; 203:4509-4515. [PMID: 34148112 DOI: 10.1007/s00203-021-02445-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
In this study, the relationships of integron 1 element, formaldehyde dehydrogenase, and orfF genes with the level of formaldehyde resistance of isolated E. coli were investigated. E. coli bacteria were isolated from apparently healthy and colibacillosis-affected broilers of Fars Province, Iran. Formaldehyde resistance level and the presence of genetic markers were measured using MIC, and PCR tests, respectively. The prevalence of integron 1 element, orfF, and formaldehyde dehydrogenase genes in E. coli isolates were 61%, 8%, and 94%, respectively. In addition, according to our cut off definition, 15% and 85% of isolates were resistant and sensitive to formaldehyde, respectively. None of the genes had a statistically significant relationship with the formaldehyde resistance; however, the isolates containing integron 1 were significantly more sensitive to formaldehyde in the MIC test than those without integron 1. Integron 1 gene cassette could carry some bacterial surface proteins and porins with different roles in bacterial cells. Formaldehyde could also interfere with the protein functions by alkylating and cross-linking, and this compound would affect bacterial cell surface proteins in advance. Through an increase in the cell surface proteins, the presence of integron 1 gene cassette might make E. coli more sensitive to formaldehyde. As integron 1 was always involved in increasing bacterial resistance to antibiotics and disinfectants such as QACs, this is the first report of bacterial induction of sensitivity to a disinfectant through integron 1. Finally, integron 1 does not always add an advantage to E. coli bacteria, and it could be assumed as a cause of vulnerability to formaldehyde.
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Affiliation(s)
- Farzad Hoseinzadeh
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mehran Ghaemi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.
| | - Hassan Sharifiyazdi
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Bahman Abdi Hachesoo
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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10
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Díaz-Jiménez D, García-Meniño I, Herrera A, Lestón L, Mora A. Microbiological risk assessment of Turkey and chicken meat for consumer: Significant differences regarding multidrug resistance, mcr or presence of hybrid aEPEC/ExPEC pathotypes of E. coli. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Avian Pathogenic Escherichia coli (APEC): An Overview of Virulence and Pathogenesis Factors, Zoonotic Potential, and Control Strategies. Pathogens 2021; 10:pathogens10040467. [PMID: 33921518 PMCID: PMC8069529 DOI: 10.3390/pathogens10040467] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) causes colibacillosis in avian species, and recent reports have suggested APEC as a potential foodborne zoonotic pathogen. Herein, we discuss the virulence and pathogenesis factors of APEC, review the zoonotic potential, provide the current status of antibiotic resistance and progress in vaccine development, and summarize the alternative control measures being investigated. In addition to the known virulence factors, several other factors including quorum sensing system, secretion systems, two-component systems, transcriptional regulators, and genes associated with metabolism also contribute to APEC pathogenesis. The clear understanding of these factors will help in developing new effective treatments. The APEC isolates (particularly belonging to ST95 and ST131 or O1, O2, and O18) have genetic similarities and commonalities in virulence genes with human uropathogenic E. coli (UPEC) and neonatal meningitis E. coli (NMEC) and abilities to cause urinary tract infections and meningitis in humans. Therefore, the zoonotic potential of APEC cannot be undervalued. APEC resistance to almost all classes of antibiotics, including carbapenems, has been already reported. There is a need for an effective APEC vaccine that can provide protection against diverse APEC serotypes. Alternative therapies, especially the virulence inhibitors, can provide a novel solution with less likelihood of developing resistance.
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Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
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Genetic Features of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Poultry in Mayabeque Province, Cuba. Antibiotics (Basel) 2021; 10:antibiotics10020107. [PMID: 33499392 PMCID: PMC7910960 DOI: 10.3390/antibiotics10020107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/13/2021] [Accepted: 01/17/2021] [Indexed: 02/07/2023] Open
Abstract
A total of 434 poultry cloacal samples were collected from seven different farms in different years (2013–2015) in the Cuban province of Mayabeque and analyzed for the presence of third-generation cephalosporin-resistant Escherichia coli (3GC-R-Ec). Sixty-two 3GC-R-Ec isolates were recovered in total from the farms, with detection rates of 2.9% in 2013, 10.3% in 2014, and 28.7% in 2015. Characterization of 32 3GC-R-Ec isolates revealed the presence of the extended-spectrum β-lactamase (ESBL) genes blaCTX-M-1 (n = 27), blaCTX-M-15 (n = 4), and blaCTX-M-1 together with blaLAP-2 (n = 1). The isolates also contained different proportions of genes conferring decreased susceptibility to sulfonamides (sul1, sul2, sul3), trimethoprim (dfrA1, dfrA7, dfrA12, dfrA14, dfrA17), tetracyclines (tet(A), tet(B)), aminoglycosides (aac(6′)-Ib-cr, strA, strB), chloramphenicol (cmlA1, floR), macrolides (mph(A), mph(D)), and quinolones (qnrS, qnrB, aac(6′)-Ib-cr) as well as mutations in the fluoroquinolone-resistance determining regions of GyrA (S83L, D87N, D87Y) and ParC (S80I, E84G). The isolates belonged to 23 different sequence types and to phylogroups A (n = 25), B1 (n = 5), and D (n = 2), and they contained plasmid-associated incompatibility groups FII, X1, HI1, HI2, N, FIA, and FIB. These findings reveal a genetically diverse population of multiresistant ESBL-producing E. coli in poultry farms in Cuba, which suggests multiple sources of contamination and the acquisition of antibiotic resistance genes.
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Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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15
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A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review. ACTA VET BRNO 2020. [DOI: 10.2754/avb202089030273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.
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Desvaux M, Dalmasso G, Beyrouthy R, Barnich N, Delmas J, Bonnet R. Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli. Front Microbiol 2020; 11:2065. [PMID: 33101219 PMCID: PMC7545054 DOI: 10.3389/fmicb.2020.02065] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli is a versatile bacterial species that includes both harmless commensal strains and pathogenic strains found in the gastrointestinal tract in humans and warm-blooded animals. The growing amount of DNA sequence information generated in the era of "genomics" has helped to increase our understanding of the factors and mechanisms involved in the diversification of this bacterial species. The pathogenic side of E. coli that is afforded through horizontal transfers of genes encoding virulence factors enables this bacterium to become a highly diverse and adapted pathogen that is responsible for intestinal or extraintestinal diseases in humans and animals. Many of the accessory genes acquired by horizontal transfers form syntenic blocks and are recognized as genomic islands (GIs). These genomic regions contribute to the rapid evolution, diversification and adaptation of E. coli variants because they are frequently subject to rearrangements, excision and transfer, as well as to further acquisition of additional DNA. Here, we review a subgroup of GIs from E. coli termed pathogenicity islands (PAIs), a concept defined in the late 1980s by Jörg Hacker and colleagues in Werner Goebel's group at the University of Würzburg, Würzburg, Germany. As with other GIs, the PAIs comprise large genomic regions that differ from the rest of the genome by their G + C content, by their typical insertion within transfer RNA genes, and by their harboring of direct repeats (at their ends), integrase determinants, or other mobility loci. The hallmark of PAIs is their contribution to the emergence of virulent bacteria and to the development of intestinal and extraintestinal diseases. This review summarizes the current knowledge on the structure and functional features of PAIs, on PAI-encoded E. coli pathogenicity factors and on the role of PAIs in host-pathogen interactions.
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Affiliation(s)
- Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, Clermont-Ferrand, France
| | - Guillaume Dalmasso
- UMR Inserm 1071, USC-INRAE 2018, M2iSH, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Racha Beyrouthy
- UMR Inserm 1071, USC-INRAE 2018, M2iSH, Université Clermont Auvergne, Clermont-Ferrand, France
- Laboratoire de Bactériologie, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Nicolas Barnich
- UMR Inserm 1071, USC-INRAE 2018, M2iSH, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julien Delmas
- UMR Inserm 1071, USC-INRAE 2018, M2iSH, Université Clermont Auvergne, Clermont-Ferrand, France
- Laboratoire de Bactériologie, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Richard Bonnet
- UMR Inserm 1071, USC-INRAE 2018, M2iSH, Université Clermont Auvergne, Clermont-Ferrand, France
- Laboratoire de Bactériologie, CHU Clermont-Ferrand, Clermont-Ferrand, France
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Bakhshi M, Zandi H, Bafghi MF, Astani A, Ranjbar VR, Vakili M. A survey for phylogenetic relationship; presence of virulence genes and antibiotic resistance patterns of avian pathogenic and uropathogenic Escherichia coli isolated from poultry and humans in Yazd, Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Papouskova A, Masarikova M, Valcek A, Senk D, Cejkova D, Jahodarova E, Cizek A. Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic. BMC Vet Res 2020; 16:189. [PMID: 32522212 PMCID: PMC7286222 DOI: 10.1186/s12917-020-02407-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 06/02/2020] [Indexed: 01/01/2023] Open
Abstract
Background Avian pathogenic Escherichia coli (APEC) can cause various extraintestinal infections in poultry, resulting in massive economic losses in poultry industry. In addition, some avian E. coli strains may have zoonotic potential, making poultry a possible source of infection for humans. Due to its extreme genetic diversity, this pathotype remains poorly defined. This study aimed to investigate the diversity of colibacillosis-associated E. coli isolates from Central European countries with a focus on the Czech Republic. Results Of 95 clinical isolates subjected to preliminary characterization, 32 were selected for whole-genome sequencing. A multi resistant phenotype was detected in a majority of the sequenced strains with the predominant resistance to β-lactams and quinolones being associated with TEM-type beta-lactamase genes and chromosomal gyrA mutations respectively. The phylogenetic analysis confirmed a great diversity of isolates, that were derived from nearly all phylogenetic groups, with predominace of B2, B1 and C phylogroups. Clusters of closely related isolates within ST23 (phylogroup C) and ST429 (phylogroup B2) indicated a possible local spread of these clones. Besides, the ST429 cluster carried blaCMY-2, − 59 genes for AmpC beta-lactamase and isolates of both clusters were generally well-equipped with virulence-associated genes, with considerable differences in distribution of certain virulence-associated genes between phylogenetically distant lineages. Other important and potentially zoonotic APEC STs were detected, incl. ST117, ST354 and ST95, showing several molecular features typical for human ExPEC. Conclusions The results support the concept of local spread of virulent APEC clones, as well as of zoonotic potential of specific poultry-associated lineages, and highlight the need to investigate the possible source of these pathogenic strains.
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Affiliation(s)
- Aneta Papouskova
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic. .,Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.
| | - Martina Masarikova
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Adam Valcek
- Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - David Senk
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Darina Cejkova
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Eva Jahodarova
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.,Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
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Díaz-Jiménez D, García-Meniño I, Fernández J, García V, Mora A. Chicken and turkey meat: Consumer exposure to multidrug-resistant Enterobacteriaceae including mcr-carriers, uropathogenic E. coli and high-risk lineages such as ST131. Int J Food Microbiol 2020; 331:108750. [PMID: 32559710 DOI: 10.1016/j.ijfoodmicro.2020.108750] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/10/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022]
Abstract
For the first time, this study evaluates consumer exposure via poultry meat to Enterobacteriaceae with capacity to develop severe extraintestinal infections by either bacterial virulence and/or antibiotic resistance traits. The characterization of 256 isolates and the assessment of five parameters, showed that 96 of 100 poultry meat samples from supermarkets of northwest Spain posed ≥ one potential risk: i) 96% carried Enterobacteriaceae resistant to antimicrobials of categories A (64% to monobactams) or B (95% to cephalosporins 3rd and 4rd- generation, quinolones and/or polymixins) of the new categorization of EMA. ii) More than one extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae species were recovered from 28% of poultry meat. iii) High-risk lineages of E. coli, including multidrug-resistant ST131-H22, were present in 62% of samples. iv) E. coli recovered from 25% of samples conformed the ExPEC status. v) E. coli from 17% of samples satisfied the UPEC status. Of note, the recovery from different samples of two E. coli CC10-A (CH11-54) carrying mcr-1.1-bearing IncX4 plasmids, and four E. coli CC10-A (eae-beta1) of the hybrid pathotype aEPEC/ExPEC. (ESBL)-producing K. pneumoniae were isolated from 27% of samples. In summary, poultry meat microbiota is a source of genetically diverse Enterobacteriaceae, resistant to relevant antimicrobials and potentially pathogenic for consumers.
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Affiliation(s)
- Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA). Instituto de Investigación del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain.; Department of Veterinary and Animal Sciences, Section of Veterinary Clinical Microbiology, University of Copenhagen, København, Denmark
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain..
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Zhu W, Fan Z, Qiu R, Chen L, Wei H, Hu B, Chen M, Wang F. Characterization of Pasteurella multocida isolates from rabbits in China. Vet Microbiol 2020; 244:108649. [PMID: 32402342 DOI: 10.1016/j.vetmic.2020.108649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 10/24/2022]
Abstract
Pasteurella multocida is the causative agent of a wide range of diseases (pasteurellosis) and is a zoonotic pathogen in humans. The molecular epidemiology of P. multocida from rabbits in some southern European countries has been characterized, and the associations of some populations with the respiratory niche or virulence factors have been suggested. However, the population structure of P. multocida from rabbits in China has not been well characterized. In this study, 30 P. multocida isolates from rabbits without epidemiological relations in China were clustered using mutilocus sequence typing (MLST). Then, the genotypes of virulence factors (capsule, lipopolysaccharides, HgbB, and PfhA) of these isolates were determined via multiplex PCR methods. Next, the virulence of the isolates in a mice model was established by determining the 50 % lethal dose. Finally, the associations between MLST types and the prevalence of genotypes, virulent strains, or clinical origins were characterized. The P. multocida isolates identified in this work included 3 major clonal complexes: CC9, CC74, and ST129. CC9 exhibited cpsA(F)L3, and was associated with a higher prevalence of rhinitis; CC74 exhibited cpsAL6, and was associated with higher prevalences of hgbB+pfhA- and pneumonia; ST129 exhibited cpsAL1, and was associated with higher prevalences of high-virulence strains and septicemia. The results provided insights into P. multocida from rabbits in China and suggested the use of strains from different populations in future P. multocida pathogenesis and vaccine studies.
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Affiliation(s)
- Weifeng Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China
| | - Zhiyu Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China
| | - Rulong Qiu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China
| | - Lu Chen
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; College of Animal Science, Tibet Agricultural & Animal Husbandry University, Linzhi, 860000, China
| | - Houjun Wei
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China
| | - Bo Hu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China
| | - Mengmeng Chen
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China
| | - Fang Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, 210014, China; National Center for Engineering Research of Veterinary Bio-products, Nanjing, 210014, China.
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Shiga toxin-producing Escherichia coli (STEC) shedding in a wild roe deer population. Vet Microbiol 2019; 239:108479. [PMID: 31767081 DOI: 10.1016/j.vetmic.2019.108479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 11/22/2022]
Abstract
Worldwide infections by Shiga toxin-producing Escherichia coli (STEC) in humans have been reported after consumption of mainly beef, but also deer meat. Not only the consumption of contaminated deer meat represents a risk, but also the transmission of STEC between deer and domestic animals should be considered. Within the framework of a telemetry study of roe deer (Capreolus capreolus) the aim was to analyse the occurrence of STEC. Due to the chance to sample some animals several times it was possible to obtain data on the repeated shedding of STEC in roe deer. In total 124 faeces or rectal swabs of 77 live trapped roe deer were collected. The isolates obtained were characterized for stx subtypes, different virulence genes, the so-called top-five serogroups, phylogenetic groups, PFGE-types and antimicrobial susceptibilities. The majority of roe deer were stx-positive whenever sampled. Twenty-eight animals were sampled more than once and were used to examine the duration of shedding STEC. The time interval of 6 persistently stx-negative tested animals was between 6 and 440d (median 49d, interquartile range (IQR) 17-258d). Ten animals excreted undistinguishable STEC strains in intervals between 4 and 778d (median 42d, IQR 22-79d). Most of the isolates were stx2b-positive, eae-negative and frequently ehlyA-positive. None of the isolates belonged to serogroup O26, O103, O111, O145 and O157, respectively. All isolates were sensitive to the antimicrobial substances tested. Although the duration of each shedding event could not be determined the results indicate long-term excretion of STEC in roe deer. This is an important consideration for the observance of good hygiene practice while field dressing of deer and preparing deer meat.
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Mortensen S, Johansen AE, Thøfner I, Christensen JP, Pors SE, Fresno AH, Møller-Jensen J, Olsen JE. Infectious potential of human derived uropathogenic Escherichia coli UTI89 in the reproductive tract of laying hens. Vet Microbiol 2019; 239:108445. [PMID: 31767071 DOI: 10.1016/j.vetmic.2019.108445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/24/2019] [Accepted: 10/03/2019] [Indexed: 12/18/2022]
Abstract
Avian pathogenic E. coli (APEC) and human uropathogenic E. coli (UPEC) harbour common virulence factors in spite of being associated with disease in different hosts. APEC strains have been shown to have zoonotic potential. In contrast, it is not known whether UPEC strains can cause infection in immunologically competent hens. The objective of the current study was to compare the ability of the well-characterized UPEC strain, UTI89, and the APEC strain, F149H1S2, to infect human and avian cells in culture and to cause salpingitis in an infection model in adult laying hens. In vitro characterization showed that the strains grew equally well in human urine, and both were able to infect human intestinal (Int407) and bladder (J82) epithelial cell lines, and they survived in avian macrophages (HD11) to the same extent. Groups of adult birds were inoculated with 108 bacteria directly into the oviduct using a surgical procedure. After an infection period of 48 h, bacterial load in the oviduct was determined by dilution series, and pathology was determined based on gross lesions and histological observations. Similar counts of UPEC UTI89 (ST95) and the APEC strain F149H1S2 (ST117) were obtained from tissues of infected birds, and salpingitis as evaluated by clinical score and histopathology was observed to a similar extent after infection with the two strains. Together, the results showed that UPEC UTI89 and APEC F149H1S2 have a similar potential for causing salpingitis in laying hens in the model used. No infection differences were observed between the UPEC UTI89 wild type and a mutant strain with knock-out of the well-known virulence gene, fimH, (UPEC UTI89ΔfimH), showing that the salpingitis model is not suitable for the detection of all UPEC virulence factors.
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Affiliation(s)
- Sisse Mortensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Andreas Eske Johansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Ida Thøfner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Jens Peter Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Susanne Elisabeth Pors
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Ana Herrero Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg, Denmark.
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Mamani R, Flament-Simon SC, García V, Mora A, Alonso MP, López C, García-Meniño I, Díaz-Jiménez D, Blanco JE, Blanco M, Blanco J. Sequence Types, Clonotypes, Serotypes, and Virotypes of Extended-Spectrum β-Lactamase-Producing Escherichia coli Causing Bacteraemia in a Spanish Hospital Over a 12-Year Period (2000 to 2011). Front Microbiol 2019; 10:1530. [PMID: 31379759 PMCID: PMC6646471 DOI: 10.3389/fmicb.2019.01530] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
The aim of the present study was to examine the prevalence and determine the molecular characteristics of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) causing bacteraemia in a Spanish Hospital over a 12-year period (2000 to 2011). As far as we know, this is the first study which has investigated and compared the serotypes, phylogroups, clonotypes, virotypes, and PFGE profiles of ST131 and non-ST131 clones of bacteraemia ESBL-EC isolates. Of the 2,427 E. coli bloodstream isolates, 96 (4.0%) were positive for ESBL production: 40 for CTX-M-15, 36 for CTX-M-14, eight for CTX-M-1, four for CTX-M-9, CTX-M-32, and SHV-12. The number of ESBL-EC increased from 1.0% during 2000 to 2005 to 5.5% during 2006-2011 (P < 0.001). The 96 ESBL-EC isolates belonged to 36 different STs. The commonest was ST131 (41 isolates), followed by ST58, ST354, ST393 and ST405 (four isolates each). Most CTX-M-15 isolates (87.5%, 35/40) were ST131, whereas the 36 CTX-M-14 isolates belonged to 23 different STs and only 3 (8.3%) of them were ST131. The 35 ST131 CTX-M-15-producing isolates belonged to the H30Rx subclone and 29 of them showed the virotype A. A drastic change in ST131 virotypes happened in 2011 due to the emergence of the virotypes E (sat, papGII, cnf1, hlyA, and kpsMII-K5) and F (sat, papGII, and kpsMII-K5) which displaced virotype A (afa/draBC, afa operon FM955459, sat, and kpsMII-K2). Although the 96 ESBL-EC isolates showed 21 O serogroups and 17 H flagellar antigens, 39 belonged to serotype O25b:H4 (ST131 isolates). The second most prevalent serotype (O15:H1) was found to be associated with another important high-risk clone (ST393). In conclusion, the ST131 was the most frequent sequence type, being the H30Rx subclone responsible for the significant increase of ESBL-EC isolates since 2006. Here, we report two new virotypes (E and F) of the H30Rx subclone emerged in 2011. Future molecular studies are needed to understand the dynamics of expansion of this successful high-risk subclone in order to prevent its spread and establish the importance of the two new virotypes.
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Affiliation(s)
- Rosalia Mamani
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Saskia Camille Flament-Simon
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Vanesa García
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - María Pilar Alonso
- Unidade de Microbioloxía Clínica, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Cecilia López
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dafne Díaz-Jiménez
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jesús E Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. coli, Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Hojabri Z, Mirmohammadkhani M, Darabi N, Arab M, Pajand O. Characterization of antibiotic-susceptibility patterns and virulence genes of five major sequence types of Escherichia coli isolates cultured from extraintestinal specimens: a 1-year surveillance study from Iran. Infect Drug Resist 2019; 12:893-903. [PMID: 31118697 PMCID: PMC6475099 DOI: 10.2147/idr.s199759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objectives Escherichia coli sequence types (STs) 69, 73, 95, 127, and 131 are major STs frequently causing extraintestinal infections. The prevalence of specific clones and their virulence and resistance profiles has not been described from Iran. The aim of this study was to characterize antimicrobial-susceptibility profiles and virulence traits of five major clones of E. coli recovered from human extraintestinal infections in Semnan, Iran. We compared these traits between major ST clones and also between O25b and O16 subgroups of the ST131 clone. Methods We characterized the five major ST clones among 335 collected E. coli isolates obtained from extraintestinal infections, and phylogenetic groups, antimicrobial susceptibility, and virulence/resistance-gene profiles of these major STs were studied. Results The highest rates of the multidrug-resistance phenotype were detected among ST131 (85.7%) and ST69 (41.7%), and trimethoprim/sulfamethoxazole resistance was detected significantly among the latter clone. Of the 151 isolates belonging to major ST clones, blaOXA-48 was detected among all except the ST127 clone, while blaNDM genes were harbored by 14 (9.2%) isolates, which all belonged to the ST131 clone. Aggregate virulence scores (median) of ST131 isolates (11) were slightly higher than ST69 (8.50) strains, but were lower than ST73 (16), ST95 (16), and ST127 (12.50) isolates. Principal-coordinate analysis revealed distinct virulence profiles with the ST131 clone. ST73, ST95 and ST131 were enriched with “urovirulence” traits, including phylogroup B2 and group B2-associated accessory traits (chuA, iutA, yfcV, papGII, usp, kpsMTII and malX) and the derived variables extraintestinal pathogenic E. coli and uropathogenic E. coli. In contrast, ST69 was depleted of these traits, but enriched with phylogroups D and E. Conclusion Our data emphasize that isolates of the ST131 clone have the ability to make a balance between resistance and virulence traits to establish a wider clone in extraintestinal pathogenic E. coli.
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Affiliation(s)
- Zoya Hojabri
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran,
| | - Majid Mirmohammadkhani
- Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran,
| | - Narges Darabi
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran,
| | - Maedeh Arab
- Student Research Committee, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Omid Pajand
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran, .,Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran,
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Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95. mSphere 2019; 4:4/1/e00333-18. [PMID: 30651401 PMCID: PMC6336079 DOI: 10.1128/msphere.00333-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection. Avian-pathogenic Escherichia coli (APEC) is a subgroup of extraintestinal pathogenic E. coli (ExPEC) presumed to be zoonotic and to represent an external reservoir for extraintestinal infections in humans, including uropathogenic E. coli (UPEC) causing urinary tract infections. Comparative genomics has previously been applied to investigate whether APEC and human ExPEC are distinct entities. Even so, whole-genome-based studies are limited, and large-scale comparisons focused on single sequence types (STs) are not available yet. In this study, comparative genomic analysis was performed on 323 APEC and human ExPEC genomes belonging to sequence type 95 (ST95) to investigate whether APEC and human ExPEC are distinct entities. Our study showed that APEC of ST95 did not constitute a unique ExPEC branch and was genetically diverse. A large genetic overlap between APEC and certain human ExPEC was observed, with APEC located on multiple branches together with closely related human ExPEC, including nearly identical APEC and human ExPEC. These results illustrate that certain ExPEC clones may indeed have the potential to cause infection in both poultry and humans. Previously described ExPEC-associated genes were found to be encoded on ColV plasmids. These virulence-associated plasmids seem to be crucial for ExPEC strains to cause avian colibacillosis and are strongly associated with strains of the mixed APEC/human ExPEC clusters. The phylogenetic analysis revealed two distinct branches consisting of exclusively closely related human ExPEC which did not carry the virulence-associated plasmids, emphasizing a lower avian virulence potential of human ExPEC in relation to an avian host. IMPORTANCE APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.
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Zhu Q, Dupont CL, Jones MB, Pham KM, Jiang ZD, DuPont HL, Highlander SK. Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. MICROBIOME 2018; 6:201. [PMID: 30409177 PMCID: PMC6225641 DOI: 10.1186/s40168-018-0579-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/17/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Travelers' diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease. RESULTS We performed a comprehensive amplicon and whole genome shotgun (WGS) metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers, all of which were negative for the known etiologic agents of TD based on standard microbiological and immunological assays. Abnormal and diverse taxonomic profiles in TD samples were revealed. WGS reads were assembled and the resulting contigs were visualized using multiple query types. A semi-manual workflow was applied to isolate independent genomes from metagenomic pools. A total of 565 genome bins were extracted, 320 of which were complete enough to be characterized as cellular genomes; 160 were viral genomes. We made predictions of the etiology of disease for many of the individual subjects based on the properties and features of the recovered genomes. Multiple patients with low-diversity metagenomes were predominated by one to several E. coli strains. Functional annotation allowed prediction of pathogenic type in many cases. Five patients were co-infected with E. coli and other members of Enterobacteriaceae, including Enterobacter, Klebsiella, and Citrobacter; these may represent blooms of organisms that appear following secretory diarrhea. New "dark matter" microbes were observed in multiple samples. In one, we identified a novel TM7 genome that phylogenetically clustered with a sludge isolate; it carries genes encoding potential virulence factors. In multiple samples, we observed high proportions of putative novel viral genomes, some of which form clusters with the ubiquitous gut virus, crAssphage. The total relative abundance of viruses was significantly higher in healthy travelers versus TD patients. CONCLUSION Our study highlights the strength of assembly-based metagenomics, especially the manually curated, visualization-assisted binning of contigs, in resolving unusual and under-characterized pathogenic profiles of human-associated microbiomes. Results show that TD may be polymicrobial, with multiple novel cellular and viral strains as potential players in the diarrheal disease.
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Affiliation(s)
- Qiyun Zhu
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
- Department of Pediatrics, University of California San Diego, 9500 Gillman Drive #0763, La Jolla, CA 92093 USA
| | | | - Marcus B. Jones
- Human Longevity, Inc., 4570 Executive Drive, La Jolla, CA 92121 USA
- Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591 USA
| | - Kevin M. Pham
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
- 2132 Calaveras Ave, Davis, CA 95616 USA
| | - Zhi-Dong Jiang
- University of Texas School of Public Health, 7000 Fannin St., Houston, TX 77030 USA
| | - Herbert L. DuPont
- University of Texas School of Public Health, 7000 Fannin St., Houston, TX 77030 USA
| | - Sarah K. Highlander
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037 USA
- Pathogen and Microbiome Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86005 USA
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Abstract
Resistance to last-line polymyxins mediated by the plasmid-borne mobile colistin resistance gene (mcr-1) represents a new threat to global human health. Here we present the complete genome sequence of an mcr-1-positive multidrug-resistant Escherichia coli strain (MS8345). We show that MS8345 belongs to serotype O2:K1:H4, has a large 241,164-bp IncHI2 plasmid that carries 15 other antibiotic resistance genes (including the extended-spectrum β-lactamase bla CTX-M-1) and 3 putative multidrug efflux systems, and contains 14 chromosomally encoded antibiotic resistance genes. MS8345 also carries a large ColV-like virulence plasmid that has been associated with E. coli bacteremia. Whole-genome phylogeny revealed that MS8345 clusters within a discrete clade in the sequence type 95 (ST95) lineage, and MS8345 is very closely related to the highly virulent O45:K1:H4 clone associated with neonatal meningitis. Overall, the acquisition of a plasmid carrying resistance to colistin and multiple other antibiotics in this virulent E. coli lineage is concerning and might herald an era where the empirical treatment of ST95 infections becomes increasingly more difficult.IMPORTANCE Escherichia coli ST95 is a globally disseminated clone frequently associated with bloodstream infections and neonatal meningitis. However, the ST95 lineage is defined by low levels of drug resistance amongst clinical isolates, which normally provides for uncomplicated treatment options. Here, we provide the first detailed genomic analysis of an E. coli ST95 isolate that has both high virulence potential and resistance to multiple antibiotics. Using the genome, we predicted its virulence and antibiotic resistance mechanisms, which include resistance to last-line antibiotics mediated by the plasmid-borne mcr-1 gene. Finding an ST95 isolate resistant to nearly all antibiotics that also has a high virulence potential is of major clinical importance and underscores the need to monitor new and emerging trends in antibiotic resistance development in this important global lineage.
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A Population-Based Surveillance Study of Shared Genotypes of Escherichia coli Isolates from Retail Meat and Suspected Cases of Urinary Tract Infections. mSphere 2018; 3:3/4/e00179-18. [PMID: 30111626 PMCID: PMC6094058 DOI: 10.1128/msphere.00179-18] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Community-acquired urinary tract infection caused by Escherichia coli is one of the most common infectious diseases in the United States, affecting approximately seven million women and costing approximately 11.6 billion dollars annually. In addition, antibiotic resistance among E. coli bacteria causing urinary tract infection continues to increase, which greatly complicates treatment. Identifying sources of uropathogenic E. coli and implementing prevention measures are essential. However, the reservoirs of uropathogenic E. coli have not been well defined. This study demonstrated that poultry sold in retail stores may serve as one possible source of uropathogenic E. coli. This finding adds to a growing body of evidence that suggests that urinary tract infection may be a food-borne disease. More research in this area can lead to the development of preventive strategies to control this common and costly infectious disease. There is increasing evidence that retail food may serve as a source of Escherichia coli that causes community-acquired urinary tract infections, but the impact of this source in a community is not known. We conducted a prospective, population-based study in one community to examine the frequency of recovery of uropathogenic E. coli genotypes from retail meat samples. We analyzed E. coli isolates from consecutively collected urine samples of patients suspected to have urinary tract infections (UTIs) at a university-affiliated health service and retail meat samples from the same geographic region. We genotyped all E. coli isolates by multilocus sequence typing (MLST) and tested them for antimicrobial susceptibility. From 2016 to 2017, we cultured 233 E. coli isolates from 230 (21%) of 1,087 urine samples and 177 E. coli isolates from 120 (28%) of 427 retail meat samples. Urine samples contained 61 sequence types (STs), and meat samples had 95 STs; 12 STs (ST10, ST38, ST69, ST80, ST88, ST101, ST117, ST131, ST569, ST906, ST1844, and ST2562) were common to both. Thirty-five (81%) of 43 meat isolates among the 12 STs were from poultry. Among 94 isolates in the 12 STs, 26 (60%) of 43 retail meat isolates and 15 (29%) of 51 human isolates were pan-susceptible (P < 0.005). We found that 21% of E. coli isolates from suspected cases of UTIs belonged to STs found in poultry. Poultry may serve as a possible reservoir of uropathogenic E. coli (UPEC). Additional studies are needed to demonstrate transmission pathways of these UPEC genotypes and their food sources. IMPORTANCE Community-acquired urinary tract infection caused by Escherichia coli is one of the most common infectious diseases in the United States, affecting approximately seven million women and costing approximately 11.6 billion dollars annually. In addition, antibiotic resistance among E. coli bacteria causing urinary tract infection continues to increase, which greatly complicates treatment. Identifying sources of uropathogenic E. coli and implementing prevention measures are essential. However, the reservoirs of uropathogenic E. coli have not been well defined. This study demonstrated that poultry sold in retail stores may serve as one possible source of uropathogenic E. coli. This finding adds to a growing body of evidence that suggests that urinary tract infection may be a food-borne disease. More research in this area can lead to the development of preventive strategies to control this common and costly infectious disease.
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Contribution of Healthy Chickens to Antimicrobial-ResistantEscherichia coliAssociated with Human Extraintestinal Infections in Egypt. Vector Borne Zoonotic Dis 2018; 18:408-416. [DOI: 10.1089/vbz.2017.2237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Comparative ecology of Escherichia coli in endangered Australian sea lion (Neophoca cinerea) pups. INFECTION GENETICS AND EVOLUTION 2018; 62:262-269. [PMID: 29730275 DOI: 10.1016/j.meegid.2018.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 02/07/2023]
Abstract
The dissemination of human-associated bacteria into the marine environment has the potential to expose wildlife populations to atypical microbes that can alter the composition of the gut microbiome or act as pathogens. The objective of the study was to determine whether endangered Australian sea lion (Neophoca cinerea) pups from two South Australian colonies, Seal Bay, Kangaroo Island and Dangerous Reef, Spencer Gulf, have been colonised by human-associated Escherichia coli. Faecal samples (n = 111) were collected to isolate E. coli, and molecular screening was applied to assign E. coli isolates (n = 94) to phylotypes and detect class 1 integrons; mobile genetic elements that confer resistance to antimicrobial agents. E. coli phylotype distribution and frequency differed significantly between colonies with phylotypes B2 and D being the most abundant at Seal Bay, Kangaroo Island (55% and 7%) and Dangerous Reef, Spencer Gulf (36% and 49%), respectively. This study reports the first case of antimicrobial resistant E. coli in free-ranging Australian sea lions through the identification of class 1 integrons from an individual pup at Seal Bay. A significant relationship between phylotype and total white cell count (WCC) was identified, with significantly higher WCC seen in pups with human-associated phylotypes at Dangerous Reef. The difference in phylotype distribution and presence of human-associated E. coli suggests that proximity to human populations can influence sea lion gut microbiota. The identification of antimicrobial resistance in a free-ranging pinniped population provides crucial information concerning anthropogenic influences in the marine environment.
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Persistent Pandemic Lineages of Uropathogenic Escherichia coli in a College Community from 1999 to 2017. J Clin Microbiol 2018; 56:JCM.01834-17. [PMID: 29436416 DOI: 10.1128/jcm.01834-17] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/01/2018] [Indexed: 01/11/2023] Open
Abstract
The incidence of drug-resistant community-acquired urinary tract infections (CA-UTI) continues to increase worldwide. In 1999 to 2000, a single lineage of uropathogenic Escherichia coli (UPEC) sequence type 69 (ST69) caused 51% of trimethoprim-sulfamethoxazole-resistant UTI in a Northern California university community. We compared the clonal distributions of UPEC and its impact on antimicrobial resistance prevalence in the same community during two periods separated by 17 years. We analyzed E. coli isolates from urine samples from patients with symptoms of UTI who visited a health service between September 2016 and May 2017 and compared them to UPEC isolates collected similarly between October 1999 and March 2000. Isolates were tested for antimicrobial drug susceptibility and genotyped by multilocus sequence typing. In 1999 to 2000, strains belonging to ST95, ST127, ST73, ST69, ST131, and ST10 caused 125 (56%) of 225 UTI cases, while the same STs caused 148 (64%) of 233 UTI cases in 2016 to 2017. The frequencies of ampicillin resistance and ciprofloxacin resistance rose from 24.4% to 41.6% (P < 0.001) and from 0.9% to 5.1% (P < 0.003), respectively. The six STs accounted for 78.6% and 72.7% of these increases, respectively. Prevalence of drug-resistant UTI in this community appears to be largely influenced by a small set of dominant UPEC STs circulating in the same community 17 years apart. Further research to determine the origin and reasons for persistence of these dominant genotypes is necessary to combat antimicrobial-resistant CA-UTI.
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Impact of human-associated Escherichia coli clonal groups in Antarctic pinnipeds: presence of ST73, ST95, ST141 and ST131. Sci Rep 2018; 8:4678. [PMID: 29549276 PMCID: PMC5856829 DOI: 10.1038/s41598-018-22943-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/16/2018] [Indexed: 01/13/2023] Open
Abstract
There is growing concern about the spreading of human microorganisms in relatively untouched ecosystems such as the Antarctic region. For this reason, three pinniped species (Leptonychotes weddellii, Mirounga leonina and Arctocephalus gazella) from the west coast of the Antartic Peninsula were analysed for the presence of Escherichia spp. with the recovery of 158 E. coli and three E. albertii isolates. From those, 23 harboured different eae variants (α1, β1, β2, ε1, θ1, κ, ο), including a bfpA-positive isolate (O49:H10-A-ST206, eae-k) classified as typical enteropathogenic E. coli. Noteworthy, 62 of the 158 E. coli isolates (39.2%) exhibited the ExPEC status and 27 (17.1%) belonged to sequence types (ST) frequently occurring among urinary/bacteremia ExPEC clones: ST12, ST73, ST95, ST131 and ST141. We found similarities >85% within the PFGE-macrorrestriction profiles of pinniped and human clinic O2:H6-B2-ST141 and O16:H5/O25b:H4-B2-ST131 isolates. The in silico analysis of ST131 Cplx genomes from the three pinnipeds (five O25:H4-ST131/PST43-fimH22-virotype D; one O16:H5-ST131/PST506-fimH41; one O25:H4-ST6252/PST9-fimH22-virotype D1) identified IncF and IncI1 plasmids and revealed high core-genome similarities between pinniped and human isolates (H22 and H41 subclones). This is the first study to demonstrate the worrisome presence of human-associated E. coli clonal groups, including ST131, in Antarctic pinnipeds.
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Chakraborty A, Adhikari P, Shenoy S, Saralaya V. Molecular characterisation of uropathogenic Escherichia coli isolates at a tertiary care hospital in South India. Indian J Med Microbiol 2018; 35:305-310. [PMID: 28681829 DOI: 10.4103/ijmm.ijmm_14_291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) express a multitude of virulence factors (VFs) to break the inertia of the mucosal barrier of the urinary tract. The aim of the present study was undertaken to characterised the UPEC strains and to correlate carriage of specific virulence markers with different phylogroups and also to correlate these findings with clinical outcome of patients. A total of 156 non-repeated, clinically significant UPEC isolates were studied. Virulent genes were determined by two set of multiplex polymerase chain reaction (PCR). Phylogenetic analysis was performed by triplex PCR methods. Antibiograms and patient's clinical outcomes were collected in a structured pro forma. Of the 156 patients infected by UPEC strains with significant bacterial counts the most common predisposing factors were diabetes (45.5%) followed by carcinoma (7%). On analysis of the VF genes of the isolates, a majority of strains (140; 90%) were possessing the fimH gene followed by iutA (98; 63%), papC (76; 49%), cnf1 (46; 29.5%), hlyA (45; 29%) and neuC (8; 5%), respectively. On phylogenetic analysis, 27 (17%) isolates were belong to phylogroup A, 16 (10%) strains to Group B1, 59 (38%) were from Group B2 and 54 (35%) were from Group D. High prevalence of antibiotic resistance was observed among the isolates. The incidence of papC, cnf1 and hlyA was significantly higher (P < 0.05) among the isolates from relapse patients. Our findings indicate that virulent as well as commensal strains are capable of causing urinary tract infection. Virulence genes as well as patients-related factors are equally responsible for the development of infections and also that virulence genes may help such isolates to persist even with appropriate chemotherapy and be responsible for recurrent infections.
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Affiliation(s)
- Arindam Chakraborty
- Department of Microbiology, Motilal Nehru Medical College, Allahabad, Uttar Pradesh, India
| | - Prabha Adhikari
- Department of Medicine, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - Shalini Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - Vishwas Saralaya
- Department of Microbiology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
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Cunha MPV, Saidenberg AB, Moreno AM, Ferreira AJP, Vieira MAM, Gomes TAT, Knöbl T. Pandemic extra-intestinal pathogenic Escherichia coli (ExPEC) clonal group O6-B2-ST73 as a cause of avian colibacillosis in Brazil. PLoS One 2017; 12:e0178970. [PMID: 28594893 PMCID: PMC5464619 DOI: 10.1371/journal.pone.0178970] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/22/2017] [Indexed: 12/25/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) represent an emerging pathogen, with pandemic strains increasingly involved in cases of urinary tract infections (UTIs), bacteremia, and meningitis. In addition to affecting humans, the avian pathotype of ExPEC, avian pathogenic E. coli (APEC), causes severe economic losses to the poultry industry. Several studies have revealed overlapping characteristics between APEC and human ExPEC, leading to the hypothesis of a zoonotic potential of poultry strains. However, the description of certain important pandemic clones, such as Sequence Type 73 (ST73), has not been reported in food sources. We characterized 27 temporally matched APEC strains from diverse poultry farms in Brazil belonging to the O6 serogroup because this serogroup is frequently described as a causal factor in UTI and septicemia in humans in Brazil and worldwide. The isolates were genotypically characterized by identifying ExPEC virulence factors, phylogenetically tested by phylogrouping and multilocus sequence type (MLST) analysis, and compared to determine their similarity employing the pulsed field gel electrophoresis (PFGE) technique. The strains harbored a large number of virulence determinants that are commonly described in uropathogenic E. coli (UPEC) and sepsis associated E. coli (SEPEC) strains and, to a lesser extent in neonatal meningitis associated E. coli (NMEC), such as pap (85%), sfa (100%), usp (100%), cnf1 (22%), kpsMTII (66%), hlyA (52%), and ibeA (4%). These isolates also yielded a low prevalence of some genes that are frequently described in APEC, such as iss (37%), tsh, ompT, and hlyF (8% each), and cvi/cva (0%). All strains were classified as part of the B2 phylogroup and sequence type 73 (ST73), with a cluster of 25 strains showing a clonal profile by PFGE. These results further suggest the zoonotic potential of some APEC clonal lineages and their possible role in the epidemiology of human ExPEC, in addition to providing the first description of the O6-B2-ST73 clonal group in poultry.
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Affiliation(s)
- Marcos Paulo Vieira Cunha
- Department of Pathology, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Andre Becker Saidenberg
- Department of Pathology, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Andrea Micke Moreno
- Department of Preventive Veterinary Medicine, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | | | - Mônica Aparecida Midolli Vieira
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Terezinha Knöbl
- Department of Pathology, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
- * E-mail:
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Delannoy S, Beutin L, Mariani-Kurkdjian P, Fleiss A, Bonacorsi S, Fach P. The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters. Front Cell Infect Microbiol 2017; 7:30. [PMID: 28224115 PMCID: PMC5293828 DOI: 10.3389/fcimb.2017.00030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/23/2017] [Indexed: 01/10/2023] Open
Abstract
Escherichia coli strains belonging to serogroups O1 and O2 are frequently associated with human infections, especially extra-intestinal infections such as bloodstream infections or urinary tract infections. These strains can be associated with a large array of flagellar antigens. Because of their frequency and clinical importance, a reliable detection of E. coli O1 and O2 strains and also the frequently associated K1 capsule is important for diagnosis and source attribution of E. coli infections in humans and animals. By sequencing the O-antigen clusters of various O1 and O2 strains we showed that the serogroups O1 and O2 are encoded by different sets of O-antigen encoding genes and identified potentially new O-groups. We developed qPCR-assays to detect the various O1 and O2 variants and the K1-encoding gene. These qPCR assays proved to be 100% sensitive and 100% specific and could be valuable tools for the investigations of zoonotic and food-borne infection of humans with O1 and O2 extra-intestinal (ExPEC) or Shiga toxin-producing E. coli (STEC) strains.
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Affiliation(s)
- Sabine Delannoy
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Lothar Beutin
- National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR)Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Institute for Biology - Microbiology, Freie Universität BerlinBerlin, Germany
| | - Patricia Mariani-Kurkdjian
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Aubin Fleiss
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Stéphane Bonacorsi
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Patrick Fach
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
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Chakraborty A, Saralaya V, Adhikari P, Shenoy S. Virulence property, phylogenetic background, and resistance pattern of Escherichia coli isolates from wound infections. CHRISMED JOURNAL OF HEALTH AND RESEARCH 2017. [DOI: 10.4103/cjhr.cjhr_48_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Madoshi BP, Kudirkiene E, Mtambo MMA, Muhairwa AP, Lupindu AM, Olsen JE. Characterisation of Commensal Escherichia coli Isolated from Apparently Healthy Cattle and Their Attendants in Tanzania. PLoS One 2016; 11:e0168160. [PMID: 27977751 PMCID: PMC5158034 DOI: 10.1371/journal.pone.0168160] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/26/2016] [Indexed: 12/13/2022] Open
Abstract
While pathogenic types of Escherichia coli are well characterized, relatively little is known about the commensal E. coli flora. In the current study, antimicrobial resistance in commensal E. coli and distribution of ERIC-PCR genotypes among isolates of such bacteria from cattle and cattle attendants on cattle farms in Tanzania were investigated. Seventeen E. coli genomes representing different ERIC-PCR types of commensal E. coli were sequenced in order to determine their possible importance as a reservoir for both antimicrobial resistance genes and virulence factors. Both human and cattle isolates were highly resistant to tetracycline (40.8% and 33.1%), sulphamethazole-trimethoprim (49.0% and 8.8%) and ampicillin (44.9% and 21.3%). However, higher proportion of resistant E. coli and higher frequency of resistance to more than two antimicrobials was found in isolates from cattle attendants than isolates from cattle. Sixteen out of 66 ERIC-PCR genotypes were shared between the two hosts, and among these ones, seven types contained isolates from cattle and cattle attendants from the same farm, suggesting transfer of strains between hosts. Genome-wide analysis showed that the majority of the sequenced cattle isolates were assigned to phylogroups B1, while human isolates represented phylogroups A, C, D and E. In general, in silico resistome and virulence factor identification did not reveal differences between hosts or phylogroups, except for lpfA and iss found to be cattle and B1 phylogroup specific. The most frequent plasmids replicon genes found in strains from both hosts were of IncF type, which are commonly associated with carriage of antimicrobial and virulence genes. Commensal E. coli from cattle and attendants were found to share same genotypes and to carry antimicrobial resistance and virulence genes associated with both intra and extraintestinal E. coli pathotypes.
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Affiliation(s)
- Balichene P. Madoshi
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Livestock Training Agency – Mpwapwa Campus, Mpwapwa, Dodoma
| | - Egle Kudirkiene
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Madundo M. A. Mtambo
- Tanzania Industrial Research Developments Organisation, TIRDO Complex, Dar es Salaam, Tanzania
| | - Amandus P. Muhairwa
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Athumani M. Lupindu
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - John E. Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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Abstract
The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.
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Giray B, Uçar FB, Aydemir SŞ. Genotypic analysis of Escherichia coli strains that cause urosepsis in the Aegean region. Turk J Med Sci 2016; 46:1518-1527. [PMID: 27966323 DOI: 10.3906/sag-1507-114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/09/2016] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND/AIM The aim of this study was to characterize strains genotypically, to determine their phylogenetic relationships, to investigate the presence of the papG gene, and to compare their antibiotic susceptibility test results. MATERIALS AND METHODS Seventy pathogenic E. coli strains were isolated from both urine and blood cultures of patients with the preliminary diagnosis of urosepsis who were referred to the Ege University Faculty of Medicine, Bacteriology Laboratory of Medical Microbiology Department in İzmir. All of these strains were examined for the papG gene and phylogenetic groups with the multiplex polymerase chain reaction technique. Pulsed-field gel electrophoresis and multilocus sequence typing (MLST) were used for epidemiologic analysis. RESULTS Phylogenetically, it was found that 16 belonged to group B2, 31 belonged to group D, 15 belonged to group A, and 7 belonged to group B1. One strain was not identified as belonging to a group. papG genes were found in 26 of 70 E. coli strains. Thirty urosepsis pathogenic E. coli strains were analyzed with MLST. Twenty-two strains were identified as new STs. CONCLUSION These findings are extremely important for Turkey and these new 22 strains should be investigated in more detail because they are new and have the potential to lead to infections.
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Affiliation(s)
- Betül Giray
- Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, İzmir, Turkey
| | - Füsun Bahriye Uçar
- Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, İzmir, Turkey
| | - Sabire Şöhret Aydemir
- Department of Medical Microbiology, Faculty of Medicine, Ege University, İzmir, Turkey
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Liu H, Chen L, Si W, Wang C, Zhu F, Li G, Liu S. Physiology and pathogenicity of cpdB deleted mutant of avian pathogenic Escherichia coli. Res Vet Sci 2016; 111:21-25. [PMID: 28266315 DOI: 10.1016/j.rvsc.2016.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 09/21/2016] [Accepted: 11/16/2016] [Indexed: 11/18/2022]
Abstract
Avian colibacillosis is one of the most common infectious diseases caused partially or entirely by avian pathogenic Escherichia coli (APEC) in birds. In addition to spontaneous infection, APEC can also cause secondary infections that result in greater severity of illness and greater losses to the poultry industry. In order to assess the role of 2', 3'-cyclic phosphodiesterase (cpdB) in APEC on disease physiology and pathogenicity, an avian pathogenic Escherichia coli-34 (APEC-34) cpdB mutant was obtained using the Red system. The cpdB mutant grew at a slower rate than the natural strain APEC-34. Scanning electron microscopy (SEM) indicated that the bacteria of the cpdB mutant were significantly longer than the bacteria observed in the natural strain (P<0.01), and that the width of the cpdB mutant was significantly smaller than its natural counterpart (P<0.01). In order to evaluate the role of cpdB in APEC in the colonization of internal organs (lung, liver and spleen) in poultry, seven-day-old SPF chicks were infected with 109CFU/chick of the cpdB mutant or the natural strain. No colonizations of cpdB mutants were observed in the internal organs 10days following the infection, though numerous natural strains were observed at 20days following infection. Additionally, the relative expression of division protein ftsZ, outer membrane protein A ompA, ferric uptake regulator fur and tryptophanase tnaA genes in the mutant strain were all significantly lower than in the natural strain (P<0.05 or P<0.01). These results suggested that cpdB is involved in the long-term colonization of APEC in the internal organs of the test subjects. The deletion of the cpdB gene also significantly affected the APEC growth and morphology.
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Affiliation(s)
- Huifang Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Disease of Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China; Northeast Agricultural University, Harbin, China
| | - Liping Chen
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Disease of Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China
| | - Wei Si
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Disease of Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China
| | - Chunlai Wang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Disease of Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China
| | - Fangna Zhu
- Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, China
| | - Guangxing Li
- Northeast Agricultural University, Harbin, China.
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Disease of Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China.
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Abstract
Several potential reservoirs for the Escherichia coli strains that cause most human extraintestinal infections (extraintestinal pathogenic E. coli; ExPEC) have been identified, including the human intestinal tract and various non-human reservoirs, such as companion animals, food animals, retail meat products, sewage, and other environmental sources. Understanding ExPEC reservoirs, chains of transmission, transmission dynamics, and epidemiologic associations will assist greatly in finding ways to reduce the ExPEC-associated disease burden. The need to clarify the ecological behavior of ExPEC is all the more urgent because environmental reservoirs may contribute to acquisition of antimicrobial resistance determinants and selection for and amplification of resistant ExPEC. In this chapter, we review the evidence for different ExPEC reservoirs, with particular attention to food and food animals, and discuss the public health implications of these reservoirs for ExPEC dissemination and transmission.
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Iguchi A, Iyoda S, Seto K, Nishii H, Ohnishi M, Mekata H, Ogura Y, Hayashi T. Six Novel O Genotypes from Shiga Toxin-Producing Escherichia coli. Front Microbiol 2016; 7:765. [PMID: 27242776 PMCID: PMC4873512 DOI: 10.3389/fmicb.2016.00765] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/06/2016] [Indexed: 11/13/2022] Open
Abstract
Serotyping is one of the typing techniques used to classify strains within the same species. O-serogroup diversification shows a strong association with the genetic diversity of O-antigen biosynthesis genes. In a previous study, based on the O-antigen biosynthesis gene cluster (O-AGC) sequences of 184 known Escherichia coli O serogroups (from O1 to O187), we developed a comprehensive and practical molecular O serogrouping (O genotyping) platform using a polymerase chain reaction (PCR) method, named E. coli O-genotyping PCR. Although, the validation assay using the PCR system showed that most of the tested strains were successfully classified into one of the O genotypes, it was impossible to classify 6.1% (35/575) of the strains, suggesting the presence of novel O genotypes. In this study, we conducted sequence analysis of O-AGCs from O-genotype untypeable Shiga toxin-producing E. coli (STEC) strains and identified six novel O genotypes; OgN1, OgN8, OgN9, OgN10, OgN12 and OgN31, with unique wzx and/or wzy O-antigen processing gene sequences. Additionally, to identify these novel O-genotypes, we designed specific PCR primers. A screen of O genotypes using O-genotype untypeable strains showed 13 STEC strains were classified into five novel O genotypes. The O genotyping at the molecular level of the O-AGC would aid in the characterization of E. coli isolates and will assist future studies in STEC epidemiology and phylogeny.
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Affiliation(s)
- Atsushi Iguchi
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki Miyazaki, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases Tokyo, Japan
| | - Kazuko Seto
- Division of Bacteriology, Osaka Prefectural Institute of Public Health Osaka, Japan
| | - Hironobu Nishii
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki Miyazaki, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases Tokyo, Japan
| | - Hirohisa Mekata
- Organization for Promotion of Tenure Track, University of MiyazakiMiyazaki, Japan; Center for Animal Disease Control, University of MiyazakiMiyazaki, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University Fukuoka, Japan
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Chakraborty A, Adhikari P, Shenoy S, Saralaya V. Virulence factor profiles, phylogenetic background, and antimicrobial resistance pattern of lactose fermenting and nonlactose fermenting Escherichia coli from extraintestinal sources. INDIAN J PATHOL MICR 2016; 59:180-4. [DOI: 10.4103/0377-4929.182032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Clonal relationship between human and avian ciprofloxacin-resistant Escherichia coli isolates in North-Eastern Algeria. Eur J Clin Microbiol Infect Dis 2015; 35:227-34. [PMID: 26634353 DOI: 10.1007/s10096-015-2534-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
The objectives of this study were to determine rates, patterns, and mechanisms of antibiotic resistance, and to assess connections between chicken commensal, human commensal, and pathogenic ciprofloxacin-resistant Escherichia coli isolates. All E. coli isolates collected from chickens, their farmers, and patients in the Constantine region (North-east Algeria) were analyzed for bla and plasmid-mediated quinolone resistance (PMQR) gene contents, phylogroups, Rep-PCR profiles, and multilocus sequence types. A high prevalence of resistance to fluoroquinolones (51.4 % to ciprofloxacin) was recorded in avian isolates. Of these, 22.2 % carried the aac(6')-Ib-cr gene, whereas lower resistance levels to these antibiotics were recorded in chicken farmers' isolates. None of the commensal isolates harbored the qnr, qepA, or oqxAB genes. One human pathogenic isolate was ertapenem-resistant and harbored the bla OXA-48 gene, 84 showed an extended-spectrum β-lactamase phenotype, with bla CTX-M-15 gene prevalent in 87.2 % of them. Seventy isolates were resistant to fluoroquinolones, with aac(6')-Ib-cr present in 72.8 %, qnrB in 5.7 %, and qnrS in 10 %. Three Rep-PCR profiles were common to chicken commensal and human pathogenic isolates (phylogroups D and B1; ST21, ST48, and ST471 respectively); one was found in both chicken and chicken-farmer commensal strains (D; ST108), while another profile was identified in a chicken-farmer commensal strain and a human pathogenic one (B1; ST19). These findings suggest clonal and epidemiologic links between chicken and human ciprofloxacin-resistant E. coli isolates and the important role that poultry may play in the epidemiology of human E. coli infections in the Constantine region.
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Damborg P, Morsing MK, Petersen T, Bortolaia V, Guardabassi L. CTX-M-1 and CTX-M-15-producing Escherichia coli in dog faeces from public gardens. Acta Vet Scand 2015; 57:83. [PMID: 26608707 PMCID: PMC4660786 DOI: 10.1186/s13028-015-0174-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/18/2015] [Indexed: 11/25/2022] Open
Abstract
Background Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are increasingly reported in dogs. The objective of this study was to provide data on the prevalence of ESBL-producing E. coli in dog faecal deposits in public gardens. Results A total of 209 faecal deposits collected in nine public gardens in Copenhagen, Denmark were screened by selective enrichment followed by plating on MacConkey agar supplemented with cefotaxime. Presumptive ESBL-producing E. coli were confirmed by MALDI-TOF MS and polymerase chain reaction (PCR) for detection of common cefotaxime resistance determinants (blaTEM, blaSHV, blaCTX-M and blaCMY-2). ESBL-producers were further characterized by multilocus sequence typing (MLST) and antimicrobial susceptibility testing using broth microdilution. Plasmids harbouring ESBL genes were characterized by S1 nuclease pulsed field gel electrophoresis, PCR-based replicon typing, and pMLST. Cefotaxime-resistant E. coli were detected in four (1.9 %) samples. Three samples harboured CTX-M-1-producing isolates, and one sample contained two CTX-M-15-producing isolates displaying distinct colony morphology. All isolates belonged to distinct sequence types (STs), including one E. coli lineage previously associated to a human-specific pathotype (ST59). blaCTX-M-1 was carried on IncI1 plasmids classified as ST3 or ST58 by pMLST, whereas blaCTX-M-15 was located on IncF/Y and non-typeable plasmids in the two strains isolated from the same sample. Conclusions The study shows that dog faeces are a vector for dissemination of CTX-M-producing E. coli within urban areas. The risk derived from human exposure to dog faeces in public gardens depends on the prevalence of these bacteria in the local dog population as well as on the owners’ practice to remove and dispose their dog’s faeces.
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Alkeskas A, Ogrodzki P, Saad M, Masood N, Rhoma NR, Moore K, Farbos A, Paszkiewicz K, Forsythe S. The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes. BMC Infect Dis 2015; 15:449. [PMID: 26497222 PMCID: PMC4620641 DOI: 10.1186/s12879-015-1210-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/13/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The most common cause of Gram-negative bacterial neonatal meningitis is E. coli K1. It has a mortality rate of 10-15 %, and neurological sequelae in 30-50 % of cases. Infections can be attributable to nosocomial sources, however the pre-colonisation of enteral feeding tubes has not been considered as a specific risk factor. METHODS Thirty E. coli strains, which had been isolated in an earlier study, from the residual lumen liquid and biofilms of neonatal nasogastric feeding tubes were genotyped using pulsed-field gel electrophoresis, and 7-loci multilocus sequence typing. Potential pathogenicity and biofilm associated traits were determined using specific PCR probes, genome analysis, and in vitro tissue culture assays. RESULTS The E. coli strains clustered into five pulsotypes, which were genotyped as sequence types (ST) 95, 73, 127, 394 and 2076 (Achman scheme). The extra-intestinal pathogenic E. coli (ExPEC) phylogenetic group B2 ST95 serotype O1:K1:NM strains had been isolated over a 2 week period from 11 neonates who were on different feeding regimes. The E. coli K1 ST95 strains encoded for various virulence traits associated with neonatal meningitis and extracellular matrix formation. These strains attached and invaded intestinal, and both human and rat brain cell lines, and persisted for 48 h in U937 macrophages. E. coli STs 73, 394 and 2076 also persisted in macrophages and invaded Caco-2 and human brain cells, but only ST394 invaded rat brain cells. E. coli ST127 was notable as it did not invade any cell lines. CONCLUSIONS Routes by which E. coli K1 can be disseminated within a neonatal intensive care unit are uncertain, however the colonisation of neonatal enteral feeding tubes may be one reservoir source which could constitute a serious health risk to neonates following ingestion.
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Affiliation(s)
- Aldukali Alkeskas
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Pauline Ogrodzki
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Mohamed Saad
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Naqash Masood
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Nasreddin R Rhoma
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Karen Moore
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, Exeter, EX4 4QD, UK.
| | - Audrey Farbos
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, Exeter, EX4 4QD, UK.
| | - Konrad Paszkiewicz
- Wellcome Trust Biomedical Informatics Hub, Biosciences, Stocker Road, University of Exeter, Exeter, EX4 4QD, UK.
| | - Stephen Forsythe
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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Wijetunge DSS, Gongati S, DebRoy C, Kim KS, Couraud PO, Romero IA, Weksler B, Kariyawasam S. Characterizing the pathotype of neonatal meningitis causing Escherichia coli (NMEC). BMC Microbiol 2015; 15:211. [PMID: 26467858 PMCID: PMC4606507 DOI: 10.1186/s12866-015-0547-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/02/2015] [Indexed: 11/26/2022] Open
Abstract
Background Neonatal meningitis-causing Escherichia coli (NMEC) is the predominant Gram-negative bacterial pathogen associated with meningitis in newborn infants. High levels of heterogeneity and diversity have been observed in the repertoire of virulence traits and other characteristics among strains of NMEC making it difficult to define the NMEC pathotype. The objective of the present study was to identify genotypic and phenotypic characteristics of NMEC that can be used to distinguish them from commensal E. coli. Methods A total of 53 isolates of NMEC obtained from neonates with meningitis and 48 isolates of fecal E. coli obtained from healthy individuals (HFEC) were comparatively evaluated using five phenotypic (serotyping, serum bactericidal assay, biofilm assay, antimicorbial susceptibility testing, and in vitro cell invasion assay) and three genotypic (phylogrouping, virulence genotyping, and pulsed-field gel electrophoresis) methods. Results A majority (67.92 %) of NMEC belonged to B2 phylogenetic group whereas 59 % of HFEC belonged to groups A and D. Serotyping revealed that the most common O and H types present in NMEC tested were O1 (15 %), O8 (11.3 %), O18 (13.2 %), and H7 (25.3 %). In contrast, none of the HFEC tested belonged to O1 or O18 serogroups. The most common serogroup identified in HFEC was O8 (6.25 %). The virulence genotyping reflected that more than 70 % of NMEC carried kpsII, K1, neuC, iucC, sitA, and vat genes with only less than 27 % of HFEC possessing these genes. All NMEC and 79 % of HFEC tested were able to invade human cerebral microvascular endothelial cells. No statistically significant difference was observed in the serum resistance phenotype between NMEC and HFEC. The NMEC strains demonstrated a greater ability to form biofilms in Luria Bertani broth medium than did HFEC (79.2 % vs 39.9 %). Conclusion The results of our study demonstrated that virulence genotyping and phylogrouping may assist in defining the potential NMEC pathotype. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0547-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D S S Wijetunge
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 115 Henning Bldg, University Park, Pennsylvania, USA.
| | - S Gongati
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 115 Henning Bldg, University Park, Pennsylvania, USA.
| | - C DebRoy
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.
| | - K S Kim
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - P O Couraud
- Department of Cell Biology, University of Paris Descartes, Paris, France.
| | - I A Romero
- Department of Biological Sciences, Open University, Milton Keynes, UK.
| | - B Weksler
- Department of Medicine, Weill Cornell Medical College in New York, New York, USA.
| | - S Kariyawasam
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, 115 Henning Bldg, University Park, Pennsylvania, USA. .,Center for Molecular Immunology and Infectious Disease, Pennsylvania State University, University Park, Pennsylvania, USA.
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Chakraborty A, Adhikari P, Shenoy S, Saralaya V. Genomic analysis and clinical importance of Escherichia coli isolate from patients with sepsis. INDIAN J PATHOL MICR 2015; 58:22-6. [PMID: 25673586 DOI: 10.4103/0377-4929.151161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
CONTEXT Escherichia coli is a major cause of bloodstream infections and death due to sepsis. Bacteremic isolates harbor a significantly greater repertoire of virulence factors (VFs) in contrast with commensal E. coli isolates. AIMS The aim was to determine the relationships between E. coli VFs, phylogenetic groups, and their clinical importance. SETTINGS AND DESIGN This descriptive study was carried out in a multi-specialty tertiary care hospital. MATERIALS AND METHODS Escherichia coli isolates from consecutive episodes of bacteremia in 100 patients were screened for their VFs, phylogenetic group, and their effect on patient's clinical outcome. Virulence genes of all isolates were determined by multiplex polymerase chain reaction (PCR). Phylogenetic analysis was performed by triplex PCR methods. Estimation of risk of death was calculated using APACHE score II calculator. RESULTS Of the 100 patients, the most common predisposing factors were diabetes (42%), followed by carcinoma (23%). On analysis of the VF genes of the isolates, a majority of strains (88%) were possessing the fimH gene followed by iutA (76%), papC (44%), cnf1 (16%), hlyA (16%) and neuC (5%) respectively. Phylogenetic analysis revealed that 25 (25%) isolates belonged to phylogroup A, 8(8%) strains to group B1, 30 (30%) were from group B2 and 37 (37%) were from group D. The incidence of iutA gene was significant in higher APACHE II score group. CONCLUSIONS Our findings indicate that virulent as well as commensal strains are capable of causing sepsis. Host related predisposing factors, adherence factors, and iron uptake are essential for the survival of the sepsis inducing strains.
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Affiliation(s)
- Arindam Chakraborty
- Department of Microbiology, Government Medical College, Ambedkar Nagar, Uttar Pradesh, India
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Abdi HA, Rashki Ghalehnoo M. Virulence Genes, Genetic Diversity, Antimicrobial Susceptibility and Phylogenetic Background of Escherichia coli Isolates. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2015. [DOI: 10.17795/ijep.25692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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