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Ko S, Nguyen HMT, Lee W, Kim D. Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms. Comput Struct Biotechnol J 2024; 23:3040-3049. [PMID: 39175796 PMCID: PMC11340603 DOI: 10.1016/j.csbj.2024.07.017] [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: 02/29/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/24/2024] Open
Abstract
Pathogenic Escherichia coli (E. coli) strains are distinguished by their diverse virulence factors, which contribute to a wide spectrum of diseases. These pathogens evolve through the horizontal transfer of virulence factors, resulting in the emergence of hybrid pathotypes with complex and heterogeneous characteristics. Recognizing their profound impact on public health, this study introduces the PIP-eco pipeline, a comprehensive analytical tool designed for the precise identification and characterization of E. coli pathotypes. This PIP-eco pipeline advances beyond traditional molecular techniques by facilitating detailed analysis of both single and hybrid pathotypes. It integrates targeted marker gene analysis, virulence factor-based phylogenetic analysis, and pathogenicity islands (PAIs) profiling to elucidate the genetic diversity of E. coli pathotypes and support their accurate classification. This integrative approach enables PIP-eco to uncover connections among various E. coli pathotypes, highlight shared virulence factors, and provide insights into their evolutionary trajectories. By utilizing experimentally validated marker genes, the pipeline ensures robust identification of pathotypes, particularly those of hybrid pathotypes. Additionally, PAI analysis offers comprehensive genetic investigations, revealing strain-specific variations and potential virulence mechanisms. As a result, the PIP-eco pipeline emerges as a useful tool for dissecting the evolutionary dynamics of E. coli and characterizing complex pathotypes, addressing the critical need for accurate detection and understanding of hybrid pathotypes.
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Affiliation(s)
- Seyoung Ko
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Huynh Minh Triet Nguyen
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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2
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Kara A, Massaro C, Giammanco GM, Alduina R, Boussoualim N. Phylogenetic Diversity, Antibiotic Resistance, and Virulence of Escherichia coli Strains from Urinary Tract Infections in Algeria. Antibiotics (Basel) 2024; 13:773. [PMID: 39200073 PMCID: PMC11350822 DOI: 10.3390/antibiotics13080773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/23/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
Urinary tract infections (UTIs) caused by Escherichia coli represent a significant public health concern due to the high virulence and antimicrobial resistance exhibited by these pathogens. This study aimed to analyze the phylogenetic diversity and antibiotic resistance profiles of Uropathogenic E. coli (UPEC) strains isolated from UTI patients in Algeria, focusing on virulence factors such as extended β-lactamase (ESBL) production, biofilm formation, and hemolytic activity. Phylogenetic grouping of 86 clinical imipenem resistant E. coli isolates showed the prevalence of group B2 (48.9%), followed by groups E (22.1%), unknown (12.8%), A (8.1%), and B1 (4.7%), and Clade I, D, Clade I, or Clade II (1.2%). The highest resistance rates were observed towards amoxicillin (86.04%), ticarcillin (82.55%), piperacillin (73.25%), nitrofurantoin (84.88%), and trimethoprim-sulfamethoxazole (51.16%). Notably, 69.8% of UPEC strains were multidrug-resistant (MDR) and 23.2% were extensively drug-resistant (XDR). Additionally, 48.9%, 42%, and 71% of strains demonstrated ESBL production, hemolytic activity, and weak biofilm production, respectively. Continuous monitoring and characterization of UPEC strains are essential to track the spread of the most resistant and virulent phylogenetic groups over time, facilitating rapid therapeutic decisions to treat infections and prevent the emergence of new resistant organisms, helping choose the most effective antibiotics and reducing treatment failure.
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Affiliation(s)
- Anfal Kara
- Laboratory of Applied Biochemistry, Faculty of Nature and Life Sciences, University Ferhat Abbas of Setif 1, Setif 19000, Algeria; (A.K.); (N.B.)
| | - Chiara Massaro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Bldg. 16, 90128 Palermo, Italy;
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Giovanni M. Giammanco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy;
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Bldg. 16, 90128 Palermo, Italy;
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy
| | - Naouel Boussoualim
- Laboratory of Applied Biochemistry, Faculty of Nature and Life Sciences, University Ferhat Abbas of Setif 1, Setif 19000, Algeria; (A.K.); (N.B.)
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3
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Anudit C, Saraisuwan P, Kimterng C, Puangmanee C, Bamphensin N, Kerdsin A. Dissemination of Urinary Escherichia coli Phylogroup B2 in Provincial and Community Hospitals in Uthai Thani, Central Thailand. Jpn J Infect Dis 2024; 77:220-226. [PMID: 38417863 DOI: 10.7883/yoken.jjid.2023.376] [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] [Indexed: 03/01/2024]
Abstract
Escherichia coli is a Gram-negative bacterium that causes a variety of clinical infections in humans, including diarrhea, sepsis, and urinary tract infection. This bacterium is a common multidrug-resistant threat in community and hospital settings worldwide. This study examined the antimicrobial susceptibility and genetic relationship based on Clermont phylotyping and enterobacterial repetitive intergenic consensus (ERIC)-PCR of 84 E. coli urinary isolates from provincial and community hospitals in Thailand. All isolates were susceptible to nitrofurantoin, and almost all isolates were susceptible to carbapenem, fosfomycin, and amikacin. High resistance rates to fluoroquinolone, ampicillin, and trimethoprim/sulfamethoxazole were observed. Clermont phylogroup B2 was predominant (n = 58). Subtyping of the B2 phylogroup revealed diverse subgroups, of which subgroup V (n = 11), VII (n = 9), III (n = 6), and II (n = 6) were most prevalent. ERIC-PCR showed that the strains of the B2 subgroups III and V were spread between provincial and community hospitals and between hospital wards. This evidence suggests the need for comprehensive infection control monitoring, with strong active surveillance at all hospital levels.
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Affiliation(s)
| | | | | | | | - Nicharee Bamphensin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Thailand
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4
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Muñoz-Cazalla A, de Quinto I, Álvaro-Llorente L, Rodríguez-Beltrán J, Herencias C. The role of bacterial metabolism in human gut colonization. Int Microbiol 2024:10.1007/s10123-024-00550-6. [PMID: 38937311 DOI: 10.1007/s10123-024-00550-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
Can we anticipate the emergence of the next pandemic antibiotic-resistant bacterial clone? Addressing such an ambitious question relies on our ability to comprehensively understand the ecological and epidemiological factors fostering the evolution of high-risk clones. Among these factors, the ability to persistently colonize and thrive in the human gut is crucial for most high-risk clones. Nonetheless, the causes and mechanisms facilitating successful gut colonization remain obscure. Here, we review recent evidence that suggests that bacterial metabolism plays a pivotal role in determining the ability of high-risk clones to colonize the human gut. Subsequently, we outline novel approaches that enable the exploration of microbial metabolism at an unprecedented scale and level of detail. A thorough understanding of the constraints and opportunities of bacterial metabolism in gut colonization will foster our ability to predict the emergence of high-risk clones and take appropriate containment strategies.
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Affiliation(s)
- Ada Muñoz-Cazalla
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Ignacio de Quinto
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Laura Álvaro-Llorente
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Cristina Herencias
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
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Wei S, Ding B, Wang G, Luo S, Zhao H, Dan X. Population characteristics of pathogenic Escherichia coli in puerperal metritis of dairy cows in Ningxia region of China: a systemic taxa distribution of virulence factors and drug resistance genes. Front Microbiol 2024; 15:1364373. [PMID: 38694808 PMCID: PMC11061491 DOI: 10.3389/fmicb.2024.1364373] [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: 01/02/2024] [Accepted: 03/28/2024] [Indexed: 05/04/2024] Open
Abstract
Escherichia coli (E. coli) is closely associated with the occurrence of puerperal metritis in dairy cows. E. coli carries some the virulence and multi-drug resistant genes, which pose a serious threat to the health of postpartum cows. In this study, E. coli was isolated and identified from the uterine contents of postpartum cows with puerperal metritis in the Ningxia region of China, and its phylogenetic subgroups were determined. Meanwhile, virulence and drug resistance genes carried by E. coli and drug sensitivity were detected, and the characteristics of virulence and drug resistance genes distribution in E. coli phylogroups were further analyzed. The results showed that the isolation rate of E. coli in puerperal metritis samples was 95.2%. E. coli was mainly divided into phylogroups B2 and D, followed by groups A and B1, and was more connected to O157:H7, O169:H4, and ECC-1470 type strains. The virulence genes were mainly dominated by ompF (100%), traT (100%), fimH (97%), papC (96%), csgA (95%), Ang43 (93.9%), and ompC (93%), and the resistance genes were dominated by TEM (99%), tetA (71.7%), aac(3)II (66.7%), and cmlA (53.5%). Additionally, it was observed that the virulence and resistance gene phenotypes could be divided into two subgroups, with subgroup B2 and D having the highest distributions. Drug sensitivity tests also revealed that the E. coli was most sensitive to the fluoroquinolones enrofloxacin, followed by macrolides, aminoglycosides, tetracyclines, β-lactams, peptides and sulfonamides, and least sensitive to lincosamides. These results imply that pathogenic E. coli, which induces puerperal metritis of dairy cows in the Ningxia region of China, primarily belongs to the group B2 and D, contains multiple virulence and drug resistance genes, Moreover, E. coli has evolved resistance to several drugs including penicillin, lincomycin, cotrimoxazole, and streptomycin. It will offer specific guidelines reference for the prevention and treatment of puerperal metritis in dairy cows with E. coli infections in the Ningxia region of China.
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Affiliation(s)
| | | | | | | | - Hongxi Zhao
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xingang Dan
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Hernández-Chiñas U, Ahumada-Cota RE, Navarro-Ocaña A, Chávez-Berrocal ME, Molina-López J, Rocha-Ramírez LM, Navarro-Cid del Prado A, Eslava CA. Phenotypic and genotypic characteristics of Escherichia coli strains isolated during a longitudinal follow-up study of chronic urinary tract infections. Front Public Health 2023; 11:1240392. [PMID: 38074750 PMCID: PMC10702777 DOI: 10.3389/fpubh.2023.1240392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Worldwide, Urinary Tract Infections (UTIs) are an important health problem with many cases reported annually, women being the most affected. UTIs are relevant because they can become a recurrent condition, associated with different factors that contribute to the chronicity of the disease (cUTI). cUTI can be classified as persistent (peUTI) when the causative agent is the same each time the infection occurs or as reinfection (reUTI) when the associated microorganism is different. The purpose of this work was to characterize Escherichia coli isolates obtained in two prospective studies of patients with cUTI, to define which of them corresponded to peUTI and which to reUTI. A total of 394 isolates of E. coli were analyzed by agglutination with specific sera, antimicrobial susceptibility by diffusion disc test, and the phylogroups and presence of genes associated with virulence by PCR assays. Additionally, in some characterized strains adherence, invasiveness, and biofilm formation were analyzed by in vitro assays. The results showed that the peUTI strains belonged mainly to the classical UPEC serogroups (O25, O75, O6), were included in the B2 phylogroup, carried a great number of virulence genes, and were adherent, invasive, and biofilm-forming. Meanwhile, reUTI strains showed great diversity of serogroups, belonged mainly in the A phylogroup, and carried fewer virulence genes. Both peUTI and reUTI strains showed extensively drug-resistant (XDR) and multidrug-resistant (MDR) profiles in the antimicrobial susceptibility test. In conclusion, it appears that peUTIs are caused principally by classical UPEC strains, while reUTIs are caused by strains that appear to be a part of the common E. coli intestinal biota. Moreover, although both peUTI and reUTI strains presented different serotypes and phylogroups, their antimicrobial resistance profile (XDR and MDR) was similar, confirming the importance of regulating prophylactic treatments and seeking alternatives for the treatment and control of cUTI. Finally, it was possible to establish the features of the E. coli strains responsible for peUTI and reUTI which could be helpful to develop a fast diagnostic methodology.
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Affiliation(s)
- Ulises Hernández-Chiñas
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Ricardo E. Ahumada-Cota
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Armando Navarro-Ocaña
- Bacteriology Laboratory, Public Health Department, Faculty of Medicine, UNAM, Mexico City, Mexico
| | - María E. Chávez-Berrocal
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - José Molina-López
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Luz M. Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City, Mexico
| | | | - Carlos A. Eslava
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
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7
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Aziz I, Noreen Z, Ijaz UZ, Gundogdu O, Hamid MH, Muhammad N, Khan A, Bokhari H. A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Sci Rep 2023; 13:6802. [PMID: 37185286 PMCID: PMC10133260 DOI: 10.1038/s41598-023-32491-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Stunted growth is an emerging global challenge affecting children under the age of 5 years in low- and middle-income countries. Despite such a high global prevalence of stunting, the mechanism of pathogenesis and the role of associated gut microbiota is poorly understood. The present study was designed to investigate the association of pathogenic strains of E. coli with the residential gut microbiota of stunted growth children. A total of 64 stool sample were collected from children aged ≤ 5 years, and were processed for isolation and molecular characterization of diarrheagenic E. coli. Selected stool samples (n = 39 including three normal controls) were then analysed for microbial community profiling using 16S ribosomal RNA (rRNA) gene sequencing. Furthermore, associations between changes in the microbiota in the presence of different E. coli strains was explored. Pathotyping of the isolated E. coli (n = 64) has shown that 39.68% belonged to one of the five pathotypes of E. coli whilst the remaining ones were non-typeable. Amongst the different pathotypes, EPEC was found to be the most prevalent (52%; n = 13), followed by EAEC (20%; n = 5), EIEC (12%; n = 3), EHEC (8%; n = 2) and ETEC 2 (8%; n = 2). Phylogrouping analysis has shown that majority of the strains belonged to B2 (28.12%). Microbial diversity is shown to be significant and varied when the samples are organized under the recovered phylogroups. Moreover, based on predictive metabolism, the colonization of these strains were found to be significantly associated with energy utilization pathways such as Denovoprine-2 and glyoxylate-by. Differential analysis has shown that Escherichia-Shigella and Enterococcus were altered for the children with stunted growth.
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Affiliation(s)
- Israr Aziz
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Zobia Noreen
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | | | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Muhammad Haroon Hamid
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Nazir Muhammad
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Abdullah Khan
- Paediatric Unit, Saidu Teaching Hospitals, Swat, Saidu Sharif, Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Biosciences, Kohsar University, Murree, Pakistan.
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Nowrouzian FL, Stadler LS, Östblom A, Lindberg E, Lina G, Adlerberth I, Wold AE. Staphylococcus aureus sequence type (ST) 45, ST30, and ST15 in the gut microbiota of healthy infants - persistence and population counts in relation to ST and virulence gene carriage. Eur J Clin Microbiol Infect Dis 2023; 42:267-276. [PMID: 36689019 PMCID: PMC9899187 DOI: 10.1007/s10096-022-04539-9] [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: 07/22/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus colonizes the anterior nares, and also the gut, particularly in infants. S. aureus is divided into lineages, termed clonal complexes (CCs), which comprise closely related sequence types (STs). While CC30 and CC45 predominate among nasal commensals, their prevalence among gut-colonizing S. aureus is unknown. Here, 67 gut commensal S. aureus strains from 49 healthy Swedish infants (aged 3 days to 12 months) were subjected to multi-locus sequence typing. The STs of these strains were related to their virulence gene profiles, time of persistence in the microbiota, and fecal population counts. Three STs predominated: ST45 (22% of the strains); ST15 (21%); and ST30 (18%). In a logistic regression, ST45 strains showed higher fecal population counts than the others, independent of virulence gene carriage. The lower fecal counts of ST15 were linked to the carriage of fib genes (encoding fibrinogen-binding proteins), while those of ST30 were linked to fib and sea (enterotoxin A) carriage. While only 11% of the ST15 and ST30 strains were acquired after 2 months of age, this was true of 53% of the ST45 strains (p = 0.008), indicating that the former may be less fit for establishment in a more mature microbiota. None of the ST45 strains was transient (persisting < 3 weeks), and persistent ST45 strains colonized for significantly longer periods than persistent strains of other STs (mean, 34 vs 22 weeks, p = 0.04). Our results suggest that ST45 strains are well-adapted for commensal gut colonization in infants, reflecting yet-unidentified traits of these strains.
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Affiliation(s)
- Forough L Nowrouzian
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden.
| | - Liselott Svensson Stadler
- Culture Collection University of Gothenburg, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Microbiology, Dahlgren's University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Anna Östblom
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
| | - Erika Lindberg
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
| | - Gerard Lina
- Centre National de Référence Des Staphylocoques, Hospices Civils de Lyon, CIRI, Université Lyon1, INSERM U1111, CNRS-UMR 5308, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10, S-413 46, Gothenburg, Sweden
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Harbaoui S, Ferjani S, Abbassi M, Saidani M, Gargueh T, Ferjani M, Hammi Y, Boutiba‐Ben Boubaker I. Genetic heterogeneity and predominance of
bla
CTX‐M
‐15
in cefotaxime‐resistant
Enterobacteriaceae
isolates colonizing hospitalized children in Tunisia. Lett Appl Microbiol 2022; 75:1460-1474. [DOI: 10.1111/lam.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- S. Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - S. Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - M.S. Abbassi
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie Tunis Tunisie
| | - M. Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
| | - T. Gargueh
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - M. Ferjani
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - Y. Hammi
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - I. Boutiba‐Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
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10
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Phylogenetic Groups/B2 Subgroup Distributions, Serogrouping and Identification of Virulence Factors in Extended-Spectrum Cephalosporin-Resistant Escherichia coli Strains Isolated from the Stool of Healthy Children Under 10 Years Old. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2022. [DOI: 10.5812/pedinfect-118889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Segregation of Escherichia coli (E. coli) into the phylogenetic groups was observed in the experiments so that group B2 contained the enteropathogenic E. coli (EPEC) strains and extraintestinal pathogenic E. coli (ExPEC). Objectives: This study aimed to identify B2 phylogenetic groups in the extended-spectrum Cephalosporins resistant E. coli isolated from the stool of healthy children under 10 years old. Methods: One hundred E. coli resistant to broad-spectrum Cephalosporins were collected from the feces of healthy children under 10. Subsequently, we grouped phylogenetic via PCR based on the genes yjaA, chuA, arpA, as well, as TspE4.C2. Then, according to Clermont et al.’s study, we used two individual multiplex PCRs for identifying B2 sub-groups (I-X subgroups). Serogroup typing with the 12 O-antigen was analyzed via PCR, and finally, 10 virulence genes (cnf1, papG, ibeA, malX, usp, cdt, eae, bfp, and afa-Dr) were identified with PCR. Results: The age range of the healthy children was between 1 and 10 years. The B2 and unknown phylogroups were the most common strains in this study. The most common B2 subgroups were I (STc131) (2%), IX (1%), V (8%), IV, V, VII (1%), IX, V (3%), IX, V, III, I (1%), IX, V, III, VII, I (%1), V, I (6%), V, III, I (3%), and V, III, VII (1%), with each subgroup carrying distinctive sets of ExPEC virulence markers. The results also showed that 29% of E. coli in the healthy children had malX and 23% had papGII. It was also found that 32% of the strains isolated from the healthy children had antigens O2 and 36% were unknown. Conclusions: In this study, 27% of the strains belonged to B2 phylogroup and 6% to B1 phylogroup. Moreover, serogroups O2, O16, and O25 were predominant and belonged to B2 phylogroup. Moreover, malX, papGII, usp, papGIII, aggR, and eae virulence genes also had the highest to lowest supply among the tested strains, respectively. Moreover, B2 isolates were shown to have further virulence-related genes in comparison to the non B2 isolates.
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Tudu R, Banerjee J, Habib M, Bandyopadhyay S, Biswas S, Kesh SS, Maity A, Batabyal S, Polley S. Prevalence and molecular characterization of extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolated from dogs suffering from diarrhea in and around Kolkata. IRANIAN JOURNAL OF VETERINARY RESEARCH 2022; 23:237-246. [PMID: 36425605 PMCID: PMC9681975 DOI: 10.22099/ijvr.2022.42543.6176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 03/17/2023]
Abstract
BACKGROUND Dogs are the favorite companion animals among humans. The close interaction between dogs and people increases the risk of antibiotic resistance spreading. Surveillance for antimicrobial resistance and the identification of ESBL-producing Escherichia coli as an indicator bacterium is an important tool for managing antimicrobial drug therapy. AIMS The present study targeted to identify and characterize ESBL-producing E. coli among dogs suffering from diarrhea in and around Kolkata. METHODS Isolation and identification of E. coli from dogs suffering from diarrhea (n=70) along with screening for the production of both ESBL and AmpC. The isolates were further characterized through antimicrobial resistance profiling, resistance genes (bla CTX-M, bla TEM, and bla SHV) screening, and phylogenetic group study. RESULTS Among the 70 isolates, 21 (30%) were confirmed ESBL producers. An antibiogram typing of ESBL-producing E. coli revealed that the majority of them were resistant to norfloxacin (85.7%) followed by tetracycline (61.90%), doxycycline (57.14%), piperacillin/tazobactam (52.38%), cotrimoxazole (47.62%), gentamicin (42.62%), amikacin (23.81%), and chloramphenicol (19.05%). Major resistance genes included bla CTX-M (100%), bla TEM (28.57%), and bla SHV (9.50%). The predominant phylogenetic groups were phylogroup A (76%) followed by phylogroup D (24%). CONCLUSION The current investigation reported a high prevalence of both ESBL and AmpC β-lactamase (AmpC) producing E. coli, co-resistance to a distinct group of antibiotics, and co-existence of different ESBL genes in dogs. Our findings highlight the importance of diagnostic antimicrobial susceptibility testing for proper antimicrobial therapy and to prevent antimicrobial resistance from spreading to humans from dogs in Kolkata and the surrounding area.
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Affiliation(s)
- R Tudu
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - J Banerjee
- Ph.D. Student in Veterinary Biochemistry, Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - Md Habib
- Ph.D. Student in Veterinary Biochemistry, Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S Bandyopadhyay
- Eastern Regional Station, Indian Veterinary Research Institute, Kolkata-700 037, West Bengal, India
| | - S Biswas
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S S Kesh
- Department of Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - A Maity
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S Batabyal
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
| | - S Polley
- Department of Veterinary Biochemistry, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, 37, K. B. Sarani, Belgachia, Kolkata-700 037, West Bengal, India
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12
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A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates. mSphere 2021; 6:e0086821. [PMID: 34935444 PMCID: PMC8722714 DOI: 10.1128/msphere.00868-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is a longitudinal study comprising 649 Escherichia coli isolates representing all 7,165 E. coli bloodstream infection (BSI) episodes recorded in a hospital (1996 to 2016). Strain analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, pulsed-field gel electrophoresis [PFGE], and whole-genome sequencing [WGS]), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs; 29 genes). The incidence of E. coli BSI increased from 1996 to 2016 (5.5 to 10.8 BSI episodes/1,000 hospitalizations, average 7 to 8/1,000). B2 isolates predominate (53%), with subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI representing 25%, 25%, 14%, and 9%, respectively. Intertwined waves of community-acquired (CA) plus health care-associated and community-onset health care-associated (HCA) and hospital-acquired (HA) episodes of both B2 and non-B2 phylogroups occurred. A remarkable increase was observed only for B2-I-STc131 (C1/C2 subclades), with oscillations for other B2 subgroups and phylogroups throughout the years. Epidemic and persistent clones (comprising isolates with highly similar/identical PFGE types and genomes differing in 6 to 173 single nucleotide polymorphisms [SNPs]) of B2-I (STc131), B2-II (STc73), B2-III (STc127), B2-IX (STc95), and B2-VI (STc12) were recovered from different patients, most at hospital admission, for long periods (2 to 17 years), and extended-spectrum beta-lactamase (ESBL) producers or resistance to ciprofloxacin in B2 isolates was almost restricted to B2-I (STc131) subclade C. STc131 contributed to increasing the B2 rates but only transiently altered the E. coli population structure. The increase of E. coli BSI was determined by waves of CA+HCA BSI episodes that predate the waves of HA BSI. Besides the risk of hospital transmission that led to temporal increases in BSI, this study suggests that E. coli populations/clones from community-based healthy individuals may occasionally have an epidemic structure and provide a source of transmissible strains influencing the HA BSI incidence. IMPORTANCE Sepsis is the third leading cause of mortality in Western countries and one of the Global Health Threats recognized by the WHO since 2017. Despite Escherichia coli constituting the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies. Our work analyzes the long-term dynamics of E. coli causing bacteremia in a single institution and reveals waves of different clonal lineages that emerge periodically and successfully spread afterward in both the community and hospitals. Because the origin of E. coli bloodstream infections is the gut, the microbiota of healthy individuals might occasionally have an epidemic structure, providing a source of E. coli strains to influence the incidence of hospital BSI. The study complements previous fractionated observations focusing on specific E. coli lineages or antibiotic-resistant isolates in the last decades and helps to understand the epidemiology of E. coli BSI and the dynamics of pandemic clones.
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13
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Jafari E, Oloomi M, Bouzari S. Characterization of antimicrobial susceptibility, extended-spectrum β-lactamase genes and phylogenetic groups of Shigatoxin producing Escherichia coli isolated from patients with diarrhea in Iran. Ann Clin Microbiol Antimicrob 2021; 20:24. [PMID: 33858427 PMCID: PMC8051076 DOI: 10.1186/s12941-021-00430-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/10/2021] [Indexed: 11/15/2022] Open
Abstract
Background Shiga toxin‐producing Escherichia coli (STEC) are among common foodborne bacterial pathogens and healthy livestock are the main source of this bacterium. Severe diseases attribute to two types of cytotoxin Stx1 and Stx2, which are also called Shiga toxin (Stx). Infection of humans with STEC may result in Acute diarrhea with or without bleeding, hemorrhagic colitis (HC) and the hemolytic uremic syndrome (HUS). As antibiotic resistance is increasingly being reported among STEC isolates obtained from livestock and patients worldwide, in this study the pattern of antibiotic resistance in clinical isolates was determined. Methods Stool samples were collected from patients with diarrhea. All samples were cultured and identified by biochemical and molecular tests. Antimicrobial susceptibility test and assessment of extended-spectrum β-lactamase (ESBL)-related genes were conducted. Moreover, phylogenetic groups were analyzed using quadruplex PCR, and DNA analysis assessed multi-locus sequence types (MLST). Results Out of 340 E. coli samples, 174 were identified as STEC by PCR. Antimicrobial susceptibility test results showed that, 99.4%, 96% and 93.1% of isolates were susceptible to imipenem/ertapenem, piperacillin–tazobactam and amikacin, respectively. The highest resistance was towards ampicillin (68.4%), followed by trimethoprim–sulfamethoxazole (59.8%), and tetracycline (57.5%). A total of 106 (60.9%) isolates were multidrug resistance (MDR) and 40.8% of isolates were determined to be extended spectrum β-lactamase producers. In 94.4% of isolates, genes responsible for ESBL production could be detected, and blaTEM was the most prevalent, followed by blaCTX-M9. Furthermore, phylogenetic grouping revealed that majority of STEC strains belonged to Group C, followed by Groups E, B2 and A. MLST unveiled diverse ST types. Conclusion A periodical surveillance studies and thorough understanding of antibiotic resistant profiles in STEC isolates could help select effective antibiotic treatment for patients and develop strategies to effectively manage food contamination and human infections.
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Affiliation(s)
- Erfaneh Jafari
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran.,National Escherichia Coli Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
| | - Mana Oloomi
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Saeid Bouzari
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran. .,National Escherichia Coli Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran.
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14
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Princisval L, Rebelo F, Williams BL, Coimbra AC, Crovesy L, Ferreira AL, Kac G. Association Between the Mode of Delivery and Infant Gut Microbiota Composition Up to 6 Months of Age: A Systematic Literature Review Considering the Role of Breastfeeding. Nutr Rev 2021; 80:113-127. [PMID: 33837424 DOI: 10.1093/nutrit/nuab008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
CONTEXT Cesarean section (CS), breastfeeding, and geographic location can influence the infant microbiota. OBJECTIVE In this systematic review, evidence of the association between mode of delivery and infant gut microbiota up to 6 months of age was evaluated, as was the role of breastfeeding in this association, according to PRISMA guidelines. DATA SOURCE The Pubmed, Web of Science, Scopus, Embase, Medical Database, and Open Grey databases were searched. DATA EXTRACTION A total of 31 observational studies with ≥2 infant stool collections up to the sixth month of age and a comparison of gut microbiota between CS and vaginal delivery (VD) were included. DATA ANALYSIS Infants born by CS had a lower abundance of Bifidobacterium and Bacteroides spp. at almost all points up to age 6 months. Populations of Lactobacillus, Bifidobacterium longum, Bifidobacterium catenulatum, and Escherichia coli were reduced in infants delivered by CS. Infants born by CS and exclusively breastfed had greater similarity with the microbiota of infants born by VD. CONCLUSIONS Species of Bifidobacterium and Bacteroides are potentially reduced in infants born by CS. Geographic location influenced bacterial colonization. SYSTEMATIC REVIEW REGISTRATION PROSPERO registration no. 42017071285.
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Affiliation(s)
- Luciana Princisval
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
| | - Fernanda Rebelo
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
| | - Brent L Williams
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
| | - Anna Carolina Coimbra
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
| | - Louise Crovesy
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
| | - Ana Lorena Ferreira
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
| | - Gilberto Kac
- Affiliation: L. Princisval, A.C. Coimbra, L. Crovesy, A.L. Ferreira, and G. Kac are with the Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Josué de Castro Nutrition Institute, Rio de Janeiro, RJ Brazil. B.L. Williams is with the Department of Epidemiology, Columbia University, Center for Infection and Immunity, New York, NY, USA. F. Rebelo is with the Oswaldo Cruz Foundation, National Institute of Women, Children and Adolescents Health Fernandes Figueira, Clinical Research Unit, Rio de Janeiro, RJ, Brazil
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15
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Jafari E, Mostaan S, Bouzari S. Characterization of Antimicrobial Susceptibility, Extended-Spectrum β-Lactamase Genes and Phylogenetic Groups of Enteropathogenic Escherichia coli Isolated from Patients with Diarrhea. Osong Public Health Res Perspect 2020; 11:327-333. [PMID: 33117638 PMCID: PMC7577383 DOI: 10.24171/j.phrp.2020.11.5.09] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objectives Infectious diarrhea is one of the most common causes of pediatric death worldwide and enteropathogenic Escherichia coli (EPEC) is one of the main causes. There are 2 subgroups of EPEC, typical and atypical, based on the presence or absence of bundle forming pili (bfp), of which atypical EPEC is considered less virulent, but not less pathogenic. Antimicrobial resistance towards atypical EPEC among children is growing and is considered a major problem. In this study the pattern of antibiotic resistance in clinical isolates was determined. Methods Using 130 isolates, antibiotic resistance patterns and phenotypes were assessed, and genotypic profiles of extended spectrum β-lactamase (ESBL) production using disc diffusion and PCR was carried out. Phylogenetic groups were analyzed using quadruplex PCR. Results There were 65 E. coli isolates identified as atypical EPEC by PCR, among which the highest antibiotic resistance was towards ampicillin, followed by trimethoprim-sulfamethoxazole, and tetracycline. Multidrug resistance was detected in 44.6% of atypical EPEC isolates. Around 33% of isolates were determined to be extended spectrum β-lactamase producers, and in 90% of isolates, genes responsible for ESBL production could be detected. Moreover, the majority of atypical EPEC strains belonged to Group E, followed by Groups B1, B2 and C. Conclusion High rates of multidrug resistance and ESBL production among atypical EPEC isolates warrant periodical surveillance studies to select effective antibiotic treatment for patients. It is considered a critical step to manage antibiotic resistance by avoiding unnecessary prescriptions for antibiotics.
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Affiliation(s)
- Erfaneh Jafari
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Saeid Mostaan
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Saeid Bouzari
- Molecular Biology Department, Pasteur Institute of Iran, Tehran, Iran
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16
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Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PLoS Genet 2020; 16:e1009065. [PMID: 33112851 PMCID: PMC7592755 DOI: 10.1371/journal.pgen.1009065] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
The genus Escherichia is composed of several species and cryptic clades, including E. coli, which behaves as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of the Escherichia genus phylogenetic diversity and including E. albertii (n = 7), E. fergusonii (n = 5), Escherichia clades (n = 32) and E. coli (n = 326), tested in a mouse model of sepsis. We found that the presence of the high-pathogenicity island (HPI), a ~35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and the sitABCD operons. We confirmed the association in vivo by deleting key genes of the HPI in E. coli strains in two phylogenetic backgrounds. We then searched for correlations between virulence, iron capture systems and in vitro growth in a subset of E. coli strains (N = 186) previously phenotyped across growth conditions, including antibiotics and other chemical and physical stressors. We found that virulence and iron capture systems are positively correlated with growth in the presence of numerous antibiotics, probably due to co-selection of virulence and resistance. We also found negative correlations between virulence, iron uptake systems and growth in the presence of specific antibiotics (i.e. cefsulodin and tobramycin), which hints at potential “collateral sensitivities” associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genus Escherichia. Bacterial isolates belonging to the genus Escherichia can be human commensals but also opportunistic pathogens, with the ability to cause extra-intestinal infection. There is therefore the need to identify the genetic elements that favour extra-intestinal virulence, so that virulent bacterial isolates can be identified through genome analysis and potential treatment strategies be developed. To reduce the influence of host variability on virulence, we have used a mouse model of sepsis to characterize the virulence of 370 strains belonging to the genus Escherichia, for which whole genome sequences were also available. We have used a statistical approach called Genome-Wide Association Study (GWAS) to show how the presence of genes that encode for iron scavenging are significantly associated with the propensity of a bacterial isolate to cause extra-intestinal infections. Taking advantage of previously generated growth data on a subset of the strains and its correlation to virulence we generated hypothesis on the relationship between iron scavenging and growth in the presence of various antimicrobials, which could have implications for developing new treatment strategies.
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Affiliation(s)
- Marco Galardini
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
- * E-mail: (MG); (ED)
| | | | | | - Bede Busby
- Genome Biology Unit, EMBL, Heidelberg, Germany
| | - Sara Dion
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Sören Schubert
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Germany
| | - Pedro Beltrao
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Erick Denamur
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
- * E-mail: (MG); (ED)
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17
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Fox TC, Clabots C, Porter SB, Bender T, Thuras P, Colpan A, Boettcher J, Johnson JR. Bacterial "Virulence" Traits and Host Demographics Predict Escherichia coli Colonization Behaviors Within Households. Open Forum Infect Dis 2020; 7:ofaa495. [PMID: 33241068 PMCID: PMC7676507 DOI: 10.1093/ofid/ofaa495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/18/2020] [Indexed: 12/22/2022] Open
Abstract
Background Although intestinal colonization precedes most extraintestinal Escherichia coli infections, colonization-promoting factors are incompletely understood. We compared within-household E. coli colonization patterns with host and bacterial traits. Methods Twenty-two veterans with a clinical E. coli isolate and their 46 human and animal household members underwent longitudinal fecal sampling. Distinct E. coli strains were characterized for phylogenetic background, virulence genes, antibiotic resistance, and colonization behaviors. Host and bacterial traits were assessed statistically as predictors of colonization behaviors. Results Among the 139 unique-by-household fecal E. coli strains, univariable predictors of colonization behavior included (i) host demographics, (ii) matching the index clinical isolate, and (iii) bacterial characteristics (2 phylogroups, 5 clonal lineages, 18 virulence genes, and molecular extraintestinal pathogenic E. coli status). Multivariable predictors of colonization behavior included veteran host, spouse host, matching the index clinical isolate, phylogroup F, ST73, hlyD (alpha hemolysin), hlyF (variant hemolysin), H7 fliC (flagellar variant), vat (vacuolating toxin), and iha (adhesin-siderophore). Conclusions Host demographics, multiple bacterial “virulence” traits, and matching the index clinical isolate predicted E. coli fecal colonization behaviors. Thus, certain bacterial characteristics may promote both colonization and pathogenicity. Future interventions directed toward such traits might prevent E. coli infections both directly and by disrupting antecedent colonization.
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Affiliation(s)
- Teresa C Fox
- Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Connie Clabots
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Stephen B Porter
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Tricia Bender
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA
| | - Paul Thuras
- Mental Health Patient Service Line, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA.,Department of Psychiatry, University of Minnesota Minneapolis, Minnesota, USA
| | - Aylin Colpan
- Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jessica Boettcher
- Infectious Diseases, University of Minnesota, Minneapolis, Minnesota, USA
| | - James R Johnson
- Infectious Diseases, Veterans Affairs Medical Center, Minneapolis, Minnesota, USA.,Infectious Diseases, University of Minnesota Minneapolis, Minnesota, USA
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18
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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