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Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:1-31. [DOI: 10.1016/bs.pmbts.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Pelegrin AC, Palmieri M, Mirande C, Oliver A, Moons P, Goossens H, van Belkum A. Pseudomonas aeruginosa: a clinical and genomics update. FEMS Microbiol Rev 2021; 45:6273131. [PMID: 33970247 DOI: 10.1093/femsre/fuab026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) has become a global medical priority that needs urgent resolution. Pseudomonas aeruginosa is a versatile, adaptable bacterial species with widespread environmental occurrence, strong medical relevance, a diverse set of virulence genes and a multitude of intrinsic and possibly acquired antibiotic resistance traits. P. aeruginosa causes a wide variety of infections and has an epidemic-clonal population structure. Several of its dominant global clones have collected a wide variety of resistance genes rendering them multi-drug resistant (MDR) and particularly threatening groups of vulnerable individuals including surgical patients, immunocompromised patients, Caucasians suffering from cystic fibrosis (CF) and more. AMR and MDR especially are particularly problematic in P. aeruginosa significantly complicating successful antibiotic treatment. In addition, antimicrobial susceptibility testing (AST) of P. aeruginosa can be cumbersome due to its slow growth or the massive production of exopolysaccharides and other extracellular compounds. For that reason, phenotypic AST is progressively challenged by genotypic methods using whole genome sequences (WGS) and large-scale phenotype databases as a framework of reference. We here summarize the state of affairs and the quality level of WGS-based AST for P. aeruginosa mostly from clinical origin.
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Affiliation(s)
- Andreu Coello Pelegrin
- bioMérieux, Data Analytics Unit, 3 Route du Port Michaud, 38390 La Balme les Grottes, France
| | - Mattia Palmieri
- bioMérieux, Data Analytics Unit, 3 Route du Port Michaud, 38390 La Balme les Grottes, France
| | - Caroline Mirande
- bioMérieux, R&D Microbiology, Route du Port Michaud, 38390 La Balme-les-Grottes, France
| | - Antonio Oliver
- Servicio de Microbiología, Módulo J, segundo piso, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Ctra. Valldemossa, 79, 07120 Palma de Mallorca, Spain
| | - Pieter Moons
- Laboratory of Medical Microbiology, University of Antwerp, Universiteitsplein 1, building S, 2610 Wilrijk, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route du Port Michaud, 38390 La Balme Les Grottes, France
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Shi J, Wu D, Su Y, Xie B. Selective enrichment of antibiotic resistance genes and pathogens on polystyrene microplastics in landfill leachate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142775. [PMID: 33082042 DOI: 10.1016/j.scitotenv.2020.142775] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 05/11/2023]
Abstract
Landfill leachate is an important reservoir of antibiotic resistance genes (ARGs) and microplastics (MPs). However, the enrichment characteristics of ARGs on MPs and the effect of MPs' presence on ARGs in surrounding leachates are little studied. Therefore, we investigated the differences of ARGs, mobile genetic elements (MGEs), bacterial communities and pathogens on polystyrene MPs, in MPs-surrounding leachate and in control (leachate with the absence of MPs). The results revealed that ARGs were selectively enriched on MPs, which was similar in three types of leachate environments. The genes strB and blaTEM were maximally enriched and mefA, ermB, tetM and tetQ were slightly enriched on MPs, and the degree of ARGs enrichment increased with time during the 60 days of the experiment. Furthermore, compared to the leachate, MPs were observed to have the higher abundances of MGEs and distinct bacterial communities, both of which were closely associated with ARGs on MPs. Pathogens were distinct and more abundant on MPs compared to that in leachate, and 11 pathogens were identified as potential hosts for ARGs on MPs. Additionally, the presence of MPs (500 mg/L) induced few changes in ARGs' abundances, MGEs' abundances and bacterial communities in MP-surrounding leachate within 60 days. Overall, this study suggested that MPs could selectively enrich ARGs and pathogens from the surrounding environments, which promoted the understanding of the combined pollution properties of MPs and ARGs.
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Affiliation(s)
- Jianhong Shi
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Engineering Research Center for Nanophotonics & Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Engineering Research Center for Nanophotonics & Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200241, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Vianello MA, Cardoso B, Fuentes-Castillo D, Moura Q, Esposito F, Fuga B, Lincopan N, Egito EST. International high-risk clone of fluoroquinolone-resistant Escherichia coli O15:H1-D-ST393 in remote communities of Brazilian Amazon. INFECTION GENETICS AND EVOLUTION 2021; 91:104808. [PMID: 33737229 DOI: 10.1016/j.meegid.2021.104808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/07/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
The global dissemination of multidrug-resistant Escherichia coli lineages belonging to high- risk clones poses a significant public health threat. Herein we report the identification and genomic profiling of two multidrug-resistant E. coli strains [BL-II-03(2) and BL-II-11(3)] belonging to the O15:H1-D-ST393 (clonal complex 31) worldwide spread clone, isolated from fecal samples of indigenous peoples belonging to two different ethnic groups of remote communities of Brazilian Amazon. Genomic analysis revealed genes and mutations conferring resistance to β-lactams [blaTEM-1], aminoglycosides [aadA5, aph(3″)-Ib, aph(6)-Id], tetracyclines [tetB], sulfamethoxazole/trimethoprim [sul1, sul2, dfrA17], and fluoroquinolones [gyrA (D87N, S83L), parC (S80I, S57T), parE (L416F)]; and presence of IncQ1, IncFIA, and IncFIB(pB171) plasmids. On the other hand, phylogenomics of globally reported E. coli ST393 assigned E. coli strains BL-II-03(2) and BL-II-11(3) to a cluster comprising human isolates from Australia, Canada, China, Sweden, and United States of America. These results might provide valuable information for understanding dissemination of intercontinental multidrug-resistant clones in remote communities with low levels of antibiotic exposure.
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Affiliation(s)
- Marco Aurelio Vianello
- Graduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Brenda Cardoso
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, Universidade of São Paulo, São Paulo, Brazil.
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Abstract
Escherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCEEscherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.
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Mahmoodi F, Rezatofighi SE, Akhoond MR. Antimicrobial resistance and metallo-beta-lactamase producing among commensal Escherichia coli isolates from healthy children of Khuzestan and Fars provinces; Iran. BMC Microbiol 2020; 20:366. [PMID: 33256594 PMCID: PMC7708168 DOI: 10.1186/s12866-020-02051-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Background The emergence of metallo-β-lactamase (MBL)-producing isolates is alarming since they carry mobile genetic elements with great ability to spread; therefore, early detection of these isolates, particularly their reservoir, is crucial to prevent their inter- and intra-care setting dissemination and establish suitable antimicrobial therapies. The current study was designed to evaluate the frequency of antimicrobial resistance (AMR), MBL producers and identification of MBL resistance genes in Escherichia coli strains isolated from fecal samples of the healthy children under 3 years old. A total of 412 fecal E. coli isolates were collected from October 2017 to December 2018. The study population included healthy infants and children aged < 3 years who did not exhibit symptoms of any diseases, especially gastrointestinal diseases. E. coli isolates were assessed to determine the pattern of AMR. E. coli isolates were assessed to determine the pattern of AMR, the production of extended spectrum β-lactamase (ESBL) and MBL by phenotypic methods. Carbapenem-resistant isolates were investigated for the presence of MBL and carbapenemase genes, plasmid profiling, and the ability of conjugation. Results In sum, AMR, multi-drug resistance (MDR) and ESBL production were observed in more than 54.9, 36.2 and 11.7% of commensal E. coli isolates, respectively. Out of six isolates resistant to imipenem and meropenem, four isolates were phenotypically detected as MBL producers. Two and one E. coli strains carried the blaNDM-1 and blaVIM-2 genes, respectively and were able to transmit imipenem resistance through conjugation. Conclusion Our findings showed that children not exposed to antibiotics can be colonized by E. coli isolates resistant to the commonly used antimicrobial compounds and can be a good indicator for the occurrence and prevalence of AMR in the community. These bacteria can act as a potential reservoir of AMR genes including MBL genes of pathogenic bacteria and lead to the dissemination of resistance mechanisms to other bacteria.
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Affiliation(s)
- Fahimeh Mahmoodi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Postal code: 6135743135, Iran
| | - Seyedeh Elham Rezatofighi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Postal code: 6135743135, Iran.
| | - Mohammad Reza Akhoond
- Mathematical Sciences and Computer Faculty, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Virulence Characteristics and Antibiotic Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Diverse Sources. Antibiotics (Basel) 2020; 9:antibiotics9090587. [PMID: 32911679 PMCID: PMC7559023 DOI: 10.3390/antibiotics9090587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is an enteric pathogen that causes several gastrointestinal ailments in humans across the world. STEC’s ability to cause ailment is attributed to the presence of a broad range of known and putative virulence factors (VFs) including those that encode Shiga toxins. A total of 51 E. coli strains belonging to serogroups O26, O45, O103, O104, O113, O121, O145, and O157 were tested for the presence of nine VFs via PCR and for their susceptibility to 17 frequently used antibiotics using the disc diffusion method. The isolates belonged to eight different serotypes, including eight O serogroups and 12 H types. The frequency of the presence of key VFs were stx1 (76.47%), stx2 (86.27%), eae (100%), ehxA (98.03%), nleA (100%), ureC (94.11%), iha (96.07%), subA (9.80%), and saa (94.11%) in the E. coli strains. All E. coli strains carried seven or more distinct VFs and, among these, four isolates harbored all tested VFs. In addition, all E. coli strains had a high degree of antibiotic resistance and were multidrug resistant (MDR). These results show a high incidence frequency of VFs and heterogeneity of VFs and MDR profiles of E. coli strains. Moreover, half of the E. coli isolates (74.5%) were resistant to > 9 classes of antibiotics (more than 50% of the tested antibiotics). Thus, our findings highlight the importance of appropriate epidemiological and microbiological surveillance and control measures to prevent STEC disease in humans worldwide.
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Assessment of antibiotic resistant coliforms from bioaerosol samples collected above a sewage-polluted river in La Paz, Bolivia. Int J Hyg Environ Health 2020; 228:113494. [DOI: 10.1016/j.ijheh.2020.113494] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/03/2020] [Accepted: 02/18/2020] [Indexed: 01/01/2023]
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Mbelle NM, Feldman C, Sekyere JO, Maningi NE, Modipane L, Essack SY. Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa. Sci Rep 2020; 10:1232. [PMID: 31988374 PMCID: PMC6985128 DOI: 10.1038/s41598-020-58012-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/09/2020] [Indexed: 11/14/2022] Open
Abstract
Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the blaCTX-M gene, whilst 41/42(97%) contained blaTEM, 36/42(86%) contained blaOXA and 35/42(83%) harboured blaSHV genes. Other resistance genes found included blaLEN, aac(6′)-lb-cr, qnrA, qnrB, qnrS, oqxAB, aad, aph, dfr, sul1, sul2, fosA, and cat genes. Fluoroquinolone and colistin resistance-conferring mutations in parC, gyrAB, pmrAB, phoPQ and kpnEF were identified. The blaLEN gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7/42(17%) isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. The blaCTX-M-15 and blaTEM-1 genes were bracketed by Tn3 transposons, ISEc9, a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the dfrA and aadA gene cassettes being the most frequent. Phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical K. pneumoniae strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.
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Affiliation(s)
- Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
| | - Charles Feldman
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | | | - Lesedi Modipane
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu/Natal, Durban, South Africa
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Antimicrobial Resistance in Bacteria: Mechanisms, Evolution, and Persistence. J Mol Evol 2019; 88:26-40. [PMID: 31659373 DOI: 10.1007/s00239-019-09914-3] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/02/2019] [Indexed: 01/29/2023]
Abstract
In recent years, we have seen antimicrobial resistance rapidly emerge at a global scale and spread from one country to the other faster than previously thought. Superbugs and multidrug-resistant bacteria are endemic in many parts of the world. There is no question that the widespread use, overuse, and misuse of antimicrobials during the last 80 years have been associated with the explosion of antimicrobial resistance. On the other hand, the molecular pathways behind the emergence of antimicrobial resistance in bacteria were present since ancient times. Some of these mechanisms are the ancestors of current resistance determinants. Evidently, there are plenty of putative resistance genes in the environment, however, we cannot yet predict which ones would be able to be expressed as phenotypes in pathogenic bacteria and cause clinical disease. In addition, in the presence of inhibitory and sub-inhibitory concentrations of antibiotics in natural habitats, one could assume that novel resistance mechanisms will arise against antimicrobial compounds. This review presents an overview of antimicrobial resistance mechanisms, and describes how these have evolved and how they continue to emerge. As antimicrobial strategies able to bypass the development of resistance are urgently needed, a better understanding of the critical factors that contribute to the persistence and spread of antimicrobial resistance may yield innovative perspectives on the design of such new therapeutic targets.
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Zaha DC, Bungau S, Aleya S, Tit DM, Vesa CM, Popa AR, Pantis C, Maghiar OA, Bratu OG, Furau C, Moleriu RD, Petre I, Aleya L. What antibiotics for what pathogens? The sensitivity spectrum of isolated strains in an intensive care unit. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:118-127. [PMID: 31207502 DOI: 10.1016/j.scitotenv.2019.06.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Antibiotic sensitivity spectrum of isolated strains differs according to hospital departments, the hospitals themselves, and countries. Discrepancies also exist in terms of antibiotic use and dosage. The aim of the present study is to compare the antibacterial agents, the types of infections, the number and type of pathogens, and the sensitivity to antibiotics used in the Intensive Care Unit (ICU) of the Emergency Clinical County Hospital of Oradea, Romania. Over a one-year period, data were gathered from the pharmacy computer system and medical records of inpatients. WHO Anatomical Therapeutic Chemical (ATC)/defined daily doses (DDD) methodology was used to assess drug administration data, and antibiotic use was expressed as DDD/1000 PD (patient days). The antibiotic susceptibility of isolated strains was expressed through the cumulative antibiogram. The overall consumption of antimicrobial agents was 1247.47 DDD/1000 PD. The most common drugs used were cephalosporins and fluoroquinolones (52.97% of the total). Ceftriaxone was the most commonly used, followed by levofloxacin. Infections of the respiratory and urinary tract were the most frequently diagnosed infections. The most commonly isolated bacteria type was Acinetobacter baumannii (22.12% overall), isolated especially from the respiratory tract and resistant to all the β-lactam antibiotics including carbapenems. Antimicrobials intake at the ICU is much higher compared to medical and surgical wards. After we tested the existence of a possible connection between antibiotic consumption and antibiotic resistance of bacteria, it was revealed that on our sample exists a poor positive association.
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Affiliation(s)
- Dana Carmen Zaha
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Selim Aleya
- Faculty of Medicine, Besançon, Chrono-Environnement Laboratory, UMR CNRS 6249, France
| | - Delia Mirela Tit
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Cosmin Mihai Vesa
- Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Amorin Remus Popa
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Carmen Pantis
- Department of Surgical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Octavian Adrian Maghiar
- Department of Surgical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Ovidiu Gabriel Bratu
- Clinical Department 3, University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
| | - Cristian Furau
- Life Sciences Department, Western University "Vasile Goldis" of Arad, Arad, Romania
| | - Radu Dumitru Moleriu
- Department of Mathematics, Faculty of Mathematics and Computer Science, West University of Timisoara, Romania
| | - Izabella Petre
- Department XII of Obstetrics and Gynecology, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania
| | - Lotfi Aleya
- Department XII of Obstetrics and Gynecology, "Victor Babes" University of Medicine and Pharmacy, Timisoara, Romania; Laboratoire Chrono-environnement, UMR CNRS 6249, Université de Franche-Comté, Besançon, France.
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Longitudinal Shedding Patterns and Characterization of Antibiotic Resistant E. coli in Pastured Goats using a Cohort Study. Antibiotics (Basel) 2019; 8:antibiotics8030136. [PMID: 31480769 PMCID: PMC6783881 DOI: 10.3390/antibiotics8030136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/05/2019] [Accepted: 08/28/2019] [Indexed: 12/17/2022] Open
Abstract
There is a scarcity of information on antibiotic resistance in goats. To understand shedding of resistant Escherichia coli in pastured goats, we collected fecal samples from a mixed age cohort over a one-year period. No antibiotic had been used on the study animals one year prior to and during the study period. Resistant isolates were detected in all age groups and prevalence in goat kids was significantly higher than adults; 43–48% vs. 8–25% respectively. The proportion of resistant isolates was higher when animals were congregated near handling facility than on pasture. Most isolates were resistant to tetracycline (51%) and streptomycin (30%), but also to antibiotics that had never been used on the farm; ampicillin (19%). TetB, bla-TEM, (aadA and strpA/strpB) genes were detected in 70%, 43%, (44% and 24%) of tetracycline, ampicillin, and streptomycin resistant isolates respectively. Resistant isolates also harbored virulent genes and some belonged to D and B2 phylogenetic groups. Thus, pastured goats, despite minimal exposure to antibiotics, are reservoirs of resistant E. coli that may contaminate the environment and food chain and spread resistant genes to pathogenic bacteria and some that are potential animal and human pathogens. Environmental sources may play a role in acquisition of resistant bacteria in pastured goats.
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Gatica J, Jurkevitch E, Cytryn E. Comparative Metagenomics and Network Analyses Provide Novel Insights Into the Scope and Distribution of β-Lactamase Homologs in the Environment. Front Microbiol 2019; 10:146. [PMID: 30804916 PMCID: PMC6378392 DOI: 10.3389/fmicb.2019.00146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/21/2019] [Indexed: 11/13/2022] Open
Abstract
The β-lactams are the largest group of clinically applied antibiotics, and resistance to these is primarily associated with β-lactamases. There is increasing understanding that these enzymes are ubiquitous in natural environments and henceforth, elucidating the global diversity, distribution, and mobility of β-lactamase-encoding genes is crucial for holistically understanding resistance to these antibiotics. In this study, we screened 232 shotgun metagenomes from ten different environments against a custom-designed β-lactamase database, and subsequently analyzed β-lactamase homologs with a suite of bioinformatic platforms including cluster and network analyses. Three interrelated β-lactamase clusters encompassed all of the human and bovine feces metagenomes, while β-lactamases from soil, freshwater, glacier, marine, and wastewater grouped within a separate "environmental" cluster that displayed high levels of inter-network connectivity. Interestingly, almost no connectivity occurred between the "feces" and "environmental" clusters. We attributed this in part to the divergence in microbial community composition (dominance of Bacteroidetes and Firmicutes vs. Proteobacteria, respectively). The β-lactamase diversity in the "environmental" cluster was significantly higher than in human and bovine feces microbiomes. Several class A, B, C, and D β-lactamase homologs (bla CTX-M, bla KPC, bla GES) were ubiquitous in the "environmental" cluster, whereas bovine and human feces metagenomes were dominated by class A (primarily cfxA) β-lactamases. Collectively, this study highlights the ubiquitous presence and broad diversity of β-lactamase gene precursors in non-clinical environments. Furthermore, it suggests that horizontal transfer of β-lactamases to human-associated bacteria may be more plausible from animals than from terrestrial and aquatic microbes, seemingly due to phylogenetic similarities.
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Affiliation(s)
- Joao Gatica
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel.,The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
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14
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Ingle DJ, Levine MM, Kotloff KL, Holt KE, Robins-Browne RM. Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nat Microbiol 2018; 3:1063-1073. [PMID: 30127495 PMCID: PMC6787116 DOI: 10.1038/s41564-018-0217-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
The dynamics of antimicrobial resistance (AMR) in developing countries are poorly understood, especially in community settings, due to a sparsity of data on AMR prevalence and genetics. We used a combination of phenotyping, genomics and antimicrobial usage data to investigate patterns of AMR amongst atypical enteropathogenic Escherichia coli (aEPEC) strains isolated from children younger than five years old in seven developing countries (four in sub-Saharan Africa and three in South Asia) over a three-year period. We detected high rates of AMR, with 65% of isolates displaying resistance to three or more drug classes. Whole-genome sequencing revealed a diversity of known genetic mechanisms for AMR that accounted for >95% of phenotypic resistance, with comparable rates amongst aEPEC strains associated with diarrhoea or asymptomatic carriage. Genetic determinants of AMR were associated with the geographic location of isolates, not E. coli lineage, and AMR genes were frequently co-located, potentially enabling the acquisition of multi-drug resistance in a single step. Comparison of AMR with antimicrobial usage data showed that the prevalence of resistance to fluoroquinolones and third-generation cephalosporins was correlated with usage, which was higher in South Asia than in Africa. This study provides much-needed insights into the frequency and mechanisms of AMR in intestinal E. coli in children living in community settings in developing countries.
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Affiliation(s)
- Danielle J Ingle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Myron M Levine
- Departments of Pediatrics and Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Karen L Kotloff
- Departments of Pediatrics and Medicine, Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Roy M Robins-Browne
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
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15
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Stoppe NDC, Silva JS, Carlos C, Sato MIZ, Saraiva AM, Ottoboni LMM, Torres TT. Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates. Front Microbiol 2017; 8:2512. [PMID: 29312213 PMCID: PMC5742620 DOI: 10.3389/fmicb.2017.02512] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 12/04/2017] [Indexed: 01/01/2023] Open
Abstract
Escherichia coli is an important microorganism in the gastrointestinal tract of warm-blooded animals. Commensal populations of E. coli consist of stable genetic isolates, which means that each individual has only one phylogenetic group (phylogroup). We evaluated the frequency of human commensal E. coli phylogroups from 116 people and observed that the majority of isolates belonged to group A. We also evaluated the frequency of phylogroups in wastewater samples and found a strong positive correlation between the phylogroup distribution in wastewater and human hosts. In order to find out if some factors, such as geographical location, and climate could influence the worldwide phylogroup distribution, we performed a meta-analysis of 39 different studies and 24 countries, including different climates, living areas, and feeding habits. Unexpectedly, our results showed no substructuring patterns of phylogroups; indicating there was no correlation between phylogroup distribution and geographic location, climate, living area, feeding habits, or date of collection.
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Affiliation(s)
- Nancy de Castro Stoppe
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil.,Núcleo de Pesquisa em Biodiversidade e Computação (BioComp-USP)-Universidade de São Paulo, São Paulo, Brazil
| | - Juliana S Silva
- Núcleo de Pesquisa em Biodiversidade e Computação (BioComp-USP)-Universidade de São Paulo, São Paulo, Brazil.,Secretaria de Estado de Saúde de Mato Grosso, Cuiabá, Brazil.,Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Carlos
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Maria I Z Sato
- Departamento de Análises Ambientais, Companhia Ambiental do Estado de São Paulo-CETESB, São Paulo, Brazil
| | - Antonio M Saraiva
- Núcleo de Pesquisa em Biodiversidade e Computação (BioComp-USP)-Universidade de São Paulo, São Paulo, Brazil.,Departamento de Engenharia de Computação e Sistemas Digitais, Escola Politécnica da USP, São Paulo, Brazil
| | - Laura M M Ottoboni
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Tatiana T Torres
- Núcleo de Pesquisa em Biodiversidade e Computação (BioComp-USP)-Universidade de São Paulo, São Paulo, Brazil.,Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
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16
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Brown-Jaque M, Calero-Cáceres W, Espinal P, Rodríguez-Navarro J, Miró E, González-López JJ, Cornejo T, Hurtado JC, Navarro F, Muniesa M. Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates. Int J Antimicrob Agents 2017; 51:434-442. [PMID: 29180282 DOI: 10.1016/j.ijantimicag.2017.11.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/07/2017] [Accepted: 11/18/2017] [Indexed: 12/31/2022]
Abstract
Phage particles have emerged as elements with the potential to mobilise antibiotic resistance genes (ARGs) in different environments, including the intestinal habitat. This study aimed to determine the occurrence of ARGs in phage particles present in faecal matter and induced from strains isolated from faeces. Nine ARGs (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, blaOXA-48, qnrA, qnrS, mecA, sul1 and armA) were quantified by qPCR in the phage DNA fractions of 150 faecal samples obtained from healthy individuals who had not received antibiotic treatment or travelled abroad in the 3 months prior to sample collection. On the suspicion that the detected particles originated from bacterial flora, 82 Escherichia coli and Klebsiella pneumoniae isolates possessing at least one identified ARG (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, armA, qnrA, qnrS and sul1) were isolated and their capacity to produce phage particles carrying these ARGs following induction was evaluated. Of 150 samples, 72.7% were positive for at least one ARG, with blaTEM and blaCTX-M-9 group being the most prevalent and abundant. Of the 82 isolates, 51 (62%) showed an increase in the number of copies of the respective ARG in the phage fraction following induction, with blaTEM, blaCTX-M-1 group, blaCTX-M-9 group and sul1 being the most abundant. Phages induced from the isolates were further purified and visualised using microscopy and their DNA showed ARG levels of up to 1010 gene copies/mL. This study highlights the abundance of phage particles harbouring ARGs and indicates that bacterial strains in the intestinal habitat could be source of these particles.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - William Calero-Cáceres
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Judith Rodríguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Juan José González-López
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Thais Cornejo
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Juan Carlos Hurtado
- ISGlobal, Barcelona Centre for International Health Research, Department of Microbiology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain.
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17
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Lopatkin AJ, Meredith HR, Srimani JK, Pfeiffer C, Durrett R, You L. Persistence and reversal of plasmid-mediated antibiotic resistance. Nat Commun 2017; 8:1689. [PMID: 29162798 PMCID: PMC5698434 DOI: 10.1038/s41467-017-01532-1] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/22/2017] [Indexed: 02/07/2023] Open
Abstract
In the absence of antibiotic-mediated selection, sensitive bacteria are expected to displace their resistant counterparts if resistance genes are costly. However, many resistance genes persist for long periods in the absence of antibiotics. Horizontal gene transfer (primarily conjugation) could explain this persistence, but it has been suggested that very high conjugation rates would be required. Here, we show that common conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics in Escherichia coli. The notion is applicable to nine plasmids from six major incompatibility groups and mixed populations carrying multiple plasmids. These results suggest that reducing antibiotic use alone is likely insufficient for reversing resistance. Therefore, combining conjugation inhibition and promoting plasmid loss would be an effective strategy to limit conjugation-assisted persistence of antibiotic resistance. It is unclear whether the transfer of plasmids carrying antibiotic resistance genes can explain their persistence when antibiotics are not present. Here, Lopatkin et al. show that conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics.
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Affiliation(s)
- Allison J Lopatkin
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Hannah R Meredith
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Jaydeep K Srimani
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Connor Pfeiffer
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Rick Durrett
- Department of Mathematics, Duke University, Durham, NC, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
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18
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Brinkac L, Voorhies A, Gomez A, Nelson KE. The Threat of Antimicrobial Resistance on the Human Microbiome. MICROBIAL ECOLOGY 2017; 74:1001-1008. [PMID: 28492988 PMCID: PMC5654679 DOI: 10.1007/s00248-017-0985-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/18/2017] [Indexed: 05/22/2023]
Abstract
Ubiquitous in nature, antimicrobial resistance (AMR) has existed long before the golden age of antimicrobials. While antimicrobial agents are beneficial to combat infection, their widespread use contributes to the increase in and emergence of novel resistant microbes in virtually all environmental niches. The human microbiome is an important reservoir of AMR with initial exposure occurring in early life. Once seeded with AMR, commensal organisms may be key contributors to the dissemination of resistance due to the interconnectedness of microbial communities. When acquired by pathogens however, AMR becomes a serious public health threat worldwide. Our ability to combat the threat of emerging resistance relies on accurate AMR detection methods and the development of therapeutics that function despite the presence of antimicrobial resistance.
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Affiliation(s)
- Lauren Brinkac
- J. Craig Venter Institute|, Rockville, MD, 20850, USA.
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa.
| | | | - Andres Gomez
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
| | - Karen E Nelson
- J. Craig Venter Institute|, Rockville, MD, 20850, USA
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
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19
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Lupan I, Carpa R, Oltean A, Kelemen BS, Popescu O. Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania. Microbes Environ 2017; 32:219-225. [PMID: 28781345 PMCID: PMC5606691 DOI: 10.1264/jsme2.me17016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county. The resistance to sulfamethoxazole and tetracycline and some of their representative resistance genes: sul1, tet(O), and tet(W) were assessed in this study. The results obtained showed that bacteria resistant to sulphonamides were more abundant than those resistant to tetracycline. The concentration of bacteria with antibiotic resistance changed after the treatment, namely, bacteria resistant to sulfamethoxazole. The removal of all bacteria and antibiotic-resistant bacteria was 98–99% and the degree of removal of bacteria resistant to tetracycline was higher than the bacteria resistant to sulfamethoxazole compared to total bacteria. The wastewater treatment plant not only contributed to elevating ARG concentrations, it also enhanced the possibility of horizontal gene transfer (HGT) by increasing the abundance of the intI1 gene. Even though the treatment process reduced the concentration of bacteria by two orders of magnitude, the wastewater treatment plant in Cluj-Napoca contributed to an increase in antibiotic-resistant bacteria concentrations up to 10 km downstream of its discharge in Someşul Mic river.
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Affiliation(s)
- Iulia Lupan
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Rahela Carpa
- Babeş Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology
| | - Andreea Oltean
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Beatrice Simona Kelemen
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Octavian Popescu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
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20
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Katakweba AAS, Muhairwa AP, Lupindu AM, Damborg P, Rosenkrantz JT, Minga UM, Mtambo MMA, Olsen JE. First Report on a Randomized Investigation of Antimicrobial Resistance in Fecal Indicator Bacteria from Livestock, Poultry, and Humans in Tanzania. Microb Drug Resist 2017; 24:260-268. [PMID: 28759321 DOI: 10.1089/mdr.2016.0297] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study provides an estimate of antimicrobial resistance in intestinal indicator bacteria from humans (n = 97) and food animals (n = 388) in Tanzania. More than 70% of all fecal samples contained tetracycline (TE), sulfamethoxazole (STX), and ampicillin (AMP)-resistant coliforms, while cefotaxime (CTX)-resistant coliforms were observed in 40% of all samples. The average Log10 colony forming units/g of CTX-resistant coliforms in samples from humans were 2.20. Of 390 Escherichia coli tested, 66.4% were resistant to TE, 54.9% to STX, 54.9% to streptomycin, and 36.4% to CTX. Isolates were commonly (65.1%) multiresistant. All CTX-resistant isolates contained blaCTX-M gene type. AMP- and vancomycin-resistant enterococci were rare, and the average concentrations in positive samples were low (log10 0.9 and 0.4, respectively). A low-to-moderate resistance (2.1-15%) was detected in 240 enterococci isolates to the drugs tested, except for rifampicin resistance (75.2% of isolates). The average number of sulII gene copies varied between Log10 5.37 and 5.68 with no significant difference between sample source, while cattle had significantly higher number of tetW genes than humans. These findings, based on randomly obtained samples, will be instrumental in designing antimicrobial resistance (AMR) intervention strategies for Tanzania.
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Affiliation(s)
- Abdul A S Katakweba
- 1 Department of Public Health, Pest Management Centre, Sokoine University of Agriculture , Morogoro, Tanzania
| | - Amandus P Muhairwa
- 2 Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture , Morogoro, Tanzania
| | - Athumani M Lupindu
- 2 Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture , Morogoro, Tanzania
| | - Peter Damborg
- 3 Department of Veterinary and Animal Sciences, University of Copenhagen , Frederiksberg C, Denmark
| | - Jesper T Rosenkrantz
- 3 Department of Veterinary and Animal Sciences, University of Copenhagen , Frederiksberg C, Denmark
| | - Uswege M Minga
- 4 Provost's Office, Tumaini University Dar es Salaam College (TUDARCo) , Dar es Salaam, Tanzania
| | - Madundo M A Mtambo
- 2 Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture , Morogoro, Tanzania
| | - John E Olsen
- 3 Department of Veterinary and Animal Sciences, University of Copenhagen , Frederiksberg C, Denmark
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21
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Medaney F, Ellis RJ, Raymond B. Ecological and genetic determinants of plasmid distribution inEscherichia coli. Environ Microbiol 2016; 18:4230-4239. [DOI: 10.1111/1462-2920.13552] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/19/2016] [Accepted: 09/26/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Frances Medaney
- School of Biological Science; Royal Holloway University of London; Egham Surrey TW20 0EX UK
| | - Richard J. Ellis
- Specialist Scientific Support Department; Animal and Plant Health Agency, APHA Weybridge, Addlestone; Surrey KT15 3NB UK
| | - Ben Raymond
- School of Biological Science; Royal Holloway University of London; Egham Surrey TW20 0EX UK
- University of Exeter, Penryn Campus; Penryn Cornwall TR10 9FE UK
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22
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Lopes GV, Michael GB, Cardoso M, Schwarz S. Antimicrobial resistance and class 1 integron-associated gene cassettes in Salmonella enterica serovar Typhimurium isolated from pigs at slaughter and abattoir environment. Vet Microbiol 2016; 194:84-92. [DOI: 10.1016/j.vetmic.2016.04.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 04/19/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
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23
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Francino MP. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol 2016; 6:1543. [PMID: 26793178 PMCID: PMC4709861 DOI: 10.3389/fmicb.2015.01543] [Citation(s) in RCA: 456] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
The human microbiome is overly exposed to antibiotics, due, not only to their medical use, but also to their utilization in farm animals and crops. Microbiome composition can be rapidly altered by exposure to antibiotics, with potential immediate effects on health, for instance through the selection of resistant opportunistic pathogens that can cause acute disease. Microbiome alterations induced by antibiotics can also indirectly affect health in the long-term. The mutualistic microbes in the human body interact with many physiological processes, and participate in the regulation of immune and metabolic homeostasis. Therefore, antibiotic exposure can alter many basic physiological equilibria, promoting long-term disease. In addition, excessive antibiotic use fosters bacterial resistance, and the overly exposed human microbiome has become a significant reservoir of resistance genes, contributing to the increasing difficulty in controlling bacterial infections. Here, the complex relationships between antibiotics and the human microbiome are reviewed, with focus on the intestinal microbiota, addressing (1) the effects of antibiotic use on the composition and function of the gut microbiota, (2) the impact of antibiotic-induced microbiota alterations on immunity, metabolism, and health, and (3) the role of the gut microbiota as a reservoir of antibiotic resistances.
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Affiliation(s)
- M P Francino
- Unitat Mixta d'Investigació en Genòmica i Salut, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública/Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
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24
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Um MM, Barraud O, Kérourédan M, Gaschet M, Stalder T, Oswald E, Dagot C, Ploy MC, Brugère H, Bibbal D. Comparison of the incidence of pathogenic and antibiotic-resistant Escherichia coli strains in adult cattle and veal calf slaughterhouse effluents highlighted different risks for public health. WATER RESEARCH 2016; 88:30-38. [PMID: 26460853 DOI: 10.1016/j.watres.2015.09.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 06/05/2023]
Abstract
The goal of this study was to investigate the involvement of bovine slaughterhouse effluents and biosolids in the risk of environmental dissemination of pathogenic and antibiotic-resistant Escherichia coli. Several samples were collected from one adult cattle and one veal calf slaughterhouse wastewater treatment plant (WWTP). The treatment process had no impact on the percentage of Shiga toxin-producing E. coli (STEC) and on the percentage of atypical enteropathogenic E. coli (aEPEC). A STEC O157:H7 was isolated from the thickened sludge of the adult cattle slaughterhouse. As thickened sludge is intended to be spread on agricultural lands, the detection of this pathogenic strain is a public health issue. The percentage of antibiotic-resistant E. coli was 5.0% and 87.5% in wastewater from the adult cattle and the veal calf slaughterhouse, respectively. These percentages were not significantly different after treatment. Integron-bearing E. coli isolates were only detected in the veal calf slaughterhouse WWTP with percentages above 50.0% for all sampling points whatever the step of the treatment process. Taken together, these findings highlighted the fact that different public health risks might be associated with adult cattle or veal calf slaughterhouses regarding the dissemination of pathogenic and antibiotic-resistant E. coli isolates into the environment.
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Affiliation(s)
- Maryse Michèle Um
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France
| | - Olivier Barraud
- Université de Limoges, UMR1092, Limoges, France; INSERM, UMR1092, Limoges, France; CHU Limoges, laboratoire de Bactériologie-Virologie-Hygiène, Limoges, France
| | - Monique Kérourédan
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France
| | - Margaux Gaschet
- Université de Limoges, UMR1092, Limoges, France; INSERM, UMR1092, Limoges, France; CHU Limoges, laboratoire de Bactériologie-Virologie-Hygiène, Limoges, France
| | | | - Eric Oswald
- INSERM UMR1043, INRA USC1360, CHU de Toulouse, Hôpital Purpan, Toulouse, France
| | | | - Marie-Cecile Ploy
- Université de Limoges, UMR1092, Limoges, France; INSERM, UMR1092, Limoges, France; CHU Limoges, laboratoire de Bactériologie-Virologie-Hygiène, Limoges, France
| | - Hubert Brugère
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France
| | - Delphine Bibbal
- INSERM UMR1043, INRA USC1360, INP-ENVT, Université de Toulouse, Toulouse, France.
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25
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Domingues S, Nielsen KM, da Silva GJ. Global dissemination patterns of common gene cassette arrays in class 1 integrons. Microbiology (Reading) 2015; 161:1313-37. [DOI: 10.1099/mic.0.000099] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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26
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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27
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Fouhy F, Stanton C, Cotter PD, Hill C, Walsh F. Proteomics as the final step in the functional metagenomics study of antimicrobial resistance. Front Microbiol 2015; 6:172. [PMID: 25784907 PMCID: PMC4347484 DOI: 10.3389/fmicb.2015.00172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/15/2015] [Indexed: 01/23/2023] Open
Abstract
The majority of clinically applied antimicrobial agents are derived from natural products generated by soil microorganisms and therefore resistance is likely to be ubiquitous in such environments. This is supported by the fact that numerous clinically important resistance mechanisms are encoded within the genomes of such bacteria. Advances in genomic sequencing have enabled the in silico identification of putative resistance genes present in these microorganisms. However, it is not sufficient to rely on the identification of putative resistance genes, we must also determine if the resultant proteins confer a resistant phenotype. This will require an analysis pipeline that extends from the extraction of environmental DNA, to the identification and analysis of potential resistance genes and their resultant proteins and phenotypes. This review focuses on the application of functional metagenomics and proteomics to study antimicrobial resistance in diverse environments.
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Affiliation(s)
- Fiona Fouhy
- Teagasc - Moorepark Food Research Centre , Fermoy, Ireland
| | - Catherine Stanton
- Teagasc - Moorepark Food Research Centre , Fermoy, Ireland ; Alimentary Pharmabiotic Centre , Cork, Ireland
| | - Paul D Cotter
- Teagasc - Moorepark Food Research Centre , Fermoy, Ireland ; Alimentary Pharmabiotic Centre , Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre , Cork, Ireland ; School of Microbiology, University College Cork , Cork, Ireland
| | - Fiona Walsh
- Department of Biology, National University of Ireland Maynooth , Maynooth, Ireland
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Xiong W, Sun Y, Ding X, Zhang Y, Zhong X, Liang W, Zeng Z. Responses of plasmid-mediated quinolone resistance genes and bacterial taxa to (fluoro)quinolones-containing manure in arable soil. CHEMOSPHERE 2015; 119:473-478. [PMID: 25108677 DOI: 10.1016/j.chemosphere.2014.07.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/10/2014] [Accepted: 07/13/2014] [Indexed: 05/16/2023]
Abstract
The aim of the present study was to investigate the fate of plasmid-mediated quinolone resistance (PMQR) genes and the disturbance of soil bacterial communities posed by (fluoro)quinolones (FQNs)-containing manure in arable soil. Representative FQNs (enrofloxacin (ENR), ciprofloxacin (CIP) and norfloxacin (NOR)), PMQR genes (qepA, oqxA, oqxB, aac(6')-Ib-cr and qnrS) and bacterial communities in untreated soil, +manure and +manure+FQNs groups were analyzed using culture independent methods. The significantly higher abundance of oqxA, oqxB and aac(6')-Ib-cr, and significantly higher abundance of qnrS in +manure group than those in untreated soil disappeared at day 30 and day 60, respectively. All PMQR genes (oqxA, oqxB, aac(6')-Ib-cr and qnrS) dissipated 1.5-1.7 times faster in +manure group than those in +manure+FQNs group. The disturbance of soil bacterial communities posed by FQNs-containing manure was also found. The results indicated that significant effects of PMQR genes (oqxA, oqxB, aac(6')-Ib and qnrS) on arable soils introduced by manure disappeared 2 month after manure application. FQNs introduced by manure slowed down the dissipation of PMQR genes. The presence of high FQNs provided a selective advantage for species affiliated to the phylum including Acidobacteria, Verrucomicrobia and Planctomycetes while suppressing Proteobacteria and Actinobacteria.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Xueyao Ding
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yiming Zhang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Xiaoxia Zhong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Wenfei Liang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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Recovery of plasmid pEMB1, whose toxin-antitoxin system stabilizes an ampicillin resistance-conferring β-lactamase gene in Escherichia coli, from natural environments. Appl Environ Microbiol 2014; 81:40-7. [PMID: 25304509 DOI: 10.1128/aem.02691-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Non-culture-based procedures were used to investigate plasmids showing ampicillin resistance properties in two different environments: remote mountain soil (Mt. Jeombong) and sludge (Tancheon wastewater treatment plant). Total DNA extracted from the environmental samples was directly transformed into Escherichia coli TOP10, and a single and three different plasmids were obtained from the mountain soil and sludge samples, respectively. Interestingly, the restriction fragment length polymorphism pattern of the plasmid from the mountain soil sample, designated pEMB1, was identical to the pattern of one of the three plasmids from the sludge sample. Complete DNA sequencing of plasmid pEMB1 (8,744 bp) showed the presence of six open reading frames, including a β-lactamase gene. Using BLASTX, the orf5 and orf6 genes were suggested to encode a CopG family transcriptional regulator and a plasmid stabilization system, respectively. Functional characterization of these genes using a knockout orf5 plasmid (pEMB1ΔparD) and the cloning and expression of orf6 (pET21bparE) indicated that these genes were antitoxin (parD) and toxin (parE) genes. Plasmid stability tests using pEMB1 and pEMB1ΔparDE in E. coli revealed that the orf5 and orf6 genes enhanced plasmid maintenance in the absence of ampicillin. Using a PCR-based survey, pEMB1-like plasmids were additionally detected in samples from other human-impacted sites (sludge samples) and two other remote mountain soil samples, suggesting that plasmids harboring a β-lactamase gene with a ParD-ParE toxin-antitoxin system occurs broadly in the environment. This study extends knowledge about the dissemination and persistence of antibiotic resistance genes in naturally occurring microbial populations.
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Abstract
Antibiotics have been a cornerstone of innovation in the fields of public health, agriculture, and medicine. However, recent studies have shed new light on the collateral damage they impart on the indigenous host-associated communities. These drugs have been found to alter the taxonomic, genomic, and functional capacity of the human gut microbiota, with effects that are rapid and sometimes persistent. Broad-spectrum antibiotics reduce bacterial diversity while expanding and collapsing membership of specific indigenous taxa. Furthermore, antibiotic treatment selects for resistant bacteria, increases opportunities for horizontal gene transfer, and enables intrusion of pathogenic organisms through depletion of occupied natural niches, with profound implications for the emergence of resistance. Because these pervasive alterations can be viewed as an uncoupling of mutualistic host-microbe relationships, it is valuable to reconsider antimicrobial therapies in the context of an ecological framework. Understanding the biology of competitive exclusion, interspecies protection, and gene flow of adaptive functions in the gut environment may inform the design of new strategies that treat infections while preserving the ecology of our beneficial constituents.
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Fouhy F, Ogilvie LA, Jones BV, Ross RP, Ryan AC, Dempsey EM, Fitzgerald GF, Stanton C, Cotter PD. Identification of aminoglycoside and β-lactam resistance genes from within an infant gut functional metagenomic library. PLoS One 2014; 9:e108016. [PMID: 25247417 PMCID: PMC4172600 DOI: 10.1371/journal.pone.0108016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/21/2014] [Indexed: 12/22/2022] Open
Abstract
The infant gut microbiota develops rapidly during the first 2 years of life, acquiring microorganisms from diverse sources. During this time, significant opportunities exist for the infant to acquire antibiotic resistant bacteria, which can become established and constitute the infant gut resistome. With increased antibiotic resistance limiting our ability to treat bacterial infections, investigations into resistance reservoirs are highly pertinent. This study aimed to explore the nascent resistome in antibiotically-naïve infant gut microbiomes, using a combination of metagenomic approaches. Faecal samples from 22 six-month-old infants without previous antibiotic exposure were used to construct a pooled metagenomic library, which was functionally screened for ampicillin and gentamicin resistance. Our library of ∼220Mb contained 0.45 ampicillin resistant hits/Mb and 0.059 gentamicin resistant hits/Mb. PCR-based analysis of fosmid clones and uncloned metagenomic DNA, revealed a diverse and abundant aminoglycoside and β-lactam resistance reservoir within the infant gut, with resistance determinants exhibiting homology to those found in common gut inhabitants, including Escherichia coli, Enterococcus sp., and Clostridium difficile, as well as to genes from cryptic environmental bacteria. Notably, the genes identified differed from those revealed when a sequence-driven PCR-based screen of metagenomic DNA was employed. Carriage of these antibiotic resistance determinants conferred substantial, but varied (2–512x), increases in antibiotic resistance to their bacterial host. These data provide insights into the infant gut resistome, revealing the presence of a varied aminoglycoside and β-lactam resistance reservoir even in the absence of selective pressure, confirming the infant resistome establishes early in life, perhaps even at birth.
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Affiliation(s)
- Fiona Fouhy
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lesley A. Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, East Sussex, United Kingdom
| | - Brian V. Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, East Sussex, United Kingdom
- Queen Victoria Hospital NHS Foundation Trust, East Grinstead, West Sussex, United Kingdom
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Anthony C. Ryan
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Eugene M. Dempsey
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Gerald F. Fitzgerald
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Alimentary Pharmabiotic Centre, Cork, Ireland
- * E-mail:
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Influence of First-Line Antibiotics on the Antibacterial Activities of Acetone Stem Bark Extract of Acacia mearnsii De Wild. against Drug-Resistant Bacterial Isolates. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:423751. [PMID: 25101132 PMCID: PMC4102002 DOI: 10.1155/2014/423751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/12/2014] [Indexed: 12/19/2022]
Abstract
Background. This study was aimed at evaluating the antibacterial activity of the acetone extract of A. mearnsii and its interactions with antibiotics against some resistant bacterial strains. Methods. The antibacterial susceptibility testing was determined by agar diffusion and macrobroth dilution methods while the checkerboard method was used for the determination of synergy between the antibiotics and the extract. Results. The results showed that the susceptibility of the different bacterial isolates was concentration dependent for the extract and the different antibiotics. With the exception of S. marcescens, the inhibition zones of the extract produced by 20 mg/mL ranged between 18 and 32 mm. While metronidazole did not inhibit any of the bacterial isolates, all the antibiotics and their combinations, except for ciprofloxacin and its combination, did not inhibit Enterococcus faecalis. The antibacterial combinations were more of being antagonistic than of being synergistic in the agar diffusion assay. From the macrobroth dilution, the extract and the antibiotics exerted a varied degree of inhibitory effect on the test organisms. The MIC values of the acetone extract which are in mg/mL are lower than those of the different antibiotics which are in μg/mL. From the checkerboard assay, the antibacterial combinations showed varied degrees of interactions including synergism, additive, indifference, and antagonism interactions. While antagonistic and additive interactions were 14.44%, indifference interaction was 22.22% and synergistic interaction was 37.78% of the antibacterial combinations against the test isolates. While the additivity/indifference interactions indicated no interactions, the antagonistic interaction may be considered as a negative interaction that could result in toxicity and suboptimal bioactivity. Conclusion. The synergistic effects of the herbal-drug combinations may be harnessed for the discovery and development of more rational evidence-based drug combinations with optimized efficiency in the prevention of multidrug resistance and therapy of multifactorial diseases.
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Affiliation(s)
- Julian Davies
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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Antibiotic Resistance in and from Nature. One Health 2014. [DOI: 10.1128/9781555818432.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Trends in human fecal carriage of extended-spectrum β-lactamases in the community: toward the globalization of CTX-M. Clin Microbiol Rev 2014; 26:744-58. [PMID: 24092853 DOI: 10.1128/cmr.00023-13] [Citation(s) in RCA: 473] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In the last 10 years, extended-spectrum β-lactamase-producing enterobacteria (ESBL-E) have become one of the main challenges for antibiotic treatment of enterobacterial infections, largely because of the current CTX-M enzyme pandemic. However, most studies have focused on hospitalized patients, though today it appears that the community is strongly affected as well. We therefore decided to devote our investigation to trends in ESBL-E fecal carriage rates and comprehensively reviewed data from studies conducted on healthy populations in various parts of the world. We show that (i) community ESBL-E fecal carriage, which was unknown before the turn of the millennium, has since increased significantly everywhere, with developing countries being the most affected; (ii) intercontinental travel may have emphasized and globalized the issue; and (iii) CTX-M enzymes, especially CTX-M-15, are the dominant type of ESBL. Altogether, these results suggest that CTX-M carriage is evolving toward a global pandemic but is still insufficiently described. Only a better knowledge of its dynamics and biology will lead to further development of appropriate control measures.
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Card RM, Warburton PJ, MacLaren N, Mullany P, Allan E, Anjum MF. Application of microarray and functional-based screening methods for the detection of antimicrobial resistance genes in the microbiomes of healthy humans. PLoS One 2014; 9:e86428. [PMID: 24466089 PMCID: PMC3899262 DOI: 10.1371/journal.pone.0086428] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/07/2013] [Indexed: 02/01/2023] Open
Abstract
The aim of this study was to screen for the presence of antimicrobial resistance genes within the saliva and faecal microbiomes of healthy adult human volunteers from five European countries. Two non-culture based approaches were employed to obviate potential bias associated with difficult to culture members of the microbiota. In a gene target-based approach, a microarray was employed to screen for the presence of over 70 clinically important resistance genes in the saliva and faecal microbiomes. A total of 14 different resistance genes were detected encoding resistances to six antibiotic classes (aminoglycosides, β-lactams, macrolides, sulphonamides, tetracyclines and trimethoprim). The most commonly detected genes were erm(B), blaTEM, and sul2. In a functional-based approach, DNA prepared from pooled saliva samples was cloned into Escherichia coli and screened for expression of resistance to ampicillin or sulphonamide, two of the most common resistances found by array. The functional ampicillin resistance screen recovered genes encoding components of a predicted AcrRAB efflux pump. In the functional sulphonamide resistance screen, folP genes were recovered encoding mutant dihydropteroate synthase, the target of sulphonamide action. The genes recovered from the functional screens were from the chromosomes of commensal species that are opportunistically pathogenic and capable of exchanging DNA with related pathogenic species. Genes identified by microarray were not recovered in the activity-based screen, indicating that these two methods can be complementary in facilitating the identification of a range of resistance mechanisms present within the human microbiome. It also provides further evidence of the diverse reservoir of resistance mechanisms present in bacterial populations in the human gut and saliva. In future the methods described in this study can be used to monitor changes in the resistome in response to antibiotic therapy.
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Affiliation(s)
- Roderick M. Card
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Philip J. Warburton
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Nikki MacLaren
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - Peter Mullany
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Elaine Allan
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
- * E-mail:
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Pallecchi L, Bartoloni A, Paradisi F, Rossolini GM. Antibiotic resistance in the absence of antimicrobial use: mechanisms and implications. Expert Rev Anti Infect Ther 2014; 6:725-32. [DOI: 10.1586/14787210.6.5.725] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
ABSTRACT
Recent studies have shown that antibiotic resistance genes are omnipresent in nature. Human use of antimicrobial compounds as therapeutics, growth-promoting agents, pesticides, etc., over the past half century have contributed to this situation.
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Varela AR, Manaia CM. Human health implications of clinically relevant bacteria in wastewater habitats. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:3550-3569. [PMID: 23508533 DOI: 10.1007/s11356-013-1594-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/25/2013] [Indexed: 06/01/2023]
Abstract
The objective of this review is to reflect on the multiple roles of bacteria in wastewater habitats with particular emphasis on their harmful potential for human health. Indigenous bacteria promote a series of biochemical and metabolic transformations indispensable to achieve wastewater treatment. Some of these bacteria may be pathogenic or harbour antibiotic resistance or virulence genes harmful for human health. Several chemical contaminants (heavy metals, disinfectants and antibiotics) may select these bacteria or their genes. Worldwide studies show that treated wastewater contain antibiotic resistant bacteria or genes encoding virulence or antimicrobial resistance, evidencing that treatment processes may fail to remove efficiently these bio-pollutants. The contamination of the surrounding environment, such as rivers or lakes receiving such effluents, is also documented in several studies. The current state of the art suggests that only some of antibiotic resistance and virulence potential in wastewater is known. Moreover, wastewater habitats may favour the evolution and dissemination of new resistance and virulence genes and the emergence of new pathogens. For these reasons, additional research is needed in order to obtain a more detailed assessment of the long-term effects of wastewater discharges. In particular, it is important to measure the human and environmental health risks associated with wastewater reuse.
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Affiliation(s)
- Ana Rita Varela
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
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Penders J, Stobberingh EE, Savelkoul PHM, Wolffs PFG. The human microbiome as a reservoir of antimicrobial resistance. Front Microbiol 2013; 4:87. [PMID: 23616784 PMCID: PMC3627978 DOI: 10.3389/fmicb.2013.00087] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 03/27/2013] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is amongst the most densely populated microbial ecosystem on earth. While the microbiome exerts numerous health beneficial functions, the high density of micro-organisms within this ecosystem also facilitates horizontal transfer of antimicrobial resistance (AMR) genes to potential pathogenic bacteria. Over the past decades antibiotic susceptibility testing of specific indicator bacteria from the microbiome, such as Escherichia coli, has been the method of choice in most studies. These studies have greatly enlarged our understanding on the prevalence and distribution of AMR and associated risk factors. Recent studies using (functional) metagenomics, however, highlighted the unappreciated diversity of AMR genes in the human microbiome and identified genes that had not been described previously. Next to metagenomics, more targeted approaches such as polymerase chain reaction for detection and quantification of AMR genes within a population are promising, in particular for large-scale epidemiological screening. Here we present an overview of the indigenous microbiota as a reservoir of AMR genes, the current knowledge on this “resistome” and the recent and upcoming advances in the molecular diagnostic approaches to unravel this reservoir.
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Affiliation(s)
- John Penders
- Department of Medical Microbiology, Maastricht University Medical Centre+ Maastricht, Netherlands
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Pallecchi L, Bartoloni A, Gotuzzo E, Rossolini GM. Antibiotic resistance in the absence of antimicrobial use. Microb Drug Resist 2013. [DOI: 10.2217/ebo.12.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Lucia Pallecchi
- Lucia Pallecchi is Assistant Professor of Microbiology and Clinical Microbiology at the University of Siena Medical School (Siena, Italy), working in the research group of Gian Maria Rossolini. Her main fields of investigation concern the dynamics of emergence and dissemination of acquired antimicrobial resistance in commensal bacteria
| | - Alessandro Bartoloni
- Alessandro Bartoloni is Associate Professor of Infectious Diseases at the University of Florence Medical School (Florence, Italy) and Director of the Infectious and Tropical Diseases Unit of the University of Florence. He has a long-standing experience in health cooperation and research projects in Latin American countries
| | - Eduardo Gotuzzo
- Eduardo Gotuzzo is Principal Professor at the Department of Medicine and Director of the ‘AvH’ Institute of Tropical Medicine and Infectious Diseases at the Peruvian University Cayetano Heredia in Lima (Peru), and he is also Head of the Department of Transmissible Diseases at the Cayetano Heredia Hospital (Lima, Peru)
| | - Gian Maria Rossolini
- Gian Maria Rossolini is Full Professor of Microbiology and Clinical Microbiology at the University of Siena Medical School and the University of Florence Medical School, and Director of the Clinical Microbiology and Virology Unit of the University of Florence. His research group’s activity is mainly focused on different aspects related to antimicrobial agents and antimicrobial resistance mechanisms
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Zhang RQ, Ying GG, Su HC, Zhou LJ, Liu YS. Antibiotic resistance and genetic diversity of Escherichia coli isolates from traditional and integrated aquaculture in South China. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2013; 48:999-1013. [PMID: 23998313 DOI: 10.1080/03601234.2013.816611] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This study investigated antibiotic resistance profiles including antibiotic resistance frequencies, resistance genes and resistance patterns in Escherichia coli strains isolated from traditional and integrated aquaculture systems in South China by using antibiotic susceptibility testing and real time polymerase chain reaction (PCR) technique. The E. coli isolates were found to be resistant to at least one antibiotic among 12 antibiotics. Higher resistance frequencies to ampicillin, sulfamethoxazole, trimethoprime, streptomycin and tetracycline were found compared to the rest antibiotics. Among the 10 tetracycline resistance genes detected in the resistant isolates, the most prevalent tetracycline resistance genes were tetA, tetW and tetB with the frequency of 69.7%, 63.5% and 21.9%, respectively. Three sulfonamide resistance genes were detected in these resistant isolates, with their detection frequencies in the following order: sul2 (55.3%) > sul3 (28.2%) > sul1 (6.2%). Four resistance genes mainly encoding extended-spectrum β-lactamases (ESBLs) were detected in these resistant isolates, with the detection frequencies of blaTEM (28.4%) > blaOXA (9.7%) > blaCTX (9.3%) > blaCARB (5.2%) > blaSHV (0.0%). It was found that the integrated aquaculture system exhibited generally higher prevalence of antibiotic resistance than the traditional aquaculture system. An integrated aquaculture system could facilitate development of bacterial resistance and spread of the antibiotic resistance genes, and consequently become an important reservoir of resistance genes.
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Affiliation(s)
- Rui-Quan Zhang
- State Key Laboratory of Organic Geochemistry, CAS Centre for PRD Environmental Pollution and Control Research, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Tianhe District, Guangzhou, China
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Labar AS, Millman JS, Ruebush E, Opintan JA, Bishar RA, Aboderin AO, Newman MJ, Lamikanra A, Okeke IN. Regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. PLoS One 2012; 7:e38142. [PMID: 22666464 PMCID: PMC3364232 DOI: 10.1371/journal.pone.0038142] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Accepted: 04/30/2012] [Indexed: 02/04/2023] Open
Abstract
Background Antimicrobial resistance is a growing international problem. We observed a 50% increase in the prevalence of trimethoprim resistance among fecal Escherichia coli from healthy Nigerian students between 1998 and 2005, a trend to increase that continued in 2009. Methods and Findings A PCR-based screen revealed that 131 (43.1%) of isolates obtained in Nigeria in 2005 and 2009 carried integron-borne dfrA cassettes. In the case of 67 (51.1%) of these isolates, the cassette was a class 1-integron-borne dfrA7 gene, which has been reported at high prevalence from E. coli isolates from other parts of Africa. Complete sequencing of a 27 Kb dfrA7-bearing plasmid from one isolate located the dfrA7 gene within a Tn21-type transposon. The transposon also contained an IS26-derived bla/sul/str element, encoding resistance to β-lactams, sulphonamides and streptomycin, and mercury resistance genes. Although the plasmid backbone was only found in 12 (5.8%) of trimethoprim-resistant isolates, dfrA7 and other transposon-borne genes were detected in 14 (16.3%) and 32 (26.3%) of trimethoprim resistant isolates collected in Nigeria in 2005 and 2009, respectively. Additionally, 37 (19.3%) of trimethoprim-resistant E. coli isolates collected between 2006 and 2008 from Ghana were positive for the dfrA7 and a transposon marker, but only 4 (2.1%) harbored the plasmid backbone. Conclusions Our data point to transposition as a principal mechanism for disseminating dfrA7 among E. coli from Nigeria and Ghana. On-going intensive use of the affordable broad-spectrum antibacterials is likely to promote selective success of a highly prevalent transposable element in West Africa.
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Affiliation(s)
- Amy S. Labar
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Jennifer S. Millman
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Ellen Ruebush
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - Japheth A. Opintan
- Department of Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Rima A. Bishar
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
| | - A. Oladipo Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Mercy J. Newman
- Department of Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Adebayo Lamikanra
- Department of Pharmaceutics, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Iruka N. Okeke
- Department of Biology, Haverford College, Haverford, Pennsylvania, United States of America
- * E-mail:
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Davies J, Ryan KS. Introducing the parvome: bioactive compounds in the microbial world. ACS Chem Biol 2012; 7:252-9. [PMID: 22074935 DOI: 10.1021/cb200337h] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe and discuss the features and functions of the "parvome", the "-ome" of the chemical world, consisting of the small molecules produced by living organisms. Here, we focus specifically on the world of microbial small molecules. Many years of natural product discovery research, coupled with recent advances and applications of genetic and genomic techniques have revealed the presence of an enormous collection of unique small molecules that are the products of cellular metabolism. As yet, we have a poor understanding of their functions and, in most cases, little knowledge of their routes of biosynthesis, although such information is accruing rapidly. In this review, we attempt to address the raison d'etre of the parvome in the bacterial world, and we propose that a better understanding of the true biological roles of natural products will permit the application of rational approaches to the more effective exploitation of their use in medicine by humankind.
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Affiliation(s)
- Julian Davies
- Department
of Microbiology and Immunology and ‡Department of Chemistry, University
of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Katherine S. Ryan
- Department
of Microbiology and Immunology and ‡Department of Chemistry, University
of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
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Guenther S, Ewers C, Wieler LH. Extended-Spectrum Beta-Lactamases Producing E. coli in Wildlife, yet Another Form of Environmental Pollution? Front Microbiol 2011; 2:246. [PMID: 22203818 PMCID: PMC3244693 DOI: 10.3389/fmicb.2011.00246] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 11/23/2011] [Indexed: 11/13/2022] Open
Abstract
Wildlife is normally not exposed to clinically used antimicrobial agents but can acquire antimicrobial resistant bacteria through contact with humans, domesticated animals and the environment, where water polluted with feces seems to be the most important vector. Escherichia coli, an ubiquitous commensal bacterial species colonizing the intestinal tract of mammals and birds, is also found in the environment. Extended-spectrum beta-lactamases producing E. coli (ESBL-E. coli) represent a major problem in human and veterinary medicine, particular in nosocomial infections. Additionally an onset of community-acquired ESBL-E. coli infections and an emergence in livestock farming has been observed in recent years, suggesting a successful transmission as well as persistence of ESBL-E. coli strains outside clinical settings. Another parallel worldwide phenomenon is the spread of ESBL-E. coli into the environment beyond human and domesticated animal populations, and this seems to be directly influenced by antibiotic practice. This might be a collateral consequence of the community-onset of ESBL-E. coli infections but can result (a) in a subsequent colonization of wild animal populations which can turn into an infectious source or even a reservoir of ESBL-E. coli, (b) in a contribution of wildlife to the spread and transmission of ESBL-E. coli into fragile environmental niches, (c) in new putative infection cycles between wildlife, domesticated animals and humans, and (d) in problems in the medical treatment of wildlife. This review aims to summarize the current knowledge on ESBL-E. coli in wildlife, in turn underlining the need for more large scale investigations, in particular sentinel studies to monitor the impact of multiresistant bacteria on wildlife.
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Affiliation(s)
- Sebastian Guenther
- Institute of Microbiology and Epizootics, Freie Universität Berlin Berlin, Germany
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Baran W, Adamek E, Ziemiańska J, Sobczak A. Effects of the presence of sulfonamides in the environment and their influence on human health. JOURNAL OF HAZARDOUS MATERIALS 2011; 196:1-15. [PMID: 21955662 DOI: 10.1016/j.jhazmat.2011.08.082] [Citation(s) in RCA: 393] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 07/22/2011] [Accepted: 08/31/2011] [Indexed: 05/26/2023]
Abstract
World production and consumption of pharmaceuticals has been steadily increasing. Anti-infectives have been particularly important in modern therapy of microbial infection. Sulfonamides have been widely used for a long time as anti-infectives and are still widely prescribed today. This review presents the most common types of sulfonamides used in healthcare and veterinary medicine and discusses the problems connected with their presence in the biosphere. Based on the analysis of over 160 papers, it was found that small amounts of sulfonamides present in the environment were mainly derived from agricultural activities. These drugs have caused changes in the population of microbes that could be potentially hazardous to human health. This human health hazard could have a global range, and administrative activities have been ineffective in risk reduction.
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Affiliation(s)
- Wojciech Baran
- Silesian Medical University, Department of General and Analytical Chemistry, Jagiellońska 4, 41-200 Sosnowiec, Poland
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Stanton TB, Humphrey SB. Persistence of antibiotic resistance: evaluation of a probiotic approach using antibiotic-sensitive Megasphaera elsdenii strains to prevent colonization of swine by antibiotic-resistant strains. Appl Environ Microbiol 2011; 77:7158-66. [PMID: 21821757 PMCID: PMC3194883 DOI: 10.1128/aem.00647-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/25/2011] [Indexed: 11/20/2022] Open
Abstract
Megasphaera elsdenii is a lactate-fermenting, obligately anaerobic bacterium commonly present in the gastrointestinal tracts of mammals, including humans. Swine M. elsdenii strains were previously shown to have high levels of tetracycline resistance (MIC=64 to >256 μg/ml) and to carry mosaic (recombinant) tetracycline resistance genes. Baby pigs inherit intestinal microbiota from the mother sow. In these investigations we addressed two questions. When do M. elsdenii strains from the sow colonize baby pigs? Can five antibiotic-sensitive M. elsdenii strains administered intragastrically to newborn pigs affect natural colonization of the piglets by antibiotic-resistant (AR) M. elsdenii strains from the mother? M. elsdenii natural colonization of newborn pigs was undetectable (<10(4) CFU/g [wet weight] of feces) prior to weaning (20 days after birth). After weaning, all pigs became colonized (4 × 10(5) to 2 × 10(8) CFU/g feces). In a separate study, 61% (76/125) of M. elsdenii isolates from a gravid sow never exposed to antibiotics were resistant to chlortetracycline, ampicillin, or tylosin. The inoculation of the sow's offspring with mixtures of M. elsdenii antibiotic-sensitive strains prevented colonization of the offspring by maternal AR strains until at least 11 days postweaning. At 25 and 53 days postweaning, however, AR strains predominated. Antibiotic susceptibility phenotypes and single nucleotide polymorphism (SNP)-based identities of M. elsdenii isolated from sow and offspring were unexpectedly diverse. These results suggest that dosing newborn piglets with M. elsdenii antibiotic-sensitive strains delays but does not prevent colonization by maternal resistant strains. M. elsdenii subspecies diversity offers an explanation for the persistence of resistant strains in the absence of antibiotic selection.
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Affiliation(s)
- Thad B Stanton
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
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Riccobono E, Pallecchi L, Mantella A, Bartalesi F, Zeballos IC, Trigoso C, Villagran AL, Bartoloni A, Rossolini GM. Carriage of antibiotic-resistant Escherichia coli among healthy children and home-raised chickens: a household study in a resource-limited setting. Microb Drug Resist 2011; 18:83-7. [PMID: 21711148 DOI: 10.1089/mdr.2011.0003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have previously observed high rates of acquired antibiotic resistance in commensal Escherichia coli from healthy children living in urban areas of Bolivia and Peru, including resistance to tetracycline and quinolones, which are not routinely used in childhood. In this work we investigated acquired resistance in commensal E. coli from healthy children and home-raised chickens in 12 households from one of the previously surveyed urban area in Bolivia, to ascertain the possibility of human-animal exchange of resistant strains in similar settings. The resistance rates to ampicillin, tetracycline, chloramphenicol, streptomycin, and trimethoprim-sulphametoxazole were overall high (≥50%) and comparable between children and chickens, whereas those to quinolones were significantly higher in chickens (81% vs. 29% for nalidixic acid; 43% vs. 10% for ciprofloxacin). Molecular characterization of tetracycline- and quinolone-resistant isolates (n = 66) from children and chickens of three selected households revealed a remarkable clonal diversity and, in some cases, the presence of the same resistant strains among children or among chickens living in the same household, but not between children and chickens. Several resistance plasmids were characterized, but inter-clonal plasmid dissemination was not detected. Overall, the results from the present study suggested that cross-transmission between children and home-raised chickens could not represent a major spreading mechanism for resistant E. coli in households of resource-limited settings with high human-animal promiscuity.
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Affiliation(s)
- Eleonora Riccobono
- Dipartimento di Biotecnologie, Sezione di Microbiologia, Università di Siena, Siena, Italy
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Heringa S, Kim J, Shepherd MW, Singh R, Jiang X. The Presence of Antibiotic Resistance and Integrons inEscherichia coliIsolated from Compost. Foodborne Pathog Dis 2010; 7:1297-304. [DOI: 10.1089/fpd.2010.0544] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Spencer Heringa
- Department of Food Science and Human Nutrition, Clemson University, Clemson, South Carolina
| | - Jinkyung Kim
- Department of Food Science and Human Nutrition, Clemson University, Clemson, South Carolina
| | - Marion W. Shepherd
- Department of Food Science and Human Nutrition, Clemson University, Clemson, South Carolina
| | - Randhir Singh
- Department of Food Science and Human Nutrition, Clemson University, Clemson, South Carolina
| | - Xiuping Jiang
- Department of Food Science and Human Nutrition, Clemson University, Clemson, South Carolina
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Bailey JK, Pinyon JL, Anantham S, Hall RM. Commensal Escherichia coli of healthy humans: a reservoir for antibiotic-resistance determinants. J Med Microbiol 2010; 59:1331-1339. [DOI: 10.1099/jmm.0.022475-0] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study examined in detail the population structure of Escherichia coli from healthy adults with respect to the prevalence of antibiotic resistance and specific resistance determinants. E. coli isolated from the faeces of 20 healthy adults not recently exposed to antibiotics was tested for resistance to ten antibiotics and for carriage of integrons and resistance determinants using PCR. Strain diversity was assessed using biochemical and molecular criteria. E. coli was present in 19 subjects at levels ranging from 2.0×104 to 1.7×108 c.f.u. (g faeces)−1. Strains resistant to one to six antibiotics were found at high levels (>30 %) in only ten individuals, but at significant levels (>0.5 %) in 14. Resistant isolates with the same phenotype from the same individual were indistinguishable, but more than one susceptible strain was sometimes found. Overall, individuals harboured one to four E. coli strains, although in 17 samples one strain was dominant (>70 % of isolates). Eighteen strains resistant to ampicillin, sulfamethoxazole, tetracycline and trimethoprim in 15 different combinations were observed. One resistant strain was carried by two unrelated individuals and a susceptible strain was shared by two cohabiting subjects. Two minority strains were derivatives of a more abundant resistant strain in the same sample, showing that continuous evolution is occurring in vivo. The trimethoprim-resistance genes dfrA1, dfrA5, dfrA7, dfrA12 or dfrA17 were in cassettes in a class 1 or class 2 integron. Ampicillin resistance was conferred by the bla
TEM gene, sulfamethoxazole resistance by sul1, sul2 or sul3 and tetracycline resistance by tetA(A) or tetA(B). Chloramphenicol resistance (cmlA1 gene) was detected only once. Phylogenetic groups A and B2 were more common than B1 and D. Commensal E. coli of healthy humans represent an important reservoir for numerous antibiotic-resistance genes in many combinations. However, measuring the true extent of resistance carriage in commensal E. coli requires in-depth analysis.
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Affiliation(s)
- Jannine K. Bailey
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Jeremy L. Pinyon
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Sashindran Anantham
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Ruth M. Hall
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
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