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Liu J, Li W, Yao C, Yu J, Zhang H. Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts. BMC Microbiol 2022; 22:158. [PMID: 35710325 PMCID: PMC9202165 DOI: 10.1186/s12866-022-02573-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/06/2022] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics. RESULTS A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine. CONCLUSIONS These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.
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Affiliation(s)
- Jiaqi Liu
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Caiqing Yao
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering (Inner Mongolia Agricultural University), Ministry of Education; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.
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Montero L, Irazabal J, Cardenas P, Graham JP, Trueba G. Extended-Spectrum Beta-Lactamase Producing- Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador. Front Microbiol 2021; 12:709418. [PMID: 34671324 PMCID: PMC8521160 DOI: 10.3389/fmicb.2021.709418] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The blaCTX–M–55, blaCTX–M 65, and blaCTX–M 15 genes were the most frequently found gene associated with the ESBL phenotype and coincided with the blaCTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.
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Affiliation(s)
- Lorena Montero
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jorge Irazabal
- Agrocalidad, Agencia de Regulación y Control Fito y Zoosanitario, Quito, Ecuador
| | - Paul Cardenas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jay P Graham
- Environmental Health Sciences Division, University of California, Berkeley, Berkeley, CA, United States
| | - Gabriel Trueba
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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3
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Bezabih YM, Sabiiti W, Alamneh E, Bezabih A, Peterson GM, Bezabhe WM, Roujeinikova A. The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community. J Antimicrob Chemother 2021; 76:22-29. [PMID: 33305801 DOI: 10.1093/jac/dkaa399] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Intestinal colonization by ESBL Escherichia coli and its association with community-acquired MDR infections is of great concern. This review determined the worldwide prevalence of human faecal ESBL E. coli carriage and its trend in the community over the past two decades. METHODS A systematic literature search was conducted using PubMed, EMBASE and Google Scholar to retrieve articles published between 1 January 2000 and 13 February 2020 that contained data on the prevalence of faecal carriage of ESBL E. coli among healthy individuals. A cumulative (for the whole period) meta-analysis was used to estimate the global and regional pooled prevalence rates. Articles were grouped into study periods of 3 years, and subgroup meta-analyses were undertaken to examine the global pooled prevalence over time. RESULTS Sixty-two articles covering 29 872 healthy persons were included in this meta-analysis. The cumulative (2003-18) global pooled prevalence of ESBL E. coli intestinal carriage in the community was 16.5% (95% CI 14.3%-18.7%; P < 0.001). The pooled prevalence showed an upward trend, increasing from 2.6% (95% CI 1.6%-4.0%) in 2003-05 to 21.1% (95% CI 15.8%-27.0%) in 2015-18. Over the whole period, the highest carriage rate was observed in South-East Asia (27%; 95% CI 2.9%-51.3%), while the lowest occurred in Europe (6.0%; 95% CI 4.6%-7.5%). CONCLUSIONS Globally, an 8-fold increase in the intestinal carriage rate of ESBL E. coli in the community has occurred over the past two decades. Prevention of its spread may require new therapeutic and public health strategies.
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Affiliation(s)
- Yihienew M Bezabih
- Arsi University College of Health Sciences, Arsi University, PO Box 0193, Asella, Ethiopia
| | - Wilber Sabiiti
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
| | | | - Alamneh Bezabih
- École nationale vétérinaire, agroalimentaire et de l'alimentation, Nantes-Atlantique, BIOEPAR (UMR1300 INRA/ONIRIS), Nantes, France
| | | | | | - Anna Roujeinikova
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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Logan LK, Medernach RL, Domitrovic TN, Rispens JR, Hujer AM, Qureshi NK, Marshall SH, Nguyen DC, Rudin SD, Zheng X, Konda S, Weinstein RA, Bonomo RA. The Clinical and Molecular Epidemiology of CTX-M-9 Group Producing Enterobacteriaceae Infections in Children. Infect Dis Ther 2019; 8:243-254. [PMID: 30772921 PMCID: PMC6522575 DOI: 10.1007/s40121-019-0237-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
Introduction The pandemic of extended-spectrum beta-lactamase-(ESBL)-producing Enterobacteriaceae (Ent) is strongly linked to the dissemination of CTX-M-type-ESBL-Ent. We sought to define the epidemiology of infections in children due to an emerging resistance type, CTX-M-9-group-producing-Ent (CTX-M-9-grp-Ent). Methods A retrospective matched case-control analysis of children with CTX-M-9-grp-Ent infections who received medical care at three Chicago area hospitals was performed. Cases were defined as children possessing extended-spectrum cephalosporin-resistant (ESC-R) infections due to blaCTX-M-9. PCR and DNA analysis assessed beta-lactamase (bla) genes, multi-locus sequence types (MLST) and phylogenetic grouping of E. coli. Controls were children with ESC-susceptible (ESC-S)-Ent infections matched one case to three controls by age, source, and hospital. The clinical-epidemiologic predictors of CTX-M-9-grp-Ent infection were assessed. Results Of 356 ESC-R-Ent isolates from children (median age 4.1 years), the CTX-M-9-group was the solely detected bla gene in 44 (12.4%). The predominant species was E. coli (91%) of virulent phylogroups D (60%) and B2 (40%). MLST revealed multiple strain types. On multivariable analysis, CTX-M-9-grp-Ent occurred more often in E. coli than other Ent genera (OR 7.4, 95% CI 2.4, 27.2), children of non-Black-White-Hispanic race (OR 7.4, 95% CI 2.4, 28.2), and outpatients (OR 4.5, 95% CI 1.7, 12.3), which was a very unexpected finding for infections due to antibiotic-resistant bacteria. Residents of South Chicago had a 6.7 times higher odds of having CTX-M-9-grp-Ent infections than those in the reference region (West), while residence in Northwestern Chicago was associated with an 81% decreased odds of infection. Other demographic, comorbidity, invasive-device, and antibiotic use differences were not found. Conclusion CTX-M-9-grp-Ent infection may be associated with patient residence and is occurring in children without traditional in-patient exposure risk factors. This suggests that among children, the community environment may be a key contributor in the spread of these resistant pathogens.
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Affiliation(s)
- Latania K Logan
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA. .,Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA. .,Cook County Health and Hospital Systems, Chicago, IL, USA.
| | - Rachel L Medernach
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - T Nicholas Domitrovic
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Jared R Rispens
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Nadia K Qureshi
- Pediatrics, Loyola University Medical Center, Maywood, IL, USA
| | - Steven H Marshall
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - David C Nguyen
- Pediatrics, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA.,Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA
| | - Susan D Rudin
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Xiaotian Zheng
- Microbiology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sreenivas Konda
- Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, IL, USA
| | - Robert A Weinstein
- Medicine, Rush University Medical Center, Rush Medical College, Chicago, IL, USA.,Cook County Health and Hospital Systems, Chicago, IL, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Case Western Reserve School of Medicine, Cleveland, OH, USA.,Pharmacology, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.,Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.,Biochemistry, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.,Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
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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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Njage PMK, Buys EM. Pathogenic and commensal Escherichia coli from irrigation water show potential in transmission of extended spectrum and AmpC β-lactamases determinants to isolates from lettuce. Microb Biotechnol 2015; 8:462-73. [PMID: 25488608 PMCID: PMC4408178 DOI: 10.1111/1751-7915.12234] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 10/07/2014] [Indexed: 11/28/2022] Open
Abstract
There are few studies on the presence of extended-spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) in bacteria that contaminate vegetables. The role of the production environment in ESBL/AmpC gene transmission is poorly understood. The occurrence of ESBL/AmpC in Escherichia coli (n = 46) from lettuce and irrigation water and the role of irrigation water in the transmission of resistant E. coli were studied. The presence of ESBL/AmpC, genetic similarity and phylogeny were typed using genotypic and phenotypic techniques. The frequency of β-lactamase gene transfer was studied in vitro. ESBLs/AmpC were detected in 35 isolates (76%). Fourteen isolates (30%) produced both ESBLs/AmpC. Prevalence was highest in E. coli from lettuce (90%). Twenty-two isolates (48%) were multi-resistant with between two and five ESBL/AmpC genes. The major ESBL determinant was the CTX-M type (34 isolates). DHA (33% of isolates) were the dominant AmpC β lactamases. There was a high conjugation efficiency among the isolates, ranging from 3.5 × 10(-2) to 1 × 10(-2) ± 1.4 × 10(-1) transconjugants per recipient. Water isolates showed a significantly higher conjugation frequency than those from lettuce. A high degree of genetic relatedness between E. coli from irrigation water and lettuce indicated possible common ancestry and pathway of transmission.
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Affiliation(s)
- Patrick M K Njage
- Department of Food Science, University of Pretoria Lynwood RoadPretoria, 0002, South Africa
| | - Elna M Buys
- Department of Food Science, University of Pretoria Lynwood RoadPretoria, 0002, South Africa
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Leimbach A, Hacker J, Dobrindt U. E. coli as an All-Rounder: The Thin Line Between Commensalism and Pathogenicity. Curr Top Microbiol Immunol 2013; 358:3-32. [PMID: 23340801 DOI: 10.1007/82_2012_303] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Skippington E, Ragan MA. Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 2011; 35:707-35. [DOI: 10.1111/j.1574-6976.2010.00261.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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9
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Assessment of bacterial antibiotic resistance transfer in the gut. Int J Microbiol 2011; 2011:312956. [PMID: 21318188 PMCID: PMC3034945 DOI: 10.1155/2011/312956] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 11/21/2010] [Accepted: 12/09/2010] [Indexed: 12/21/2022] Open
Abstract
We assessed horizontal gene transfer between bacteria in the gastrointestinal (GI) tract. During the last decades, the emergence of antibiotic resistant strains and treatment failures of bacterial infections have increased the public awareness of antibiotic usage. The use of broad spectrum antibiotics creates a selective pressure on the bacterial flora, thus increasing the emergence of multiresistant bacteria, which results in a vicious circle of treatments and emergence of new antibiotic resistant bacteria. The human gastrointestinal tract is a massive reservoir of bacteria with a potential for both receiving and transferring antibiotic resistance genes. The increased use of fermented food products and probiotics, as food supplements and health promoting products containing massive amounts of bacteria acting as either donors and/or recipients of antibiotic resistance genes in the human GI tract, also contributes to the emergence of antibiotic resistant strains. This paper deals with the assessment of antibiotic resistance gene transfer occurring in the gut.
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Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, Kirn TJ, Bushman FD, Artis D. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 2010; 3:148-58. [PMID: 19940845 PMCID: PMC2824244 DOI: 10.1038/mi.2009.132] [Citation(s) in RCA: 312] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Despite widespread use of antibiotics, few studies have measured their effects on the burden or diversity of bacteria in the mammalian intestine. We developed an oral antibiotic treatment protocol and characterized its effects on murine intestinal bacterial communities and immune cell homeostasis. Antibiotic administration resulted in a 10-fold reduction in the amount of intestinal bacteria present and sequencing of 16S rDNA segments revealed significant temporal and spatial effects on luminal and mucosal-associated communities including reductions in luminal Firmicutes and mucosal-associated Lactobacillus species, and persistence of bacteria belonging to the Bacteroidetes and Proteobacteria phyla. Concurrently, antibiotic administration resulted in reduced RELM beta production, and reduced production of interferon-gamma and interleukin-17A by mucosal CD4(+) T lymphocytes. This comprehensive temporal and spatial metagenomic analyses will provide a resource and framework to test the influence of bacterial communities in murine models of human disease.
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Affiliation(s)
- David A. Hill
- University of Pennsylvania School of Veterinary Medicine, Department of Pathobiology, 314 Hill Pavilion, 380 South University Avenue Philadelphia, PA 19104-4539, Tel: 215 898-7920, Fax: 215 746-2295,
| | - Christian Hoffmann
- University of Pennsylvania School of Medicine, Department of Microbiology, 402C Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, Tel: 215 573-8732, Fax: 215 573-4856,
| | - Michael C. Abt
- University of Pennsylvania School of Veterinary Medicine, Department of Pathobiology, 314 Hill Pavilion, 380 South University Avenue Philadelphia, PA 19104-4539, Tel: 215 898-7920, Fax: 215 746-2295,
| | - Yurong Du
- University of Pennsylvania School of Veterinary Medicine, Department of Pathobiology, 314 Hill Pavilion, 380 South University Avenue Philadelphia, PA 19104-4539, Tel: 215 898-7920, Fax: 215 746-2295,
| | - Dmytro Kobuley
- University of Pennsylvania School of Veterinary Medicine, Department of Pathobiology, 314 Hill Pavilion, 380 South University Avenue Philadelphia, PA 19104-4539, Tel: 215 898-7920, Fax: 215 746-2295,
| | - Thomas J. Kirn
- University of Pennsylvania School of Veterinary Medicine, Department of Pathobiology, 314 Hill Pavilion, 380 South University Avenue Philadelphia, PA 19104-4539, Tel: 215 898-7920, Fax: 215 746-2295,
| | - Frederic D. Bushman
- University of Pennsylvania School of Medicine, Department of Microbiology, 402C Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, Tel: 215 573-8732, Fax: 215 573-4856, ,joint corresponding authors, please address editorial correspondence to David Artis
| | - David Artis
- University of Pennsylvania School of Veterinary Medicine, Department of Pathobiology, 314 Hill Pavilion, 380 South University Avenue Philadelphia, PA 19104-4539, Tel: 215 898-7920, Fax: 215 746-2295, ,joint corresponding authors, please address editorial correspondence to David Artis
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Beaume M, Hernandez D, Francois P, Schrenzel J. New approaches for functional genomic studies in staphylococci. Int J Med Microbiol 2009; 300:88-97. [PMID: 20005775 DOI: 10.1016/j.ijmm.2009.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Functional transcriptomics studies have resulted in interesting insights into Staphylococcus aureus diversity and pathogenicity. Here we review the principles, advantages and disadvantages of recent technical developments in the field of transcriptomics and their potential impact on S. aureus research.
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Affiliation(s)
- Marie Beaume
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland
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12
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Huyghe A, Francois P, Schrenzel J. Characterization of microbial pathogens by DNA microarrays. INFECTION GENETICS AND EVOLUTION 2008; 9:987-95. [PMID: 19061975 PMCID: PMC7128123 DOI: 10.1016/j.meegid.2008.10.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 10/21/2008] [Accepted: 10/26/2008] [Indexed: 02/01/2023]
Affiliation(s)
- Antoine Huyghe
- Genomic Research Laboratory, Infectious Diseases Service, University of Geneva Hospitals, Micheli-du-Crest 24, 1211 Geneva 14, Geneva, Switzerland.
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