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Pepper IL, Brooks JP, Gerba CP. Antibiotic Resistant Bacteria in Municipal Wastes: Is There Reason for Concern? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3949-3959. [PMID: 29505255 DOI: 10.1021/acs.est.7b04360] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recently, there has been increased concern about the presence of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARG), in treated domestic wastewaters, animal manures and municipal biosolids. The concern is whether these additional sources of ARB contribute to antibiotic resistance levels in the environment, that is, "environmental antibiotic resistance." ARB and ARG occur naturally in soil and water, and it remains unclear whether the introduction of ARB in liquid and solid municipal and animal wastes via land application have any significant impact on the background levels of antibiotic resistance in the environment, and whether they affect human exposure to ARB. In this current review, we examine and re-evaluate the incidence of ARB and ARG resulting from land application activities, and offer a new perspective on the threat of antibiotic resistance to public health via exposure from nonclinical environmental sources. Based on inputs of ARBs and ARGs from land application, their fate in soil due to soil microbial ecology principles, and background indigenous levels of ARBs and ARGs already present in soil, we conclude that while antibiotic resistance levels in soil are increased temporally by land application of wastes, their persistence is not guaranteed and is in fact variable, and often contradictory based on application site. Furthermore, the application of wastes may not produce the most direct impact of ARGs and ARB on public health. Further investigation is still warranted in agriculture and public health, including continued scrutiny of antibiotic use in both sectors.
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Affiliation(s)
- Ian L Pepper
- Water and Energy Sustainable Technology Center (WEST) , The University of Arizona , 2959 W. Calle Agua Nueva , Tucson , Arizona 85745 , United States
| | - John P Brooks
- Genetics and Sustainable Agriculture Research Unit, USDA ARS , Mississippi State , Mississippi , 39762 , United States
| | - Charles P Gerba
- Water and Energy Sustainable Technology Center (WEST) , The University of Arizona , 2959 W. Calle Agua Nueva , Tucson , Arizona 85745 , United States
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52
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Bok E, Mazurek J, Myc A, Stosik M, Wojciech M, Baldy-Chudzik K. Comparison of Commensal Escherichia coli Isolates from Adults and Young Children in Lubuskie Province, Poland: Virulence Potential, Phylogeny and Antimicrobial Resistance. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040617. [PMID: 29597292 PMCID: PMC5923659 DOI: 10.3390/ijerph15040617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/14/2022]
Abstract
Commensal Escherichia coli population is a dynamic structure which may be important in the pathogenesis of extraintestinal infections. The aim of this study was the comparison of genetic diversity of commensal E. coli isolates from two age group—adults and young children. E. coli strains were isolated on MacConkey agar and identified by biochemical tests. Determination of four major phylogenetic groups, identification of virulence genes and antimicrobial resistance determinants were performed by using multiplex or simplex PCR. Phenotypic analysis of resistance was based on disc-diffusion method. The prevalence of virulence genes was significantly higher among isolates from adults than from young children. Phylogroup B2 predominated among E. coli from adults, whereas phylogroup A was the most common in isolates from young children. The analyses of antimicrobial resistance revealed that resistance to at least one antimicrobial agent and multidrug-resistance were detected significantly more frequent in the isolates from adults than from young children. This study documented that the commensal E. coli isolates from adults showed greater genetic diversity than from young children and constitutes a substantial reservoir of the virulence genes typical for extraintestinal pathogenic E. coli.
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Affiliation(s)
- Ewa Bok
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
| | - Justyna Mazurek
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
| | - Andrzej Myc
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
- Laboratory of Virology, Department of Immunology of Infectious Diseases, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland.
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI 48109-5648, USA.
| | - Michał Stosik
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
| | - Magdalena Wojciech
- Department of Mathematical Statistics and Econometrics, Faculty of Mathematics, Computer Science and Econometrics, University of Zielona Góra, 65-516 Zielona Góra, Poland.
| | - Katarzyna Baldy-Chudzik
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
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53
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Nogacka AM, Salazar N, Arboleya S, Suárez M, Fernández N, Solís G, de Los Reyes-Gavilán CG, Gueimonde M. Early microbiota, antibiotics and health. Cell Mol Life Sci 2018; 75:83-91. [PMID: 28988290 PMCID: PMC11105232 DOI: 10.1007/s00018-017-2670-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022]
Abstract
The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance. Exposure to antibiotics, either prenatally or postnatally, is common in early life mainly due to the use of intrapartum prophylaxis or to the administration of antibiotics in C-section deliveries. However, we are still far from understanding the impact of early antibiotics and their long-term effects. Increased risk of non-communicable diseases, such as allergies or obesity, has been observed in individuals exposed to antibiotics during early infancy. Moreover, the impact of antibiotics on the establishment of the infant gut resistome, and on the role of the microbiota as a reservoir of resistance genes, should be evaluated in the context of the problems associated with the increasing number of antibiotic resistant pathogenic strains. In this article, we review and discuss the above-mentioned issues with the aim of encouraging debate on the actions needed for understanding the impact of early life antibiotics upon human microbiota and health and for developing strategies aimed at minimizing this impact.
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Affiliation(s)
- Alicja M Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marta Suárez
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Nuria Fernández
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Gonzalo Solís
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain.
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54
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Ma Q, Fu Y, Sun H, Huang Y, Li L, Yu Q, Dinnyes A, Sun Q. Antimicrobial resistance of Lactobacillus spp. from fermented foods and human gut. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.07.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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55
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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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Impact of "Raised without Antibiotics" Beef Cattle Production Practices on Occurrences of Antimicrobial Resistance. Appl Environ Microbiol 2017; 83:AEM.01682-17. [PMID: 28887421 DOI: 10.1128/aem.01682-17] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/05/2017] [Indexed: 01/04/2023] Open
Abstract
The specific antimicrobial resistance (AMR) decreases that can be expected from reducing antimicrobial (AM) use in U.S. beef production have not been defined. To address this data gap, feces were recovered from 36 lots of "raised without antibiotics" (RWA) and 36 lots of "conventional" (CONV) beef cattle. Samples (n = 719) were collected during harvest and distributed over a year. AMR was assessed by (i) the culture of six AM-resistant bacteria (ARB), (ii) quantitative PCR (qPCR) for 10 AMR genes (ARGs), (iii) a qPCR array of 84 ARGs, and (iv) metagenomic sequencing. Generally, AMR levels were similar, but some were higher in CONV beef cattle. The prevalence of third-generation cephalosporin-resistant (3GCr) Escherichia coli was marginally different between production systems (CONV, 47.5%; RWA, 34.8%; P = 0.04), but the seasonal effect (summer, 92.8%; winter, 48.3%; P < 0.01) was greater. Erythromycin-resistant (ERYr) Enterococcus sp. concentrations significantly differed between production systems (CONV, 1.91 log10 CFU/g; RWA, 0.73 log10 CFU/g; P < 0.01). Levels of aadA1, ant(6)-I, bla ACI, erm(A), erm(B), erm(C), erm(F), erm(Q), tet(A), tet(B), tet(M), and tet(X) ARGs were higher (P < 0.05) in the CONV system. Aggregate abundances of all 43 ARGs detected by metagenomic sequencing and the aggregate abundances of ARGs in the aminoglycoside, β-lactam, macrolide-lincosamide-streptogramin B (MLS), and tetracycline AM classes did not differ (log2 fold change < 1.0) between CONV and RWA systems. These results suggest that further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.IMPORTANCE The majority of antimicrobial (AM) use in the United States is for food-animal production, leading to concerns that typical AM use patterns during "conventional" (CONV) beef cattle production in the United States contribute broadly to antimicrobial resistance (AMR) occurrence. In the present study, levels of AMR were generally similar between CONV and "raised without antibiotics" (RWA) cattle. Only a limited number of modest AMR increases was observed in CONV cattle, primarily involving macrolide-lincosamide-streptogramin B (MLS) and tetracycline resistance. Macrolides (tylosin) and tetracyclines (chlortetracycline) are administered in-feed for relatively long durations to reduce liver abscesses. To ensure judicious AM use, the animal health, economic, and AMR impacts of shorter duration in-feed administration of these AMs should be examined. However, given the modest AMR reductions observed, further reductions of AM use in U.S. beef cattle production may not yield significant AMR reductions beyond MLS and tetracycline resistance.
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57
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Rose G, Shaw AG, Sim K, Wooldridge DJ, Li MS, Gharbia S, Misra R, Kroll JS. Antibiotic resistance potential of the healthy preterm infant gut microbiome. PeerJ 2017; 5:e2928. [PMID: 28149696 PMCID: PMC5270596 DOI: 10.7717/peerj.2928] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/20/2016] [Indexed: 01/06/2023] Open
Abstract
Background Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. Results Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. Conclusions We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.
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Affiliation(s)
- Graham Rose
- Genomics Research Unit, Public Health England , London , United Kingdom
| | - Alexander G Shaw
- Department of Medicine, Imperial College London , London , United Kingdom
| | - Kathleen Sim
- Department of Medicine, Imperial College London , London , United Kingdom
| | | | - Ming-Shi Li
- Department of Medicine, Imperial College London , London , United Kingdom
| | - Saheer Gharbia
- Genomics Research Unit, Public Health England , London , United Kingdom
| | - Raju Misra
- Genomics Research Unit, Public Health England , London , United Kingdom
| | - John Simon Kroll
- Section of Paediatrics, Department of Medicine, Imperial College London , London , United Kingdom
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58
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Halimi S, Mirsalehian A. Assessment and comparison of probiotic potential of four Lactobacillus species isolated from feces samples of Iranian infants. Microbiol Immunol 2016; 60:73-81. [PMID: 26648174 DOI: 10.1111/1348-0421.12352] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/02/2015] [Accepted: 12/01/2015] [Indexed: 02/03/2023]
Abstract
The probiotic potential of Lactobacillus species isolated from infant feces was investigated. For this study, the antibiotic susceptibility, tolerance in gut-related conditions, antimicrobial activity, and ability to adhere to a human colorectal adenocarcinoma cell line (Caco-2 cells) of four common Lactobacillus species (Lactobacillus paracasei [n = 15], Lactobacillus rhamnosus [n = 45], Lactobacillus gasseri [n = 20] and Lactobacillus fermentum [n = 18]) were assessed. Most isolates that which were sensitive to imipenem, ampicillin, gentamycin, erythromycin and tetracycline were selected for other tests. L. gasseri isolates had the greatest sensitivity to gastric and intestinal fluids (<10% viability). L. fermentum (FH5, FH13 and FH18) had the highest adhesion to Caco-2 cells. The lowest antibacterial activity against pathogenic bacteria was shown by L. gasseri strains in spot tests. Furthermore, non-adjusted cell-free culture supernatants with low pH had greater antimicrobial activity, which was related to organic acid. The results showed that some isolates of L. rhamnosus and L. fermentum are suitable for use as a probiotic.
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Affiliation(s)
- Shahnaz Halimi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Akbar Mirsalehian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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59
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Safety evaluation of AB-LIFE® (Lactobacillus plantarum CECT 7527, 7528 and 7529): Antibiotic resistance and 90-day repeated-dose study in rats. Food Chem Toxicol 2016; 92:117-28. [DOI: 10.1016/j.fct.2016.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/12/2016] [Accepted: 03/21/2016] [Indexed: 01/07/2023]
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60
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Guillard T, Pons S, Roux D, Pier GB, Skurnik D. Antibiotic resistance and virulence: Understanding the link and its consequences for prophylaxis and therapy. Bioessays 2016; 38:682-93. [PMID: 27248008 DOI: 10.1002/bies.201500180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
"Antibiotic resistance is usually associated with a fitness cost" is frequently accepted as common knowledge in the field of infectious diseases. However, with the advances in high-throughput DNA sequencing that allows for a comprehensive analysis of bacterial pathogenesis at the genome scale, including antibiotic resistance genes, it appears that this paradigm might not be as solid as previously thought. Recent studies indicate that antibiotic resistance is able to enhance bacterial fitness in vivo with a concomitant increase in virulence during infections. As a consequence, strategies to minimize antibiotic resistance turn out to be not as simple as initially believed. Indeed, decreased antibiotic use may not be sufficient to let susceptible strains outcompete the resistant ones. Here, we put in perspective these findings and review alternative approaches, such as preventive and therapeutic anti-bacterial immunotherapies that have the potential to by-pass the classic antibiotics.
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Affiliation(s)
- Thomas Guillard
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Laboratoire de Bactériologie-Virologie-Hygiène hospitalière, Hôpital Robert Debré - CHU de Reims, UFR de Médecine, Université de Reims Champagne-Ardenne, Reims, France
| | - Stéphanie Pons
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Damien Roux
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,INSERM, IAME, UMR 1137, Paris, France.,Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, Colombes, France
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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61
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Yang Z, Guo Z, Qiu C, Li Y, Feng X, Liu Y, Zhang Y, Pang P, Wang P, Zhou Q, Han L, Dai W. Preliminary analysis showed country-specific gut resistome based on 1267 feces samples. Gene 2016; 581:178-82. [DOI: 10.1016/j.gene.2016.01.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/29/2015] [Accepted: 01/19/2016] [Indexed: 11/30/2022]
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62
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von Wintersdorff CJH, Wolffs PFG, Savelkoul PHM, Nijsen RRR, Lau S, Gerhold K, Hamelmann E, Penders J. The gut resistome is highly dynamic during the first months of life. Future Microbiol 2016; 11:501-10. [PMID: 27064174 DOI: 10.2217/fmb.15.154] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
AIM We investigated the longitudinal development of several antibiotic resistance genes (ARGs) of the infant gut resistome during the first months after birth. MATERIALS & METHODS Fecal samples from 120 infants collected at the ages of 5, 13 and 31 weeks were analyzed and subjected to qPCR for the detection of several ARGs. RESULTS The prevalence of ARGs significantly increased for ermB, tetM and tetQ, while it decreased for aac(6')-aph(2'). Birth mode and breastfeeding significantly affected tetQ prevalence. Correlations to bacterial taxa suggest that fluctuations in some ARGs are (partly) attributed to shifts in bacteroides colonization rates. CONCLUSION Acquisition of ARGs in the gut microbiota occurs shortly after birth and resistome composition fluctuates over the course of several months, reflecting changes in microbial community structure.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology & Infection Control, VU University Medical Center, Amsterdam
| | - Rianne R R Nijsen
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Susanne Lau
- Department of Pediatrics, Pneumology & Immunology, Charité Medical University Berlin, Berlin, Germany
| | - Kerstin Gerhold
- Department of Pediatrics & Child Health, Section of Pediatric Rheumatology, Winnipeg, Manitoba, Canada
| | - Eckard Hamelmann
- Children's Hospital, Ev. Hospital Bielefeld (EvKB), Bielefeld, Germany
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition & Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.,Department of Medical Microbiology, Caphri School for Public Health & Primary Care, Maastricht University Medical Center+, Maastricht, The Netherlands
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63
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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: 447] [Impact Index Per Article: 55.9] [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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64
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Abstract
Probiotics are live microorganisms, mainly belonging to the genera Lactobacillus and Bifidobacterium, although also strain of other species are commercialized, that have a beneficial effect on the host. From the perspective of antibiotic use, probiotics have been observed to reduce the risk of certain infectious disease such as certain types of diarrhea and respiratory tract infection. This may be accompanied with a reduced need of antibiotics for secondary infections. Antibiotics tend to be effective against most common diseases, but increasingly resistance is being observed among pathogens. Probiotics are specifically selected to not contribute to the spread of antibiotic resistance and not carry transferable antibiotic resistance. Concomitant use of probiotics with antibiotics has been observed to reduce the incidence, duration and/or severity of antibiotic-associated diarrhea. This contributes to better adherence to the antibiotic prescription and thereby reduces the evolution of resistance. To what extent probiotics directly reduce the spread of antibiotic resistance is still much under investigation; but maintaining a balanced microbiota during antibiotic use may certainly provide opportunities for reducing the spread of resistances. Key messages Probiotics may reduce the risk for certain infectious diseases and thereby reduce the need for antibiotics. Probiotics may reduce the risk for antibiotic-associated diarrhea Probiotics do not contribute to the spread of antibiotic resistance and may even reduce it.
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Affiliation(s)
| | - Sofia Forssten
- a Active Nutrition, DuPont Nutrition and Health , Kantvik , Finland
| | | | - Anna Lyra
- a Active Nutrition, DuPont Nutrition and Health , Kantvik , Finland
| | - Buffy Stahl
- c DuPont Health and Nutrition , Madison , WI , USA
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65
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Thiemann S, Smit N, Strowig T. Antibiotics and the Intestinal Microbiome : Individual Responses, Resilience of the Ecosystem, and the Susceptibility to Infections. Curr Top Microbiol Immunol 2016; 398:123-146. [PMID: 27738912 DOI: 10.1007/82_2016_504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The intestinal microbiota is a diverse ecosystem containing thousands of microbial species, whose metabolic activity affects many aspects of human physiology. Large-scale surveys have demonstrated that an individual's microbiota composition is shaped by factors such as diet and the use of medications, including antibiotics. Loss of overall diversity and in some cases loss of single groups of bacteria as a consequence of antibiotic treatment in humans has been associated with enhanced susceptibility toward gastrointestinal infections and with enhanced weight gain and obesity in young children. Moreover, the extensive use of antibiotics has led to an increased abundance of antibiotic resistance genes (ARGs) within commensal bacteria that can be transferred to invading pathogens, which complicates the treatment of bacterial infections. In this review, we provide insight into the complex interplay between the microbiota and antibiotics focussing on (i) the effect of antibiotics on the composition of the microbiota, (ii) the impact of antibiotics on gastrointestinal infections, and (iii) finally the role of the microbiota as reservoir for ARGs. We also discuss how targeted manipulation of the microbiota may be used as an innovative therapeutic approach to reduce the incidence of bacterial infections as well as resulting complications.
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Affiliation(s)
| | - Nathiana Smit
- Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Brunswick, Germany.
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Antimicrobial consumption and resistance in five Gram-negative bacterial species in a hospital from 2003 to 2011. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 48:647-54. [DOI: 10.1016/j.jmii.2014.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 11/27/2013] [Accepted: 04/15/2014] [Indexed: 11/18/2022]
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Fitch FM, Carmo-Rodrigues MS, Oliveira VGS, Gaspari MV, Dos Santos A, de Freitas JB, Pignatari ACC. β-Lactam Resistance Genes: Characterization, Epidemiology, and First Detection of blaCTX-M-1 and blaCTX-M-14 in Salmonella spp. Isolated from Poultry in Brazil-Brazil Ministry of Agriculture's Pathogen Reduction Program. Microb Drug Resist 2015; 22:164-71. [PMID: 26380894 DOI: 10.1089/mdr.2015.0143] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Salmonella spp. are widespread in nature; however, human infections occur mainly through ingestion of contaminated food, specially poultry and eggs. In Brazil, the Ministry of Agriculture (MAPA) oversees food production in general, with the goal of preventing transmission of pathogens through the food chain. In 2004, MAPA initiated a program to monitor and control levels of Salmonella in poultry during slaughter. This study analyzes isolates from MAPA's program for β-lactam resistance and the resistance genes involved, as well as the geographic distributions of potentially clonal populations of resistant isolates within Brazil. Initially, 1,939 Salmonella spp. isolated between 2004 and 2011 were examined. These isolates were tested for antimicrobial susceptibility, and 100 isolates resistant or intermediate to ampicillin and ceftriaxone were screened initially for the presence of blaSHV, blaTEM, blaOXA, blaPSA, blaCMY-1, and blaCMY-2 genes. There were 55 isolates whose resistance genes were not identified by this panel and these isolates are the subject of this report. These 55 isolates were differentiated into 31 distinct ribogroups, with multiple β-lactam resistance genes, including AmpC blaCMY, blaTEM, blaCTX-M-1, blaCTX-M-2, blaCTX-M-8, and blaCTX-M-14. Isolates carrying variants of blaCTX-M were identified in three geographic regions. Salmonella carrying particular genetic variants of blaCTX-M and belonging to the same ribogroup were identified from multiple poultry slaughtering facilities. In some instances, these presumptive clonal-related isolates were from facilities over 300 miles apart, indicating potential clonal spread between two geographic regions. This is the first report of blaCTX-M-1 and blaCTX-M-14 in Salmonella in Brazil.
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Affiliation(s)
| | | | | | | | - Amaury Dos Santos
- 2 Ministry of Agriculture and Food Supply , LANAGRO, Campinas, Brazil
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68
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High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples. J Dev Orig Health Dis 2015; 7:35-44. [PMID: 26353938 DOI: 10.1017/s2040174415001506] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gastrointestinal tract (GIT) microbiota has been identified as an important reservoir of antibiotic resistance genes (ARGs) that can be horizontally transferred to pathogenic species. Maternal GIT microbes can be transmitted to the offspring, and recent work indicates that such transfer starts before birth. We have used culture-independent genetic screenings to explore whether ARGs are already present in the meconium accumulated in the GIT during fetal life and in feces of 1-week-old infants. We have analyzed resistance to β-lactam antibiotics (BLr) and tetracycline (Tcr), screening for a variety of genes conferring each. To evaluate whether ARGs could have been inherited by maternal transmission, we have screened perinatal fecal samples of the 1-week-old babies' mothers, as well as a mother-infant series including meconium, fecal samples collected through the infant's 1st year, maternal fecal samples and colostrum. Our results reveal a high prevalence of BLr and Tcr in both meconium and early fecal samples, implying that the GIT resistance reservoir starts to accumulate even before birth. We show that ARGs present in the mother may reach the meconium and colostrum and establish in the infant GIT, but also that some ARGs were likely acquired from other sources. Alarmingly, we identified in both meconium and 1-week-olds' samples a particularly elevated prevalence of mecA (>45%), six-fold higher than that detected in the mothers. The mecA gene confers BLr to methicillin-resistant Staphylococcus aureus, and although its detection does not imply the presence of this pathogen, it does implicate the young infant's GIT as a noteworthy reservoir of this gene.
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Huang Y, Zhang L, Tiu L, Wang HH. Characterization of antibiotic resistance in commensal bacteria from an aquaculture ecosystem. Front Microbiol 2015; 6:914. [PMID: 26441859 PMCID: PMC4561822 DOI: 10.3389/fmicb.2015.00914] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/20/2015] [Indexed: 12/03/2022] Open
Abstract
The objective of the study was to improve the understanding of antibiotic resistance (AR) ecology through characterization of antibiotic-resistant commensal isolates associated with an aquaculture production system. A total of 4767 isolates non-susceptible to sulfamethoxazole/trimethoprim (Sul/Tri), tetracycline (Tet), erythromycin (Erm), or cefotaxime (Ctx), originated from fish, feed, and environmental samples of an aquaculture farm with no known history of antibiotic applications were examined. Close to 80% of the isolates exhibited multi-drug resistance in media containing the corresponding antibiotics, and representative AR genes were detected in various isolates by PCR, with feed isolates had the highest positive rate detected. Identified AR gene carriers involved 18 bacterial genera. Selected AR genes led to acquired resistance in other bacteria by transformation. The AR traits in many isolates were stable in the absence of selective pressure. AR-rich feed and possibly environmental factors may contribute to AR in the aquaculture ecosystem. For minimum inhibitory concentration test, brain heart infusion medium was found more suitable for majority of the bacteria examined than cation-adjusted Mueller Hinton broth, with latter being the recommended medium for clinical isolates by standard protocol. The data indicated a need to update the methodology due to genetic diversity of microbiota for better understanding of the AR ecology.
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Affiliation(s)
- Ying Huang
- Department of Food Science and Technology, The Ohio State University, Columbus, OHUSA
| | - Lu Zhang
- Department of Food Science and Technology, The Ohio State University, Columbus, OHUSA
| | - Laura Tiu
- South Centers, The Ohio State University, Piketon, OHUSA
| | - Hua H. Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OHUSA
- Department of Microbiology, The Ohio State University, Columbus, OHUSA
- School of Biological Sciences, Fudan University, Yangpu, ShanghaiChina
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Huang Y, Zhang L, Wang HH. Identification of a New Tetracycline Resistance Determinant tet47 from Fish Intestine. J Food Prot 2015; 78:1581-5. [PMID: 26219374 DOI: 10.4315/0362-028x.jfp-15-025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To better understand food safety risks, functional genomic analysis was conducted to identify undescribed antibiotic resistance genes in fish samples from an aquaculture fish farm in Ohio. A fosmid genomic library from pooled DNA of antibiotic-resistant isolates was used to screen for resistance genes against tetracycline (Tet). A new Tet-resistant determinant designated as tet 47 was identified, with the original hosts being Providencia spp. from fish intestine. The new gene was also found to confer Tet resistance in Escherichia coli. Fish and byproducts were shown to be possible carriers that may disseminate new, functional, and potentially transmissible antibiotic resistance determinants through food, feed, and environmental contacts.
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Affiliation(s)
- Ying Huang
- Department of Food Science and Technology, 2015 Fyffe Court, The Ohio State University, Columbus, Ohio 43210, USA
| | - Lu Zhang
- Department of Food Science and Technology, 2015 Fyffe Court, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hua H Wang
- Department of Food Science and Technology, 2015 Fyffe Court, The Ohio State University, Columbus, Ohio 43210, USA; 2Department of Microbiology, 484 West 12th Avenue, The Ohio State University, Columbus, Ohio 43210, USA.
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Gibson MK, Crofts TS, Dantas G. Antibiotics and the developing infant gut microbiota and resistome. Curr Opin Microbiol 2015; 27:51-6. [PMID: 26241507 DOI: 10.1016/j.mib.2015.07.007] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/12/2015] [Indexed: 02/07/2023]
Abstract
The microbial communities colonizing the human gut are tremendously diverse and highly personal. The composition and function of the microbiota play important roles in human health and disease, and considerable research has focused on understanding the ecological forces shaping these communities. While it is clear that factors such as diet, genotype of the host, and environment influence the adult gut microbiota community composition, recent work has emphasized the importance of early-life assembly dynamics in both the immediate and long-term personalized nature of the gut microbiota. While the mature adult gut microbiota is believed to be relatively stable, the developing infant gut microbiota (IGM) is highly dynamic and prone to disruption by external factors, including antibiotic exposure. Studies have revealed both transient and persistent alterations to the adult gut microbiota community resulting from antibiotic treatment later in life. As antibiotics are routinely prescribed at a greater rate in the first years of life, the impact of these interventions on the developing IGM is emerging as a key research priority. In addition to understanding the impact of these disruptions on the infant gut microbial architecture and related host diseases, we need to understand the contribution of early life antibiotics to the selection of antibiotic resistance gene reservoirs in the microbiota, and their threat to successful treatment of infectious disease. Here we review the current understanding of the developmental progression of the IGM and the impact of antibiotic therapies on its composition and encoded reservoir of antibiotic resistance genes.
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Affiliation(s)
- Molly K Gibson
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Terence S Crofts
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA; Department of Biomedical Engineering, Washington University, St Louis, MO, USA.
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Moore AM, Ahmadi S, Patel S, Gibson MK, Wang B, Ndao MI, Deych E, Shannon W, Tarr PI, Warner BB, Dantas G. Gut resistome development in healthy twin pairs in the first year of life. MICROBIOME 2015; 3:27. [PMID: 26113976 PMCID: PMC4480905 DOI: 10.1186/s40168-015-0090-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/05/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND The early life of the human host marks a critically important time for establishment of the gut microbial community, yet the developmental trajectory of gut community-encoded resistance genes (resistome) is unknown. We present a longitudinal study of the fecal antibiotic resistome of healthy amoxicillin-exposed and antibiotic-naive twins and their mothers during the first year of life. RESULTS We extracted metagenomic DNA (mgDNA) from fecal samples collected from three healthy twin pairs at three timepoints (1 or 2 months, 6 or 7 months, and 11 months) and from their mothers (collected at delivery). The mgDNA was used to construct metagenomic expression libraries in an Escherichia coli host. These libraries were screened for antibiotic resistance, and functionally selected resistance genes were sequenced and annotated. A diverse fecal resistome distinct from the maternal resistome was apparent by 2 months of age, and infants' fecal resistomes included resistance to clinically important broad-spectrum beta-lactam antibiotics (e.g., piperacillin-tazobactam, aztreonam, cefepime) not found in their mothers. Dissemination of resistance genes among members of a given family was positively correlated with sharing of those same resistance genes between unrelated families, potentially identifying within-family sharing as a marker of resistance genes emerging in the human community at large. Finally, we found a distinct developmental trajectory for a community-encoded function: chloramphenicol resistance. All study subjects at all timepoints harbored chloramphenicol resistance determinants, but multidrug efflux pumps (rarely found in mothers) were the primary effectors of chloramphenicol resistance in young infants. Chloramphenicol acetyltransferases were more common in mothers than in infants and were found in nearly all the infants at later timepoints. CONCLUSIONS Our results suggest that healthy 1-2-month-old infants' gut microbes harbor clinically relevant resistance genes distinct from those of their mothers, and that family-specific shared environmental factors early in life shape resistome development.
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Affiliation(s)
- Aimee M. Moore
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sara Ahmadi
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Sanket Patel
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Molly K. Gibson
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Bin Wang
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
| | - Malick I. Ndao
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Elena Deych
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - William Shannon
- />Department of Biostatistics, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Phillip I. Tarr
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Department of Molecular Microbiology, Washington University in St. School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Barbara B. Warner
- />Department of Pediatrics, Washington University in St Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
| | - Gautam Dantas
- />Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110 USA
- />Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108 USA
- />Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130 USA
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Impact of Ciprofloxacin and Clindamycin Administration on Gram-Negative Bacteria Isolated from Healthy Volunteers and Characterization of the Resistance Genes They Harbor. Antimicrob Agents Chemother 2015; 59:4410-6. [PMID: 25987611 DOI: 10.1128/aac.00068-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/21/2015] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to assess the impact of ciprofloxacin, clindamycin, and placebo administration on culturable Gram-negative isolates and the antibiotic resistance genes they harbor. Saliva and fecal samples were collected from healthy human volunteers before and at intervals, up to 1 year after antibiotic administration. Samples were plated on selective and nonselective media to monitor changes in different colony types or bacterial species. Following ciprofloxacin administration, there was a decrease of Escherichia coli in feces and after clindamycin administration a decrease of Bacteroides in feces and Leptotrichia in saliva, which all returned to pretreatment levels within 1 to 4 months. Ciprofloxacin administration also resulted in an increase in ciprofloxacin-resistant Veillonella in saliva, which persisted for 12 months. Additionally, 949 aerobic and anaerobic isolates purified from ciprofloxacin- and clindamycin-containing plates were screened for the presence of resistance genes. Resistance gene carriage was widespread in isolates from all three treatment groups, and no association was observed between genes and antibiotic administration. Although the anaerobic component of the microbiota was not a major reservoir of aerobe-associated antimicrobial resistance (AMR) genes, we detected the sulfonamide resistance gene sul2 in anaerobic isolates. The longitudinal nature of the study allowed identification of distinct Escherichia coli clones harboring multiple resistance genes, including one carrying an extended-spectrum β-lactamase blaCTX-M group 9 gene, which persisted in the gut for up to 4 months. This study provided insight into the effects of antibiotic administration on healthy microbiota and the diversity of resistance genes harbored therein.
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Anjum MF. Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota. Future Microbiol 2015; 10:317-20. [DOI: 10.2217/fmb.15.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Done HY, Venkatesan AK, Halden RU. Does the Recent Growth of Aquaculture Create Antibiotic Resistance Threats Different from those Associated with Land Animal Production in Agriculture? AAPS JOURNAL 2015; 17:513-24. [PMID: 25700799 DOI: 10.1208/s12248-015-9722-z] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/17/2015] [Indexed: 11/30/2022]
Abstract
Important antibiotics in human medicine have been used for many decades in animal agriculture for growth promotion and disease treatment. Several publications have linked antibiotic resistance development and spread with animal production. Aquaculture, the newest and fastest growing food production sector, may promote similar or new resistance mechanisms. This review of 650+ papers from diverse sources examines parallels and differences between land-based agriculture of swine, beef, and poultry and aquaculture. Among three key findings was, first, that of 51 antibiotics commonly used in aquaculture and agriculture, 39 (or 76%) are also of importance in human medicine; furthermore, six classes of antibiotics commonly used in both agriculture and aquaculture are also included on the World Health Organization's (WHO) list of critically important/highly important/important antimicrobials. Second, various zoonotic pathogens isolated from meat and seafood were observed to feature resistance to multiple antibiotics on the WHO list, irrespective of their origin in either agriculture or aquaculture. Third, the data show that resistant bacteria isolated from both aquaculture and agriculture share the same resistance mechanisms, indicating that aquaculture is contributing to the same resistance issues established by terrestrial agriculture. More transparency in data collection and reporting is needed so the risks and benefits of antibiotic usage can be adequately assessed.
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Affiliation(s)
- Hansa Y Done
- Center for Environmental Security, The Biodesign Institute, Arizona State University, 781 E. Terrace Mall, Tempe, Arizona, 85287, USA
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Ioannidis A, Magana M, Bologa CG, Oprea TI, Paulsen IT, Tegos GP. Defining the microbial effluxome in the content of the host-microbiome interaction. Front Pharmacol 2015; 6:31. [PMID: 25745401 PMCID: PMC4333769 DOI: 10.3389/fphar.2015.00031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 02/04/2015] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anastasios Ioannidis
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese Sparta, Greece ; Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital Athens, Greece
| | - Maria Magana
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese Sparta, Greece
| | - Cristian G Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center Albuquerque, NM, USA
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center Albuquerque, NM, USA ; Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark Lyngby, Denmark
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University NSW, Australia
| | - George P Tegos
- Torrey Pines Institute for Molecular Studies, Port St. Lucie FL, USA ; Department of Dermatology, Harvard Medical School Boston, MA, USA ; Wellman Center for Photomedicine, Massachusetts General Hospital Boston MA, USA
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Kirchner M, Mafura M, Hunt T, Abu-Oun M, Nunez-Garcia J, Hu Y, Weile J, Coates A, Card R, Anjum MF. Antimicrobial resistance characteristics and fitness of Gram-negative fecal bacteria from volunteers treated with minocycline or amoxicillin. Front Microbiol 2014; 5:722. [PMID: 25566232 PMCID: PMC4269195 DOI: 10.3389/fmicb.2014.00722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 12/02/2014] [Indexed: 11/13/2022] Open
Abstract
A yearlong study was performed to examine the effect of antibiotic administration on the bacterial gut flora. Gram-negative facultative anaerobic bacteria were recovered from the feces of healthy adult volunteers administered amoxicillin, minocycline or placebo, and changes determined in antimicrobial resistance (AMR) gene carriage. Seventy percent of the 1039 facultative anaerobic isolates recovered were identified by MALDI-TOF as Escherichia coli. A microarray used to determine virulence and resistance gene carriage demonstrated that AMR genes were widespread in all administration groups, with the most common resistance genes being blaTEM, dfr, strB, tet(A), and tet(B). Following amoxicillin administration, an increase in the proportion of amoxicillin resistant E. coli and a three-fold increase in the levels of blaTEM gene carriage was observed, an effect not observed in the other two treatment groups. Detection of virulence genes, including stx1A, indicated not all E. coli were innocuous commensals. Approximately 150 E. coli collected from 6 participants were selected for pulse field gel electrophoresis (PFGE), and a subset used for characterisation of plasmids and Phenotypic Microarrays (PM). PFGE indicated some E. coli clones had persisted in volunteers for up to 1 year, while others were transient. Although there were no unique characteristics associated with plasmids from persistent or transient isolates, PM assays showed transient isolates had greater adaptability to a range of antiseptic biocides and tetracycline; characteristics which were lost in some, but not all persistent isolates. This study indicates healthy individuals carry bacteria harboring resistance to a variety of antibiotics and biocides in their intestinal tract. Antibiotic administration can have a temporary effect of selecting bacteria, showing co-resistance to multiple antibiotics, some of which can persist within the gut for up to 1 year.
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Affiliation(s)
- Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Muriel Mafura
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Theresa Hunt
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Manal Abu-Oun
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Javier Nunez-Garcia
- Specialist Scientific Services Department, Animal and Plant Health Agency Addlestone, UK
| | - Yanmin Hu
- Department of Medical Microbiology, Institute of Infection and Immunity, St. George's University of London London, UK
| | - Jan Weile
- Institute for Laboratory and Transfusion Medicine at the Heart and Diabetes Centre NRW, University Hospital of the Ruhr University Bochum, Germany
| | - Anthony Coates
- Department of Medical Microbiology, Institute of Infection and Immunity, St. George's University of London London, UK
| | - Roderick Card
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency Addlestone, UK
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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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79
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Molecular identification and quantification of tetracycline and erythromycin resistance genes in Spanish and Italian retail cheeses. BIOMED RESEARCH INTERNATIONAL 2014; 2014:746859. [PMID: 25302306 PMCID: PMC4180643 DOI: 10.1155/2014/746859] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/21/2014] [Accepted: 08/27/2014] [Indexed: 11/17/2022]
Abstract
Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K), tet(L), tet(M), tet(O), tet(S), and tet(W), and two with respect to erythromycin, that is, erm(B) and erm(F). The most common resistance genes in the analysed cheeses were tet(S), tet(W), tet(M), and erm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18log10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W)-carrying cheeses, though the similarity of the sequences suggests this tet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.
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80
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Wei T, Miyanaga K, Tanji Y. Persistence of antibiotic-resistant and -sensitive Proteus mirabilis strains in the digestive tract of the housefly (Musca domestica) and green bottle flies (Calliphoridae). Appl Microbiol Biotechnol 2014; 98:8357-66. [DOI: 10.1007/s00253-014-5846-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/21/2014] [Accepted: 05/21/2014] [Indexed: 11/30/2022]
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81
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Seale J, Millar M. Perinatal vertical transmission of antibiotic-resistant bacteria: a systematic review and proposed research strategy. BJOG 2014; 121:923-8. [PMID: 24674346 DOI: 10.1111/1471-0528.12746] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND Antibiotic-resistant bacteria contribute to both early- and late-onset sepsis and outbreaks in neonatal intensive care units (NICUs). The extent to which vertical transmission of these resistant bacteria contributes to colonisation or infection of vulnerable infants in NICUs is unclear. Risk factors for vertical transmission of antibiotic-resistant bacteria are not well described. OBJECTIVES To identify studies describing vertical transmission of antibiotic-resistant bacteria, risk factors for transmission and the impact of colonisation on neonatal outcomes. SEARCH STRATEGY EMBASE, CINAHL, Cochrane, PubMed, and MEDLINE databases were searched using selected terminology. Titles and abstracts were screened by two reviewers. Selected papers were reviewed in full by two individuals to ascertain whether they fulfilled the inclusion criteria. SELECTION CRITERIA Any original article investigating perinatal vertical transmission of antibiotic-resistant bacteria between a mother and neonate was included. DATA COLLECTION AND ANALYSIS Data were extracted on study design, organism, antibiotic resistance, and means of ascertaining vertical transmission. MAIN RESULTS Five papers out of 4839 titles fulfilled the inclusion criteria. Four studies were predominantly observational and one was a case report. Each demonstrated perinatal transmission. No study reported risk factors for the transmission of resistant bacteria or the impact of colonisation on neonatal outcomes. AUTHOR'S CONCLUSIONS There is an absence of research into the perinatal transmission of resistant organisms despite the potential implications of such a situation. We outline objectives that need to be addressed in future research and describe a study design to ascertain the prevalence and risk factors for vertical transmission.
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Affiliation(s)
- J Seale
- Department of Infection, Barts Health NHS Trust, London, UK
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83
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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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84
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Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, Qin X, Tarr PI, Dantas G. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One 2013; 8:e78822. [PMID: 24236055 PMCID: PMC3827270 DOI: 10.1371/journal.pone.0078822] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/10/2013] [Indexed: 12/13/2022] Open
Abstract
Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000), and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301). We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway). This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. The observed transferability of gut-associated resistance genes to a gram-negative (E. coli) host also suggests that the potential for gut-associated resistomes to threaten human health by mediating antibiotic resistance in pathogens warrants further investigation.
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Affiliation(s)
- Aimée M. Moore
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sanket Patel
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kevin J. Forsberg
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bin Wang
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gayle Bentley
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yasmin Razia
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Gastroenterology, Department of Pediatrics, Children’s Hospital and Regional Medical Center, Seattle, Washington, United States of America
| | - Xuan Qin
- Department of Microbiology, Seattle Children’s Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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85
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Kirchner M, Mafura M, Hunt T, Card R, Anjum M. Antibiotic resistance gene profiling of faecal and oral anaerobes collected during an antibiotic challenge trial. Anaerobe 2013; 23:20-2. [DOI: 10.1016/j.anaerobe.2013.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/29/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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86
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Impact of manure fertilization on the abundance of antibiotic-resistant bacteria and frequency of detection of antibiotic resistance genes in soil and on vegetables at harvest. Appl Environ Microbiol 2013; 79:5701-9. [PMID: 23851089 DOI: 10.1128/aem.01682-13] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Consumption of vegetables represents a route of direct human exposure to bacteria found in soil. The present study evaluated the complement of bacteria resistant to various antibiotics on vegetables often eaten raw (tomato, cucumber, pepper, carrot, radish, lettuce) and how this might vary with growth in soil fertilized inorganically or with dairy or swine manure. Vegetables were sown into field plots immediately following fertilization and harvested when of marketable quality. Vegetable and soil samples were evaluated for viable antibiotic-resistant bacteria by plate count on Chromocult medium supplemented with antibiotics at clinical breakpoint concentrations. DNA was extracted from soil and vegetables and evaluated by PCR for the presence of 46 gene targets associated with plasmid incompatibility groups, integrons, or antibiotic resistance genes. Soil receiving manure was enriched in antibiotic-resistant bacteria and various antibiotic resistance determinants. There was no coherent corresponding increase in the abundance of antibiotic-resistant bacteria enumerated from any vegetable grown in manure-fertilized soil. Numerous antibiotic resistance determinants were detected in DNA extracted from vegetables grown in unmanured soil. A smaller number of determinants were additionally detected on vegetables grown only in manured and not in unmanured soil. Overall, consumption of raw vegetables represents a route of human exposure to antibiotic-resistant bacteria and resistance determinants naturally present in soil. However, the detection of some determinants on vegetables grown only in freshly manured soil reinforces the advisability of pretreating manure through composting or other stabilization processes or mandating offset times between manuring and harvesting vegetables for human consumption.
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87
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Rolain JM. Food and human gut as reservoirs of transferable antibiotic resistance encoding genes. Front Microbiol 2013; 4:173. [PMID: 23805136 PMCID: PMC3690338 DOI: 10.3389/fmicb.2013.00173] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/10/2013] [Indexed: 12/12/2022] Open
Abstract
The increase and spread of antibiotic resistance (AR) over the past decade in human pathogens has become a worldwide health concern. Recent genomic and metagenomic studies in humans, animals, in food and in the environment have led to the discovery of a huge reservoir of AR genes called the resistome that could be mobilized and transferred from these sources to human pathogens. AR is a natural phenomenon developed by bacteria to protect antibiotic-producing bacteria from their own products and also to increase their survival in highly competitive microbial environments. Although antibiotics are used extensively in humans and animals, there is also considerable usage of antibiotics in agriculture, especially in animal feeds and aquaculture. The aim of this review is to give an overview of the sources of AR and the use of antibiotics in these reservoirs as selectors for emergence of AR bacteria in humans via the food chain.
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Affiliation(s)
- Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée Infection, Aix-Marseille Université Marseille, France
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88
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Antibiotic administration routes significantly influence the levels of antibiotic resistance in gut microbiota. Antimicrob Agents Chemother 2013; 57:3659-66. [PMID: 23689712 DOI: 10.1128/aac.00670-13] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study examined the impact of oral exposure to antibiotic-resistant bacteria and antibiotic administration methods on antibiotic resistance (AR) gene pools and the profile of resistant bacteria in host gastrointestinal (GI) tracts using C57BL/6J mice with natural gut microbiota. Mice inoculated with a mixture of tet(M)-carrying Enterococcus spp. or blaCMY-2-carrying Escherichia coli were treated with different doses of tetracycline hydrochloride (Tet) or ampicillin sodium (Amp) and delivered via either feed or intravenous (i.v.) injection. Quantitative PCR assessment of mouse fecal samples revealed that (i) AR gene pools were below the detection limit in mice without prior inoculation of AR gene carriers regardless of subsequent exposure to corresponding antibiotics; (ii) oral exposure to high doses of Tet and Amp in mice inoculated with AR gene carriers led to rapid enrichment of corresponding AR gene pools in feces; (iii) significantly less or delayed development of AR in the GI tract of the AR carrier-inoculated mice was observed when the same doses of antibiotics were administered via i.v. injection rather than oral administration; and (iv) antibiotic dosage, and maybe the excretion route, affected AR in the GI tract. The shift of dominant AR bacterial populations in the gut microbiota was consistent with the dynamics of AR gene pools. The emergence of endogenous resistant bacteria in the gut microbiota corresponding to drug exposure was also observed. Together, these data suggest that oral administration of antibiotics has a prominent effect on AR amplification and development in gut microbiota, which may be minimized by alternative drug administration approaches, as illustrated by i.v. injection in this study and proper drug selection.
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89
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Tetracycline resistance genes acquired at birth. Arch Microbiol 2013; 195:447-51. [DOI: 10.1007/s00203-012-0864-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/09/2012] [Accepted: 12/16/2012] [Indexed: 10/27/2022]
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90
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Ye L, Lu Z, Li X, Shi L, Huang Y, Wang HH. Antibiotic-resistant bacteria associated with retail aquaculture products from Guangzhou, China. J Food Prot 2013; 76:295-301. [PMID: 23433377 DOI: 10.4315/0362-028x.jfp-12-288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study examined the prevalence of antibiotic-resistant (ART) bacteria and representative antibiotic resistance (AR)-encoding genes associated with several aquaculture products from retail markets in Guangzhou, China. ART commensal bacteria were found in 100% of the products examined. Among 505 multidrug-resistant isolates examined, close to one-fourth contained intI and sul1 genes: 15% contained sul2 and 5% contained tet (E). Incidences of β-lactamase-encoding genes bla(TEM), bla(CMY) and erythromycin resistance determinants ermB and ermC were 4.5, 1.7, 1.3, and 0.3%, respectively. Most of the ART isolates identified from the rinse water were Aeromonas spp.; those from intestines belonged to the Enterobacteriaceae. Plasmid-associated intI and AR-encoding genes were identified in several ART isolates by Southern hybridization. Three multidrug resistance-encoding plasmids were transferred into Escherichia coli DH5 a by chemical transformation and led to acquired AR in the transformants. In addition, the AR traits in many isolates were quite stable, even in the absence of selective pressure. Further studies are needed to reveal risk factors associated with the aquaculture production chain for targeted AR mitigation.
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Affiliation(s)
- Lei Ye
- College of Light Industry and Food Technology, South China University of Technology, Guangzhou 510640, China
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91
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Comparative analysis of Shigella sonnei biotype g isolated from paediatric populations in Egypt, 1999-2005. Epidemiol Infect 2012; 141:1614-24. [PMID: 22989417 DOI: 10.1017/s0950268812002002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Strain characteristics of 51 Shigella sonnei isolates obtained from children seeking medical care (MC) and 48 isolates recovered during a prospective diarrhoea birth cohort (BC) study were compared. Biochemical characterization and antibiotic susceptibility testing determined that all S. sonnei isolates were biotype g and multidrug-resistant. Plasmid profiling identified 15 closely related patterns and XbaI pulsed-field gel electrophoresis confirmed the high degree of genetic similarity between isolates. All S. sonnei isolates harboured ipaH and class II integrase genes and 84∙3 and 80% of the MC and BC isolates, respectively carried the sen gene. Neither the class I integrase nor the set gene was detected. Our results indicate that S. sonnei isolates associated with severe diarrhoea were indistinguishable from those associated with mild diarrhoea. Additional genetic tests with greater discrimination might offer an opportunity to determine genetic differences within the globally disseminating biotype g clone.
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92
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Goodwin KD, McNay M, Cao Y, Ebentier D, Madison M, Griffith JF. A multi-beach study of Staphylococcus aureus, MRSA, and enterococci in seawater and beach sand. WATER RESEARCH 2012; 46:4195-4207. [PMID: 22652414 DOI: 10.1016/j.watres.2012.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Revised: 04/01/2012] [Accepted: 04/02/2012] [Indexed: 06/01/2023]
Abstract
Incidences of Staphylococcus aureus and methicillin resistant S. aureus (MRSA) have risen worldwide prompting a need to better understand routes of human exposure and whether standard bacterial water quality monitoring practices adequately account for this potential threat. Beach water and sand samples were analyzed during summer months for S. aureus, enterococci, and MRSA at three southern California beaches (Avalon, Doheny, Malibu Surfrider). S. aureus frequently was detected in samples of seawater (59%, n = 328) and beach sand (53%, n = 358). MRSA sometimes was detected in seawater (1.6%, n = 366) and sand (2.7%, n = 366) at relatively low concentrations. Site specific differences were observed, with Avalon Beach presenting the highest concentrations of S. aureus and Malibu Surfrider the lowest in both seawater and sand. S. aureus concentrations in seawater and sand were correlated to each other and to a variety of other parameters. Multiple linear regression on the combined beach data indicated that significant explanatory variables for S. aureus in seawater were S. aureus in sand, water temperature, enterococci in seawater, and the number of swimmers. In sand, S. aureus concentrations were related to S. aureus in seawater, water temperature, enterococci in seawater, and inversely to surf height classification. Only the correlation to water temperature held for individually analyzed beaches and for S. aureus concentrations in both seawater and sand. To provide context for these results, the prevalence of S. aureus in sand was compared to published fomite studies, and results suggested that beach prevalence was similar to that in homes.
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Affiliation(s)
- Kelly D Goodwin
- National Oceanic and Atmospheric Administration, AOML, 4301 Rickenbacker Cswy, Miami, FL 33149, USA.
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93
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Antibiotic resistance: how much do we know and where do we go from here? Appl Environ Microbiol 2011; 77:7093-5. [PMID: 21908629 DOI: 10.1128/aem.06565-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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94
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Persistent, toxin-antitoxin system-independent, tetracycline resistance-encoding plasmid from a dairy Enterococcus faecium isolate. Appl Environ Microbiol 2011; 77:7096-103. [PMID: 21784909 DOI: 10.1128/aem.05168-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A tetracycline-resistant (Tet(r)) dairy Enterococcus faecium isolate designated M7M2 was found to carry both tet(M) and tet(L) genes on a 19.6-kb plasmid. After consecutive transfer in the absence of tetracycline, the resistance-encoding plasmid persisted in 99% of the progenies. DNA sequence analysis revealed that the 19.6-kb plasmid contained 28 open reading frames (ORFs), including a tet(M)-tet(L)-mob gene cluster, as well as a 10.6-kb backbone highly homologous (99.9%) to the reported plasmid pRE25, but without an identified toxin-antitoxin (TA) plasmid stabilization system. The derived backbone plasmid without the Tet(r) determinants exhibited a 100% retention rate in the presence of acridine orange, suggesting the presence of a TA-independent plasmid stabilization mechanism, with its impact on the persistence of a broad spectrum of resistance-encoding traits still to be elucidated. The tet(M)-tet(L) gene cluster from M7M2 was functional and transmissible and led to acquired resistance in Enterococcus faecalis OG1RF by electroporation and in Streptococcus mutans UA159 by natural transformation. Southern hybridization showed that both the tet(M) and tet(L) genes were integrated into the chromosome of S. mutans UA159, while the whole plasmid was transferred to and retained in E. faecalis OG1RF. Quantitative real-time reverse transcription-PCR (RT-PCR) indicated tetracycline-induced transcription of both the tet(M) and tet(L) genes of pM7M2. The results indicated that multiple mechanisms might have contributed to the persistence of antibiotic resistance-encoding genes and that the plasmids pM7M2, pIP816, and pRE25 are likely correlated evolutionarily.
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