1
|
Garcia CR, Norfolk WA, Howard AK, Glatter AL, Beaudry MS, Mallis NA, Welton M, Glenn TC, Lipp EK, Ottesen EA. Long-term gut colonization with ESBL-producing Escherichia coli in participants without known risk factors from the southeastern United States. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.03.24302254. [PMID: 38370669 PMCID: PMC10871458 DOI: 10.1101/2024.02.03.24302254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on culture-based screening of stool samples, 4.5% of 555 participants carried ESBL-Es. This is slightly higher than reported in studies conducted 2012-2015, which found carriage rates of 2.5-3.9% in healthy U.S. residents. All ESBL-E confirmed isolates (n=25) were identified as Escherichia coli. Isolates belonged to 11 sequence types, with 48% classified as ST131. Ninety six percent of ESBL-E isolates carried a blaCTX-M gene. Isolated ESBL-Es frequently carried virulence genes as well as multiple classes of antibiotic resistance genes. Long-term colonization was common, with 64% of ESBL-E positive participants testing positive when rescreened three months later. One participant yielded isolates belonging to two different E. coli sequence types that carried blaCTX-M-1 genes on near-identical plasmids, suggesting intra-gut plasmid transfer. Isolation of E. coli on media without antibiotics revealed that ESBL-E. coli typically made up a minor fraction of the overall gut E. coli population, although in some cases they were the dominant strain. ESBL-E carriage was not associated with a significantly different stool microbiome composition. However, some microbial taxa were differentially abundant in ESBL-E carriers. Together, these results suggest that a small subpopulation of US residents are long-term, asymptomatic carriers of ESBL-Es, and may serve as an important reservoir for community spread of these ESBL genes.
Collapse
Affiliation(s)
| | - William A. Norfolk
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Center for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amanda K. Howard
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Amanda L. Glatter
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Megan S. Beaudry
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Nicholas A. Mallis
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Michael Welton
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| | - Travis C. Glenn
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
| | - Erin K. Lipp
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, USA
| | | |
Collapse
|
2
|
O’Neill L, Manzanilla EG, Ekhlas D, Leonard FC. Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract. Antibiotics (Basel) 2023; 12:1616. [PMID: 37998818 PMCID: PMC10669415 DOI: 10.3390/antibiotics12111616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.
Collapse
Affiliation(s)
- Lorcan O’Neill
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| | - Edgar García Manzanilla
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| | - Daniel Ekhlas
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin D15 DY05, Ireland
| | - Finola C. Leonard
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| |
Collapse
|
3
|
Sheng H, Wu S, Xue Y, Zhao W, Caplan AB, Hovde CJ, Minnich SA. Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance. PLoS One 2023; 18:e0291520. [PMID: 37699034 PMCID: PMC10497133 DOI: 10.1371/journal.pone.0291520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.
Collapse
Affiliation(s)
- Haiqing Sheng
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah Wu
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Yansong Xue
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Wei Zhao
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Allan B. Caplan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Carolyn J. Hovde
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Scott A. Minnich
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| |
Collapse
|
4
|
Kim SK, Lee JB, Lee HT, Han D, Yoon JW. Development of antisense peptide-peptide nucleic acids against fluoroquinolone-resistant Escherichia coli. J Antimicrob Chemother 2023:dkad203. [PMID: 37390375 DOI: 10.1093/jac/dkad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Fluoroquinolones (FQs) are potent and broad-spectrum antibiotics commonly used to treat MDR bacterial infections, but bacterial resistance to FQs has emerged and spread rapidly around the world. The mechanisms for FQ resistance have been revealed, including one or more mutations in FQ target genes such as DNA gyrase (gyrA) and topoisomerase IV (parC). Because therapeutic treatments for FQ-resistant bacterial infections are limited, it is necessary to develop novel antibiotic alternatives to minimize or inhibit FQ-resistant bacteria. OBJECTIVES To examine the bactericidal effect of antisense peptide-peptide nucleic acids (P-PNAs) that can block the expression of DNA gyrase or topoisomerase IV in FQ-resistant Escherichia coli (FRE). METHODS A set of antisense P-PNA conjugates with a bacterial penetration peptide were designed to inhibit the expression of gyrA and parC and were evaluated for their antibacterial activities. RESULTS Antisense P-PNAs, ASP-gyrA1 and ASP-parC1, targeting the translational initiation sites of their respective target genes significantly inhibited the growth of the FRE isolates. In addition, ASP-gyrA3 and ASP-parC2, which bind to the FRE-specific coding sequence within the gyrA and parC structural genes, respectively, showed selective bactericidal effects against FRE isolates. CONCLUSIONS Our results demonstrate the potential of targeted antisense P-PNAs as antibiotic alternatives against FQ-resistance bacteria.
Collapse
Affiliation(s)
- Se Kye Kim
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Jun Bong Lee
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Hyung Tae Lee
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Dalmuri Han
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Jang Won Yoon
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| |
Collapse
|
5
|
McCallum GE, Rossiter AE, Quraishi MN, Iqbal TH, Kuehne SA, van Schaik W. Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts. Microb Genom 2023; 9:mgen001030. [PMID: 37272920 PMCID: PMC10327510 DOI: 10.1099/mgen.0.001030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/11/2023] [Indexed: 06/06/2023] Open
Abstract
The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.
Collapse
Affiliation(s)
- Gregory E. McCallum
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Tariq H. Iqbal
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Sarah A. Kuehne
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
6
|
Malin JJ, von Wintersdorff CJH, Penders J, Savelkoul PHM, Wolffs PFG. Longitudinal fluctuations of common antimicrobial resistance genes in the gut microbiomes of healthy Dutch individuals. Int J Antimicrob Agents 2023; 61:106716. [PMID: 36640847 DOI: 10.1016/j.ijantimicag.2023.106716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/22/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
The human gut microbiome is an important reservoir of antimicrobial resistance genes (ARGs), collectively termed the 'resistome'. To date, few studies have examined the dynamics of the human gut resistome in healthy individuals. Previously, the authors observed high rates of ARG acquisition and significant abundance shifts during international travel. In order to provide insight into commonly occurring dynamics, this study investigated longitudinal fluctuations in prevalent ARGs (cfxA, tetM and ermB) in the resistomes of non-travelling healthy volunteers. In addition, this study assessed the prevalence of acquirable ARGs (blaCTX-M, qnrB, qnrS, vanA and vanB) over time. Faecal samples from 23 participants were collected at baseline and after 2 and 4 weeks. DNA was isolated, and ARG quantification was performed by quantitative polymerase chain reaction adjusting for the total amount of bacterial 16S rDNA. vanA and qnrS were not detected in any of the samples, while the prevalence rates of vanB of non-enterococcal origin and qnrB were 73.9% and 5.7%, respectively. The ß-lactamase encoding blaCTX-M was detected in 17.4% of healthy participants. The results were compared with previous data from 122 travellers. ARG acquisitions observed in travellers were rare in non-travelling individuals during 4 weeks of follow-up, supporting the hypothesis of ARG acquisition during international travel. However, median -1.04- to 1.04-fold abundance changes were observed for 100% of cfxA, tetM and ermB, which did not differ from those found in travellers. Thus, common abundance shifts in prevalent ARGs of the gut resistome were found to occur independent of travel behaviour.
Collapse
Affiliation(s)
- Jakob J Malin
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands.
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Medical Microbiology, Care and Public Health Research Institute CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| |
Collapse
|
7
|
Kessler C, Hou J, Neo O, Buckner MMC. In situ, in vivo, and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome. FEMS Microbiol Rev 2022; 47:6807411. [PMID: 36341518 PMCID: PMC9841969 DOI: 10.1093/femsre/fuac044] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence, and manipulability of horizontal gene transfer in the gut microbiome.
Collapse
Affiliation(s)
- Celia Kessler
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Jingping Hou
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Onalenna Neo
- Institute of Microbiology and Infection College of Medical and Dental Sciences Biosciences Building University Road West University of Birmingham, B15 2TT, United Kingdom
| | - Michelle M C Buckner
- Corresponding author: Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, United Kingdom. Tel: +44 (0)121 415 8758; E-mail:
| |
Collapse
|
8
|
Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries. Nat Microbiol 2022; 7:1337-1347. [PMID: 35927336 PMCID: PMC9417982 DOI: 10.1038/s41564-022-01184-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/23/2022] [Indexed: 12/29/2022]
Abstract
Early development of the microbiome has been shown to affect general health and physical development of the infant and, although some studies have been undertaken in high-income countries, there are few studies from low- and middle-income countries. As part of the BARNARDS study, we examined the rectal microbiota of 2,931 neonates (term used up to 60 d) with clinical signs of sepsis and of 15,217 mothers screening for blaCTX-M-15, blaNDM, blaKPC and blaOXA-48-like genes, which were detected in 56.1%, 18.5%, 0% and 4.1% of neonates’ rectal swabs and 47.1%, 4.6%, 0% and 1.6% of mothers’ rectal swabs, respectively. Carbapenemase-positive bacteria were identified by MALDI-TOF MS and showed a high diversity of bacterial species (57 distinct species/genera) which exhibited resistance to most of the antibiotics tested. Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae/E. cloacae complex, the most commonly found isolates, were subjected to whole-genome sequencing analysis and revealed close relationships between isolates from different samples, suggesting transmission of bacteria between neonates, and between neonates and mothers. Associations between the carriage of antimicrobial resistance genes (ARGs) and healthcare/environmental factors were identified, and the presence of ARGs was a predictor of neonatal sepsis and adverse birth outcomes. Analysis of gut microbiota of mothers and its neonates—as part of the BARNARDS study—reveals associations between β-lactamase gene carriage and neonatal sepsis risk in low-income settings.
Collapse
|
9
|
Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes 2022; 14:2055944. [PMID: 35332832 PMCID: PMC8959533 DOI: 10.1080/19490976.2022.2055944] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.
Collapse
Affiliation(s)
- Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Haley Anne Hallowell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kalia Koutouvalis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jotham Suez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA,CONTACT Jotham Suez Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, Maryland, USA, 21205
| |
Collapse
|
10
|
Sheikh SW, Ali A, Ahsan A, Shakoor S, Shang F, Xue T. Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli. Antibiotics (Basel) 2021; 10:522. [PMID: 34063307 PMCID: PMC8147483 DOI: 10.3390/antibiotics10050522] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.
Collapse
Affiliation(s)
- Salma Waheed Sheikh
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Asma Ahsan
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Punjab, Pakistan;
| | - Sidra Shakoor
- Station de Neucfchateau, CIRAD, 97130 Sainte-Marie, Capesterre Belle Eau, Guadeloupe, France;
| | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| |
Collapse
|
11
|
Yakimov A, Bakhlanova I, Baitin D. Targeting evolution of antibiotic resistance by SOS response inhibition. Comput Struct Biotechnol J 2021; 19:777-783. [PMID: 33552448 PMCID: PMC7843400 DOI: 10.1016/j.csbj.2021.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 01/08/2023] Open
Abstract
Antibiotic resistance is acquired in response to antibiotic therapy by activating SOS-depended mutagenesis and horizontal gene transfer pathways. Compounds able to inhibit SOS response are extremely important to develop new combinatorial strategies aimed to block mutagenesis. The regulators of homologous recombination involved in the processes of DNA repair should be considered as potential targets for blocking. This review highlights the current knowledge of the protein targets for the evolution of antibiotic resistance and the inhibitory effects of some new compounds on this pathway.
Collapse
Affiliation(s)
- Alexander Yakimov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina, Russian Federation
| | - Irina Bakhlanova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina, Russian Federation.,Kurchatov Genome Center - PNPI, Gatchina, Russian Federation
| | - Dmitry Baitin
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina, Russian Federation.,Kurchatov Genome Center - PNPI, Gatchina, Russian Federation
| |
Collapse
|
12
|
Decano AG, Tran N, Al-Foori H, Al-Awadi B, Campbell L, Ellison K, Mirabueno LP, Nelson M, Power S, Smith G, Smyth C, Vance Z, Woods C, Rahm A, Downing T. Plasmids shape the diverse accessory resistomes of Escherichia coli ST131. Access Microbiol 2020; 3:acmi000179. [PMID: 33997610 PMCID: PMC8115979 DOI: 10.1099/acmi.0.000179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and we examined this here using a preterm infant resistome. We found that individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes.
Collapse
Affiliation(s)
- Arun Gonzales Decano
- School of Biotechnology, Dublin City University, Ireland.,Present address: School of Medicine, University of St., Andrews, UK
| | - Nghia Tran
- School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Ireland
| | | | | | | | - Kevin Ellison
- School of Biotechnology, Dublin City University, Ireland
| | - Louisse Paolo Mirabueno
- School of Biotechnology, Dublin City University, Ireland.,Present address: National Institute of Agricultural Botany - East Malling Research, Kent, UK
| | - Maddy Nelson
- School of Biotechnology, Dublin City University, Ireland
| | - Shane Power
- School of Biotechnology, Dublin City University, Ireland
| | | | - Cian Smyth
- School of Biotechnology, Dublin City University, Ireland.,Present address: Dept of Biology, Maynooth University, Dublin, Ireland
| | - Zoe Vance
- School of Genetics & Microbiology, Trinity College Dublin, Ireland
| | | | - Alexander Rahm
- School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Ireland.,Present address: GAATI Lab, Université de la Polynésie Française, Puna'auia, French Polynesia
| | - Tim Downing
- School of Biotechnology, Dublin City University, Ireland
| |
Collapse
|
13
|
Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB. The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy. Life Sci 2020; 262:118562. [PMID: 33038378 DOI: 10.1016/j.lfs.2020.118562] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023]
Abstract
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
Collapse
Affiliation(s)
- Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
14
|
Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. Microorganisms 2020; 8:microorganisms8060827. [PMID: 32486334 PMCID: PMC7355805 DOI: 10.3390/microorganisms8060827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.
Collapse
|
15
|
Baumgartner M, Bayer F, Pfrunder-Cardozo KR, Buckling A, Hall AR. Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples. PLoS Biol 2020; 18:e3000465. [PMID: 32310938 PMCID: PMC7192512 DOI: 10.1371/journal.pbio.3000465] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/30/2020] [Accepted: 04/02/2020] [Indexed: 01/05/2023] Open
Abstract
Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g., via resource competition) but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonisation by focal E. coli but also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic-resistance evolution of individual species.
Collapse
Affiliation(s)
- Michael Baumgartner
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florian Bayer
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Katia R. Pfrunder-Cardozo
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Alex R. Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
16
|
Vikram A, Miller E, Arthur TM, Bosilevac JM, Wheeler TL, Schmidt JW. Food Service Pork Chops from Three U.S. Regions Harbor Similar Levels of Antimicrobial Resistance Regardless of Antibiotic Use Claims. J Food Prot 2019; 82:1667-1676. [PMID: 31532250 DOI: 10.4315/0362-028x.jfp-19-139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pork products from animals "raised without antibiotics" (RWA) are assumed to harbor lower levels of antimicrobial resistance (AMR) than conventional (CONV) pork products with no claims regarding use of antimicrobial agents during production. A total of 372 pork chop samples from CONV (n = 190) and RWA (n = 182) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TETr) E. coli, third-generation cephalosporin-resistant (3GCr) E. coli, Salmonella enterica, TETr Salmonella, 3GCr Salmonella, nalidixic acid-resistant Salmonella, Enterococcus spp., TETr Enterococcus, erythromycin-resistant Enterococcus, Staphylococcus aureus, and methicillin-resistant S. aureus. Production system did not significantly impact the detection of cultured bacteria (P > 0.05). Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). Quantitative PCR was used to assess the abundances of the following 10 AMR genes: aac(6')-Ie-aph(2″)-Ia, aadA1, blaCMY-2, blaCTX-M, blaKPC-2, erm(B), mecA, tet(A), tet(B), and tet(M). For all 10 AMR genes, abundances did not differ significantly (P > 0.05) between production systems. These results suggest that use of antimicrobial agents during swine production minimally impacts the AMR of bacteria in pork chops.
Collapse
Affiliation(s)
- Amit Vikram
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA (ORCID: https://orcid.org/0000-0001-9035-0474 [T.M.A.]; https://orcid/org/0000-0002-6571-9097 [T.L.W.]; https://orcid.org/0000-0003-0494-2436 [J.W.S.])
| | - Eric Miller
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA (ORCID: https://orcid.org/0000-0001-9035-0474 [T.M.A.]; https://orcid/org/0000-0002-6571-9097 [T.L.W.]; https://orcid.org/0000-0003-0494-2436 [J.W.S.])
| | - Terrance M Arthur
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA (ORCID: https://orcid.org/0000-0001-9035-0474 [T.M.A.]; https://orcid/org/0000-0002-6571-9097 [T.L.W.]; https://orcid.org/0000-0003-0494-2436 [J.W.S.])
| | - Joseph M Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA (ORCID: https://orcid.org/0000-0001-9035-0474 [T.M.A.]; https://orcid/org/0000-0002-6571-9097 [T.L.W.]; https://orcid.org/0000-0003-0494-2436 [J.W.S.])
| | - Tommy L Wheeler
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA (ORCID: https://orcid.org/0000-0001-9035-0474 [T.M.A.]; https://orcid/org/0000-0002-6571-9097 [T.L.W.]; https://orcid.org/0000-0003-0494-2436 [J.W.S.])
| | - John W Schmidt
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA (ORCID: https://orcid.org/0000-0001-9035-0474 [T.M.A.]; https://orcid/org/0000-0002-6571-9097 [T.L.W.]; https://orcid.org/0000-0003-0494-2436 [J.W.S.])
| |
Collapse
|
17
|
Anjum M, Madsen JS, Nesme J, Jana B, Wiese M, Jasinskytė D, Nielsen DS, Sørensen SJ, Dalsgaard A, Moodley A, Bortolaia V, Guardabassi L. Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous Escherichia coli. Antimicrob Agents Chemother 2019; 63:e02528-18. [PMID: 30885897 PMCID: PMC6496067 DOI: 10.1128/aac.02528-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/19/2019] [Indexed: 11/20/2022] Open
Abstract
The gut is a hot spot for transfer of antibiotic resistance genes from ingested exogenous bacteria to the indigenous microbiota. The objective of this study was to determine the fate of two nearly identical blaCMY-2-harboring plasmids introduced into the human fecal microbiota by two Escherichia coli strains isolated from a human and from poultry meat. The chromosome and the CMY-2-encoding plasmid of both strains were labeled with distinct fluorescent markers (mCherry and green fluorescent protein [GFP]), allowing fluorescence-activated cell sorting (FACS)-based tracking of the strain and the resident bacteria that have acquired its plasmid. Each strain was introduced into an established in vitro gut model (CoMiniGut) inoculated with individual feces from ten healthy volunteers. Fecal samples collected 2, 6, and 24 h after strain inoculation were analyzed by FACS and plate counts. Although the human strain survived better than the poultry meat strain, both strains transferred their plasmids to the fecal microbiota at concentrations as low as 102 CFU/ml. Strain survival and plasmid transfer varied significantly depending on inoculum concentration and individual fecal microbiota. Identification of transconjugants by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revealed that the plasmids were predominantly acquired by Enterobacteriaceae species, such as E. coli and Hafnia alvei Our experimental data demonstrate that exogenous E. coli of human or animal origin can readily transfer CMY-2-encoding IncI1 plasmids to the human fecal microbiota. Small amounts of the exogenous strain are sufficient to ensure plasmid transfer if the strain is able to survive the gastric environment.
Collapse
Affiliation(s)
- Mehreen Anjum
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bimal Jana
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Maria Wiese
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Džiuginta Jasinskytė
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Luca Guardabassi
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
| |
Collapse
|
18
|
Khueychai S, Jangpromma N, Daduang S, Klaynongsruang S. Effects of alkaline hydrolysis and storage conditions on the biological activity of ostrich egg white. J FOOD PROCESS PRES 2019. [DOI: 10.1111/jfpp.13921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Siriporn Khueychai
- Department of Biochemistry, Faculty of Science Khon Kaen University Khon Kaen Thailand
- The Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science Khon Kaen University Khon Kaen Thailand
| | - Nisachon Jangpromma
- The Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science Khon Kaen University Khon Kaen Thailand
- Department of Integrated Science, Forensic Science Program, Faculty of Science Khon Kaen University Khon Kaen Thailand
| | - Sakda Daduang
- The Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science Khon Kaen University Khon Kaen Thailand
- Division of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences Khon Kaen University Khon Kaen Thailand
| | - Sompong Klaynongsruang
- Department of Biochemistry, Faculty of Science Khon Kaen University Khon Kaen Thailand
- The Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Faculty of Science Khon Kaen University Khon Kaen Thailand
| |
Collapse
|
19
|
Dynamics of Resistance Plasmids in Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization. Antimicrob Agents Chemother 2019; 63:AAC.02201-18. [PMID: 30745391 DOI: 10.1128/aac.02201-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/05/2019] [Indexed: 01/01/2023] Open
Abstract
Extended-spectrum β-lactamase-producing Enterobacteriaceae (EPE) are a major cause of bloodstream infections, and the colonization rate of EPE in the gut microbiota of individuals lacking prior hospitalization or comorbidities is increasing. In this study, we performed an in-depth investigation of the temporal dynamics of EPE and their plasmids during one year by collecting fecal samples from three patients initially seeking medical care for urinary tract infections. In two of the patients, the same strain that caused the urinary tract infection (UTI) was found at all consecutive samplings from the gut microbiota, and no other EPEs were detected, while in the third patient the UTI strain was only found in the initial UTI sample. Instead, this patient presented a complex situation where a mixed microbiota of different EPE strain types, including three different E. coli ST131 variants, as well as different bacterial species, was identified over the course of the study. Different plasmid dynamics were displayed in each of the patients, including the spread of plasmids between different strain types over time and the transposition of bla CTX-M-15 from the chromosome to a plasmid, followed by subsequent loss through homologous recombination. Small cryptic plasmids were found in all isolates from all patients, and they appear to move frequently between different strains in the microbiota. In conclusion, we could demonstrate an extensive variation of EPE strain types, plasmid composition, rearrangements, and horizontal gene transfer of genetic material illustrating the high dynamics nature and interactive environment of the gut microbiota during post-UTI carriage.
Collapse
|
20
|
Li J, Rettedal EA, van der Helm E, Ellabaan M, Panagiotou G, Sommer MOA. Antibiotic Treatment Drives the Diversification of the Human Gut Resistome. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:39-51. [PMID: 31026582 PMCID: PMC6520913 DOI: 10.1016/j.gpb.2018.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/10/2018] [Accepted: 12/17/2018] [Indexed: 01/13/2023]
Abstract
Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.
Collapse
Affiliation(s)
- Jun Li
- Department of Infectious Diseases and Public Health, Colleague of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong Special Administrative Region, China; School of Data Science, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | - Eric van der Helm
- Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark
| | - Mostafa Ellabaan
- Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, 07745 Jena, Germany; Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark.
| |
Collapse
|
21
|
Knudsen PK, Gammelsrud KW, Alfsnes K, Steinbakk M, Abrahamsen TG, Müller F, Bohlin J. Transfer of a bla CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses. Sci Rep 2018; 8:280. [PMID: 29321570 PMCID: PMC5762863 DOI: 10.1038/s41598-017-18659-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/14/2017] [Indexed: 01/08/2023] Open
Abstract
Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven bla CTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains. All isolates contained bla CTX-M-1-carrying Incl1 plasmids that shared a common 101 kb backbone differing by only four SNPs. The plasmids harboured by the three different E. coli strains varied within limited regions suggestive of recombination events, according to the phylogenetic topology of the genomes of the isolates harbouring them. The findings strongly suggest that horizontal transfer of a bla CTX-M-1-carrying plasmid had occurred within the patient´s gut. The study illustrates the within-host diversity of faecally carried resistant E. coli isolates and highlights the value of collecting multiple bacterial colonies from longitudinally collected samples to assess faecal carriage of resistant enterobacteria. The clustering of the plasmids with the corresponding E. coli strains carrying them indicates that the plasmids appear to have adapted to their respective E. coli hosts.
Collapse
Affiliation(s)
- Per Kristian Knudsen
- Department of Paediatric Medicine, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway.
| | - Karianne Wiger Gammelsrud
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway
| | - Kristian Alfsnes
- Department of Molecular Biology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, PB 4404 Nydalen, 0403, Oslo, Norway
| | - Martin Steinbakk
- Department of Antibiotic Resistance and Infection Prevention, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, PB 4404 Nydalen, 0403, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Paediatric Medicine, Division of Paediatric and Adolescent Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway
| | - Fredrik Müller
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, PB 1171 Blindern, 0318, Oslo, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424, Oslo, Norway
| | - Jon Bohlin
- Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, PB 4404 Nydalen, 0403, Oslo, Norway
| |
Collapse
|
22
|
Gumpert H, Kubicek-Sutherland JZ, Porse A, Karami N, Munck C, Linkevicius M, Adlerberth I, Wold AE, Andersson DI, Sommer MOA. Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment. Front Microbiol 2017; 8:1852. [PMID: 29018426 PMCID: PMC5622998 DOI: 10.3389/fmicb.2017.01852] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics. Using whole genome sequencing, we observed large genomic deletions, bacteriophage infections, as well as the loss and acquisition of plasmids in these lineages during their colonization of the human gut. In particular, we captured the exchange of multidrug resistance genes, and identified a clinically relevant conjugative plasmid mediating the transfer. This resistant transconjugant lineage was maintained for months, demonstrating that antibiotic resistance genes can disseminate and persist in the gut microbiome; even in absence of antibiotic selection. Furthermore, through in vivo competition assays, we suggest that the resistant transconjugant can persist through a fitness advantage in the mouse gut in spite of a fitness cost in vitro. Our findings highlight the dynamic nature of the human gut microbiota and provide the first genomic description of antibiotic resistance gene transfer between bacteria in the unperturbed human gut. These results exemplify that conjugative plasmids, harboring resistance determinants, can transfer and persists in the gut in the absence of antibiotic treatment.
Collapse
Affiliation(s)
- Heidi Gumpert
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.,Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | | | - Andreas Porse
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Marius Linkevicius
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Agnes E Wold
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
23
|
Hoelzer K, Wong N, Thomas J, Talkington K, Jungman E, Coukell A. Antimicrobial drug use in food-producing animals and associated human health risks: what, and how strong, is the evidence? BMC Vet Res 2017; 13:211. [PMID: 28676125 PMCID: PMC5496648 DOI: 10.1186/s12917-017-1131-3] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 06/23/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Antimicrobial resistance is a public health threat. Because antimicrobial consumption in food-producing animals contributes to the problem, policies restricting the inappropriate or unnecessary agricultural use of antimicrobial drugs are important. However, this link between agricultural antibiotic use and antibiotic resistance has remained contested by some, with potentially disruptive effects on efforts to move towards the judicious or prudent use of these drugs. MAIN TEXT The goal of this review is to systematically evaluate the types of evidence available for each step in the causal pathway from antimicrobial use on farms to human public health risk, and to evaluate the strength of evidence within a 'Grades of Recommendations Assessment, Development and Evaluation'(GRADE) framework. The review clearly demonstrates that there is compelling scientific evidence available to support each step in the causal pathway, from antimicrobial use on farms to a public health burden caused by infections with resistant pathogens. Importantly, the pathogen, antimicrobial drug and treatment regimen, and general setting (e.g., feed type) can have significant impacts on how quickly resistance emerges or spreads, for how long resistance may persist after antimicrobial exposures cease, and what public health impacts may be associated with antimicrobial use on farms. Therefore an exact quantification of the public health burden attributable to antimicrobial drug use in animal agriculture compared to other sources remains challenging. CONCLUSIONS Even though more research is needed to close existing data gaps, obtain a better understanding of how antimicrobial drugs are actually used on farms or feedlots, and quantify the risk associated with antimicrobial use in animal agriculture, these findings reinforce the need to act now and restrict antibiotic use in animal agriculture to those instances necessary to ensure the health and well-being of the animals.
Collapse
Affiliation(s)
- Karin Hoelzer
- The Pew Charitable Trusts, 901 E Street NW, Washington, DC 20004 USA
| | - Nora Wong
- The Pew Charitable Trusts, 901 E Street NW, Washington, DC 20004 USA
| | - Joe Thomas
- The Pew Charitable Trusts, 901 E Street NW, Washington, DC 20004 USA
| | - Kathy Talkington
- The Pew Charitable Trusts, 901 E Street NW, Washington, DC 20004 USA
| | - Elizabeth Jungman
- The Pew Charitable Trusts, 901 E Street NW, Washington, DC 20004 USA
| | - Allan Coukell
- The Pew Charitable Trusts, 901 E Street NW, Washington, DC 20004 USA
| |
Collapse
|
24
|
Porse A, Gumpert H, Kubicek-Sutherland JZ, Karami N, Adlerberth I, Wold AE, Andersson DI, Sommer MOA. Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut. Front Cell Infect Microbiol 2017; 7:126. [PMID: 28447026 PMCID: PMC5388698 DOI: 10.3389/fcimb.2017.00126] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of Escherichia coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive fitness experiments to assess the role of this highly disseminated virulence plasmid in gut colonization, but found no evidence for a direct benefit of plasmid carriage. Through plasmid stability assays, we demonstrate that this plasmid is maintained in a parasitic manner, by strong first-line inheritance mechanisms, acting on the single-cell level, rather than providing a direct survival advantage in the gut. Investigating the ecology of endemic accessory genetic elements, in their pathogenic hosts and native environment, is of vital importance if we want to understand the evolution and persistence of highly virulent and drug resistant bacterial isolates.
Collapse
Affiliation(s)
- Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkLyngby, Denmark
| | - Heidi Gumpert
- Department of Clinical Microbiology, Hvidovre University HospitalHvidovre, Denmark
| | | | - Nahid Karami
- Department of infectious Diseases, University of Gothenburg, Sahlgrenska AcademyGothenburg, Sweden
| | - Ingegerd Adlerberth
- Department of infectious Diseases, University of Gothenburg, Sahlgrenska AcademyGothenburg, Sweden
| | - Agnes E Wold
- Department of infectious Diseases, University of Gothenburg, Sahlgrenska AcademyGothenburg, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical CentreUppsala, Sweden
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkLyngby, Denmark
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Ter Kuile BH, Kraupner N, Brul S. The risk of low concentrations of antibiotics in agriculture for resistance in human health care. FEMS Microbiol Lett 2016; 363:fnw210. [PMID: 27609231 DOI: 10.1093/femsle/fnw210] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
The contribution of antibiotic resistance originally selected for in the agricultural sector to resistance in human pathogens is not known exactly, but is unlikely to be negligible. It is estimated that 50% to 80% of all antibiotics used are applied in agriculture and the remainder for treating infections in humans. Since dosing regimens are less controlled in agriculture than in human health care, veterinary and environmental microbes are often exposed to sublethal levels of antibiotics. Exposure to sublethal drug concentrations must be considered a risk factor for de novo resistance, transfer of antimicrobial resistant (AMR) genes, and selection for already existing resistance. Resistant zoonotic agents and commensal strains carrying AMR genes reach the human population by a variety of routes, foodstuffs being only one of these. Based on the present knowledge, short treatments with the highest dose that does not cause unacceptable side-effects may be optimal for achieving therapeutic goals while minimizing development of resistance. Novel approaches such as combination or alternating therapy are promising, but need to be explored further before they can be implemented in daily practice.
Collapse
Affiliation(s)
- Benno H Ter Kuile
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands Office for Risk Assessment and Research, Netherlands Food and Consumer Product Safety Authority, Catharijnesingel 59, 3511 GG Utrecht, the Netherlands
| | - Nadine Kraupner
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands
| |
Collapse
|
27
|
Toutain PL, Ferran AA, Bousquet-Melou A, Pelligand L, Lees P. Veterinary Medicine Needs New Green Antimicrobial Drugs. Front Microbiol 2016; 7:1196. [PMID: 27536285 PMCID: PMC4971058 DOI: 10.3389/fmicb.2016.01196] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023] Open
Abstract
Given that: (1) the worldwide consumption of antimicrobial drugs (AMDs) used in food-producing animals will increase over the coming decades; (2) the prudent use of AMDs will not suffice to stem the rise in human antimicrobial resistance (AMR) of animal origin; (3) alternatives to AMD use are not available or not implementable, there is an urgent need to develop novel AMDs for food-producing animals. This is not for animal health reasons, but to break the link between human and animal resistomes. In this review we establish the feasibility of developing for veterinary medicine new AMDs, termed "green antibiotics," having minimal ecological impact on the animal commensal and environmental microbiomes. We first explain why animal and human commensal microbiota comprise a "turnstile" exchange, between the human and animal resistomes. We then outline the ideal physico-chemical, pharmacokinetic, and pharmacodynamic properties of a veterinary green antibiotic and conclude that they can be developed through a rational screening of currently used AMD classes. The ideal drug will be hydrophilic, of relatively low potency, slow clearance and small volume of distribution. It should be eliminated principally by the kidney as inactive metabolite(s). For oral administration, bioavailability can be enhanced by developing lipophilic pro-drugs. For parenteral administration, slow-release formulations of existing eco-friendly AMDs with a short elimination half-life can be developed. These new eco-friendly veterinary AMDs can be developed from currently used drug classes to provide alternative agents to those currently used in veterinary medicine and mitigate animal contributions to the human AMR problem.
Collapse
Affiliation(s)
- Pierre-Louis Toutain
- Ecole Nationale Vétérinaire de Toulouse, Institut National de la Recherche Agronomique, TOXALIM, Université de ToulouseToulouse, France
| | - Aude A. Ferran
- Ecole Nationale Vétérinaire de Toulouse, Institut National de la Recherche Agronomique, TOXALIM, Université de ToulouseToulouse, France
| | - Alain Bousquet-Melou
- Ecole Nationale Vétérinaire de Toulouse, Institut National de la Recherche Agronomique, TOXALIM, Université de ToulouseToulouse, France
| | - Ludovic Pelligand
- Comparative Biomedical Sciences, The Royal Veterinary CollegeHatfield, UK
| | - Peter Lees
- Comparative Biomedical Sciences, The Royal Veterinary CollegeHatfield, UK
| |
Collapse
|
28
|
Herrero-Fresno A, Zachariasen C, Hansen MH, Nielsen A, Hendriksen RS, Nielsen SS, Olsen JE. Apramycin treatment affects selection and spread of a multidrug-resistant Escherichia coli strain able to colonize the human gut in the intestinal microbiota of pigs. Vet Res 2016; 47:12. [PMID: 26739225 PMCID: PMC4704421 DOI: 10.1186/s13567-015-0291-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/04/2015] [Indexed: 11/30/2022] Open
Abstract
The effect of apramycin treatment on transfer and selection of an Escherichia coli strain (E. coli 912) in the intestine of pigs was analyzed through an in vivo experiment. The strain was sequenced and assigned to the sequence type ST101 and serotype O11. It carried resistance genes to apramycin/gentamicin, sulphonamide, tetracycline, hygromycin B, β-lactams and streptomycin [aac(3)-IV, sul2, tet(X), aph(4), blaTEM-1 and strA/B], with all but tet(X) located on the same conjugative plasmid. Nineteen pigs were randomly allocated into two inoculation groups, one treated with apramycin (pen 2) and one non-treated (pen 3), along with a non-inoculated control group (pen 1). Two pigs of pen 2 and 3 were inoculated intragastrically with a rifampicin resistant variant of the strain. Apramycin treatment in pen 2 was initiated immediately after inoculation. Strain colonization was assessed in the feces from all pigs. E. coli 912 was shown to spread to non-inoculated pigs in both groups. The selective effect did not persist beyond 3 days post-treatment, and the strain was not detected from this time point in pen 2. We demonstrated that E. coli 912 was able to spread between pigs in the same pen irrespective of treatment, and apramycin treatment resulted in significantly higher counts compared to the non-treated group. This represents the first demonstration of how antimicrobial treatment affects spread of resistant bacteria in pig production. The use of apramycin may lead to enhanced spread of gentamicin-resistant E. coli. Since gentamicin is a first-choice drug for human bacteremia, this is of concern.
Collapse
Affiliation(s)
- Ana Herrero-Fresno
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Camilla Zachariasen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Monica Hegstad Hansen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Alexander Nielsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Rene S Hendriksen
- WHO Collaborating Centre for Antimicrobial Resistance in Food-borne Pathogens and EU Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Søren Saxmose Nielsen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - John Elmerdahl Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Jurado-Rabadán S, de la Fuente R, Ruiz-Santa-Quiteria JA, Orden JA, de Vries LE, Agersø Y. Detection and linkage to mobile genetic elements of tetracycline resistance gene tet(M) in Escherichia coli isolates from pigs. BMC Vet Res 2014; 10:155. [PMID: 25015125 PMCID: PMC4105395 DOI: 10.1186/1746-6148-10-155] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 07/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Escherichia coli the genes involved in the acquisition of tetracycline resistance are mainly tet(A) and tet(B). In addition, tet(M) is the most common tetracycline resistance determinant in enterococci and it is associated with conjugative transposons and plasmids. Although tet(M) has been identified in E. coli, to our knowledge, there are no previous reports studying the linkage of the tet(M) gene in E. coli to different mobile genetic elements. The aim of this study was to determine the occurrence of tet(A), tet(B), and tet(M) genes in doxycycline-resistant E. coli isolates from pigs, as well as the detection of mobile genetic elements linked to tet(M) in E. coli and its possible transfer from enterococci. RESULTS tet(A) was the most frequently detected gene (87.9%) in doxycycline-resistant isolates. tet(M) was found in 13.1% E. coli isolates. The tet(M) gene was detected in relation with conjugative transposons in 10 out of 36 enterococci isolates analyzed but not in any of E. coli isolates positive for tet(M). Southern blot showed that in E. coli and in most of the enterococci isolates the tet(M) gene was carried on a plasmid. According to the phylogenetic analysis, E. coli contained a new tet(M) allele grouping separately. Mating experiments revealed that tet(M) was carried on a mobile element successfully transferred between enterococci and between enterococci and E. coli. CONCLUSIONS The detection of tet(M) in E. coli isolates from pigs was higher than expected. In our study, tet(M) detected in E. coli seems not to have been transferred from enterococci, although it can not be ruled out that the horizontal transfer of this gene occurred from other intestinal tract bacteria.
Collapse
Affiliation(s)
| | | | - José A Ruiz-Santa-Quiteria
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain.
| | | | | | | |
Collapse
|
31
|
Machado AMD, Sommer MOA. Human intestinal cells modulate conjugational transfer of multidrug resistance plasmids between clinical Escherichia coli isolates. PLoS One 2014; 9:e100739. [PMID: 24955767 PMCID: PMC4067368 DOI: 10.1371/journal.pone.0100739] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/30/2014] [Indexed: 12/29/2022] Open
Abstract
Bacterial conjugation in the human gut microbiota is believed to play a major role in the dissemination of antibiotic resistance genes and virulence plasmids. However, the modulation of bacterial conjugation by the human host remains poorly understood and there is a need for controlled systems to study this process. We established an in vitro co-culture system to study the interaction between human intestinal cells and bacteria. We show that the conjugation efficiency of a plasmid encoding an extended spectrum beta-lactamase is reduced when clinical isolates of Escherichia coli are co-cultured with human intestinal cells. We show that filtered media from co-cultures contain a factor that reduces conjugation efficiency. Protease treatment of the filtered media eliminates this inhibition of conjugation. This data suggests that a peptide or protein based factor is secreted on the apical side of the intestinal cells exposed to bacteria leading to a two-fold reduction in conjugation efficiency. These results show that human gut epithelial cells can modulate bacterial conjugation and may have relevance to gene exchange in the gut.
Collapse
Affiliation(s)
| | - Morten O. A. Sommer
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- * E-mail:
| |
Collapse
|
32
|
Huddleston JR. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Infect Drug Resist 2014; 7:167-76. [PMID: 25018641 PMCID: PMC4073975 DOI: 10.2147/idr.s48820] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacterial infections are becoming increasingly difficult to treat due to widespread antibiotic resistance among pathogens. This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs. Finally, implications for antibiotic usage and the development of resistant infections and persistence of antibiotic resistance genes in populations as a result of horizontal gene transfer in the large intestine will be discussed.
Collapse
|
33
|
Abstract
UNLABELLED The genome sequences of intestinal Bacteroidales strains reveal evidence of extensive horizontal gene transfer. In vitro studies of Bacteroides and other bacteria have addressed mechanisms of conjugative transfer and some phenotypic outcomes of these DNA acquisitions in the recipient, such as the acquisition of antibiotic resistance. However, few studies have addressed the horizontal transfer of genetic elements between bacterial species coresident in natural microbial communities, especially microbial ecosystems of humans. Here, we examine the genomes of Bacteroidales species from two human adults to identify genetic elements that were likely transferred among these Bacteroidales while they were coresident in the intestine. Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity. These five regions are not found in any other sequenced Bacteroidetes genome at this level of identity and are likely all integrative conjugative elements (ICEs). Such highly similar and unique regions occur in only 0.4% of phylogenetically representative mock communities, providing strong evidence that these five regions were transferred between coresident strains in these subjects. In addition to the requisite proteins necessary for transfer, these elements encode proteins predicted to increase fitness, including orphan DNA methylases that may alter gene expression, fimbriae synthesis proteins that may facilitate attachment and the utilization of new substrates, putative secreted antimicrobial molecules, and a predicted type VI secretion system (T6SS), which may confer a competitive ecological advantage to these strains in their complex microbial ecosystem. IMPORTANCE By analyzing Bacteroidales strains coresident in the gut microbiota of two human adults, we provide strong evidence for extensive interspecies and interfamily transfer of integrative conjugative elements within the intestinal microbiota of individual humans. In the recipient strain, we show that the conjugative elements themselves can be modified by the transposition of insertion sequences and retroelements from the recipient's genome, with subsequent transfer of these modified elements to other members of the microbiota. These data suggest that the genomes of our gut bacteria are substantially modified by other, coresident members of the ecosystem, resulting in highly personalized Bacteroidales strains likely unique to that individual. The genetic content of these ICEs suggests that their transfer from successful adapted members of an ecosystem confers beneficial properties to the recipient, increasing its fitness and allowing it to better compete within its particular personalized gut microbial ecosystem.
Collapse
|
34
|
Yue M, Schifferli DM. Allelic variation in Salmonella: an underappreciated driver of adaptation and virulence. Front Microbiol 2014; 4:419. [PMID: 24454310 PMCID: PMC3882659 DOI: 10.3389/fmicb.2013.00419] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/20/2013] [Indexed: 01/08/2023] Open
Abstract
Salmonella enterica causes substantial morbidity and mortality in humans and animals. Infection and intestinal colonization by S. enterica require virulence factors that mediate bacterial binding and invasion of enterocytes and innate immune cells. Some S. enterica colonization factors and their alleles are host restricted, suggesting a potential role in regulation of host specificity. Recent data also suggest that colonization factors promote horizontal gene transfer of antimicrobial resistance genes by increasing the local density of Salmonella in colonized intestines. Although a profusion of genes are involved in Salmonella pathogenesis, the relative importance of their allelic variation has only been studied intensely in the type 1 fimbrial adhesin FimH. Although other Salmonella virulence factors demonstrate allelic variation, their association with specific metadata (e.g., host species, disease or carrier state, time and geographic place of isolation, antibiotic resistance profile, etc.) remains to be interrogated. To date, genome-wide association studies (GWAS) in bacteriology have been limited by the paucity of relevant metadata. In addition, due to the many variables amid metadata categories, a very large number of strains must be assessed to attain statistically significant results. However, targeted approaches in which genes of interest (e.g., virulence factors) are specifically sequenced alleviates the time-consuming and costly statistical GWAS analysis and increases statistical power, as larger numbers of strains can be screened for non-synonymous single nucleotide polymorphisms (SNPs) that are associated with available metadata. Congruence of specific allelic variants with specific metadata from strains that have a relevant clinical and epidemiological history will help to prioritize functional wet-lab and animal studies aimed at determining cause-effect relationships. Such an approach should be applicable to other pathogens that are being collected in well-curated repositories.
Collapse
Affiliation(s)
- Min Yue
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Dieter M Schifferli
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania Philadelphia, PA, USA
| |
Collapse
|
35
|
Severe sepsis facilitates intestinal colonization by extended-spectrum-β-lactamase-producing Klebsiella pneumoniae and transfer of the SHV-18 resistance gene to Escherichia coli during antimicrobial treatment. Antimicrob Agents Chemother 2013; 58:1039-46. [PMID: 24277046 DOI: 10.1128/aac.01632-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Infections caused by multidrug-resistant pathogens are frequent and life threatening in critically ill patients. To investigate whether severe sepsis affects gut colonization by resistant pathogens and genetic exchange between opportunistic pathogens, we tested the intestinal-colonization ability of an extended-spectrum beta-lactamase-producing Klebsiella pneumoniae strain carrying the SHV-18 resistance gene and the transfer ability of the resistance gene to endogenous Escherichia coli under ceftriaxone treatment in rats with burn injury only or severe sepsis induced by burns plus endotoxin exposure. Without ceftriaxone treatment, the K. pneumoniae strain colonized the intestine in both septic and burned rats for a short time, with clearance occurring earlier in burn-only rats but never in sham burn rats. In both burned and septic rats, the colonization level of the challenge strain dropped at the beginning and then later increased during ceftriaxone treatment, after which it declined gradually. This pattern coincided with the change in resistance of K. pneumoniae to ceftriaxone during and after ceftriaxone treatment. Compared with burn-only injury, severe sepsis had a more significant effect on the change in antimicrobial resistance to ceftriaxone. Only in septic rats was the resistance gene successfully transferred from the challenge strain to endogenous E. coli during ceftriaxone treatment; the gene persisted for at least 4 weeks after ceftriaxone treatment. We concluded that severe sepsis can facilitate intestinal colonization by an exogenous resistant pathogen and the transfer of the resistance gene to a potential endogenous pathogen during antimicrobial treatment.
Collapse
|
36
|
Brooks JW, Roberts EL, Kocher K, Kariyawasam S, DebRoy C. Fatal pneumonia caused by Extraintestinal Pathogenic Escherichia coli (ExPEC) in a juvenile cat recovered from an animal hoarding incident. Vet Microbiol 2013; 167:704-7. [PMID: 24041770 DOI: 10.1016/j.vetmic.2013.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/13/2013] [Accepted: 08/16/2013] [Indexed: 11/17/2022]
Abstract
The current study describes isolation of Extraintestinal Pathogenic Escherichia coli (ExPEC) from a juvenile male cat that died after being rescued from an animal hoarding incident. Grossly, there was evidence of pneumonia and renal abscessation. Histologically, there was diffuse interstitial pneumonia with necrosis and necrotizing and suppurative nephritis with colonies of coccobacilli. Within the lung, kidney, and mesentery there was necrotizing and suppurative vasculitis with thrombosis and coccobacilli. E. coli strain belonging to serotype O6:H1 that carried many of the virulence genes associated with ExPEC was isolated from the lung and kidney. The cat was part of a community of approximately 60 cats that lived in a house in a residential neighborhood, in which multiple cats had died. The case was of major significance to public health, as first responders, animal health professionals, and other community members were likely exposed to ExPEC, which is known to have zoonotic potential. It is important that pet owners, animal health and public health professionals, and first responders be made aware of the potential for zoonotic diseases.
Collapse
Affiliation(s)
- Jason W Brooks
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | |
Collapse
|
37
|
Shkoporov AN, Khokhlova EV, Kulagina EV, Smeianov VV, Kuchmiy AA, Kafarskaya LI, Efimov BA. Analysis of a novel 8.9kb cryptic plasmid from Bacteroides uniformis, its long-term stability and spread within human microbiota. Plasmid 2012. [PMID: 23201047 DOI: 10.1016/j.plasmid.2012.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analysis of plasmid content in dominant Bacteroidales order intestinal strains isolated from the same child at a 5 year interval identified a 8.9 kb plasmid in Bacteroides uniformis BUN24 strain isolated at age 6 and indistinguishably sized plasmids in the isolates of B. uniformis, B. vulgatus, B. intesinalis, and Parabacteroides distasonis at age 11. We sequenced a B. uniformis BUN24 plasmid, designated pBUN24, and using molecular surveys of diverse species we established that this 8944bp molecule (G+C content 43.5%) represents a novel family of small cryptic Bacteroidales plasmids. The replication region of pBUN24 was experimentally localized to a 1707-bp fragment that includes a putative repA gene, coding for a protein of Rep_3 superfamily of replication proteins of theta-type plasmids preceded by a putative iteron-containing origin of replication. The other open reading frames (ORFs) identified in pBUN24 sequence include a putative tad-ata-type toxin-antitoxin and mobA-mobB mobilization modules, as well as seven additional cryptic ORFs. The interaction of Tad and Ada components demonstrated by a pull-down assay and the toxicity of Tad in Escherichia coli host suggests the functionality of the plasmid addiction module. Re-sequencing of plasmids in two Bacteroides strains isolated at the age of 11 showed 100% nucleotide identity to pBUN24. This data supports the notion that this plasmid is transmissible to other Bacteroidales strains in the natural ecosystem. The possible roles of toxin-antitoxin system and other proteins encoded by pBUN24 in providing an apparent ecological advantage to the plasmid-harbouring strains of a bacterial symbiont in the human gut deserve further investigation.
Collapse
Affiliation(s)
- Andrei N Shkoporov
- Department of Microbiology and Virology, The Russian National Research Medical University, 1, Ostrovitjanova St., Moscow 117997, Russia.
| | | | | | | | | | | | | |
Collapse
|
38
|
Kalil JA, Halperin SA, Langley JM. Human challenge studies: a review of adequacy of reporting methods and results. Future Microbiol 2012; 7:481-95. [PMID: 22439725 DOI: 10.2217/fmb.12.15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Since the 1940s, researchers have purposefully infected healthy adult humans with pathogenic organisms to study how these pathogens cause disease and can be treated and prevented. 'Challenge studies' can be safe, ethical, extremely informative and an efficient use of resources during the clinical development of vaccines, but knowledge of this form of clinical research trial is not widespread. A review of the human challenge literature was performed to determine whether common elements of challenge studies can be identified in the articles published to date. The review demonstrated incomplete reporting of study characteristics deemed necessary for the correct interpretation and application of human challenge study results and for the accurate replication of study methodology. An unofficial extension of the Consolidated Standards of Reporting Trials (CONSORT) statement is proposed.
Collapse
Affiliation(s)
- Jennifer A Kalil
- Canadian Center for Vaccinology, Sanofi Pasteur Vaccine Challenge Unit, Dalhousie University & IWK Health Centre, Halifax, Nova Scotia, Canada
| | | | | |
Collapse
|
39
|
Sheikh AA, Checkley S, Avery B, Chalmers G, Bohaychuk V, Boerlin P, Reid-Smith R, Aslam M. Antimicrobial Resistance and Resistance Genes in Escherichia coli Isolated from Retail Meat Purchased in Alberta, Canada. Foodborne Pathog Dis 2012; 9:625-31. [DOI: 10.1089/fpd.2011.1078] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ali Ahmad Sheikh
- Agriculture and Agri-Food Canada, Lacombe Research Centre, Lacombe, Alberta, Canada
| | - Sylvia Checkley
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Brent Avery
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Valerie Bohaychuk
- Agri-Food Laboratories Branch, Alberta Agriculture and Rural Development, Edmonton, Alberta, Canada
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Richard Reid-Smith
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Mueen Aslam
- Agriculture and Agri-Food Canada, Lacombe Research Centre, Lacombe, Alberta, Canada
| |
Collapse
|
40
|
Nilsson O. Vancomycin resistant enterococci in farm animals - occurrence and importance. Infect Ecol Epidemiol 2012; 2:IEE-2-16959. [PMID: 22957131 PMCID: PMC3426332 DOI: 10.3402/iee.v2i0.16959] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 03/16/2012] [Accepted: 03/28/2012] [Indexed: 11/14/2022] Open
Abstract
The view on enterococci has over the years shifted from harmless commensals to opportunistic but important pathogens mainly causing nosocomial infections. One important part of this development is the emergence of vancomycin resistance enterococci (VRE). The term VRE includes several combinations of bacterial species and resistance genes of which the most clinically important is Enterococcus faecium with vanA type vancomycin resistance. This variant is also the most common VRE among farm animals. The reason for VRE being present among farm animals is selection by extensive use of the vancomycin analog avoparcin for growth promotion. Once the use of avoparcin was discontinued, the prevalence of VRE among farm animals decreased. However, VRE are still present among farm animals and by spread via food products they could potentially have a negative impact on public health. This review is based on the PhD thesis Vancomycin Resistant Enterococci in Swedish Broilers - Emergence, Epidemiology and Elimination and makes a short summary of VRE in humans and food producing animals. The specific situation regarding VRE in Swedish broiler production is also mentioned.
Collapse
Affiliation(s)
- Oskar Nilsson
- Department of Animal health and Antimicrobial strategies, National Veterinary Institute, Uppsala, Sweden
| |
Collapse
|
41
|
Technical specifications for the analysis and reporting of data on antimicrobial resistance (AMR) in the European Union Summary Report. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2587] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
|
42
|
Ogilvie LA, Firouzmand S, Jones BV. Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome. Bioeng Bugs 2012; 3:13-31. [PMID: 22126801 PMCID: PMC3329251 DOI: 10.4161/bbug.3.1.17883] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.
Collapse
Affiliation(s)
- Lesley A Ogilvie
- Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | | | | |
Collapse
|
43
|
Kich JD, Coldebella A, Morés N, Nogueira MG, Cardoso M, Fratamico PM, Call JE, Fedorka-Cray P, Luchansky JB. Prevalence, distribution, and molecular characterization of Salmonella recovered from swine finishing herds and a slaughter facility in Santa Catarina, Brazil. Int J Food Microbiol 2011; 151:307-13. [DOI: 10.1016/j.ijfoodmicro.2011.09.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 09/14/2011] [Accepted: 09/24/2011] [Indexed: 11/28/2022]
|
44
|
Antibiotics and the resistant microbiome. Curr Opin Microbiol 2011; 14:556-63. [DOI: 10.1016/j.mib.2011.07.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 07/02/2011] [Indexed: 11/19/2022]
|
45
|
Andam CP, Gogarten JP. Biased gene transfer and its implications for the concept of lineage. Biol Direct 2011; 6:47. [PMID: 21943000 PMCID: PMC3191353 DOI: 10.1186/1745-6150-6-47] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 09/23/2011] [Indexed: 11/10/2022] Open
Abstract
Background In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct. Results We present the evolutionary histories of three aminoacyl-tRNA synthetases (aaRS) to illustrate that the concept of organismal lineage in the prokaryotic world is defined by both vertical inheritance and reticulations due to HGT. The acquisition of a novel gene from a distantly related taxon can be considered as a shared derived character that demarcates a group of organisms, as in the case of the spirochaete Phenylalanyl-tRNA synthetase (PheRS). On the other hand, when organisms transfer genetic material with their close kin, the similarity and therefore relatedness observed among them is essentially shaped by gene transfer. Studying the distribution patterns of divergent genes with identical functions, referred to as homeoalleles, can reveal preferences for transfer partners. We describe the very ancient origin and the distribution of the archaeal homeoalleles for Threonyl-tRNA synthetases (ThrRS) and Seryl-tRNA synthetases (SerRS). Conclusions Patterns created through biased HGT can be undistinguishable from those created through shared organismal ancestry. A re-evaluation of the definition of lineage is necessary to reflect genetic relatedness due to both HGT and vertical inheritance. In most instances, HGT bias will maintain and strengthen similarity within groups. Only in cases where HGT bias is due to other factors, such as shared ecological niche, do patterns emerge from gene phylogenies that are in conflict with those reflecting shared organismal ancestry. Reviewers This article was reviewed by W. Ford Doolittle, François-Joseph Lapointe, and Frederic Bouchard.
Collapse
Affiliation(s)
- Cheryl P Andam
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA.
| | | |
Collapse
|
46
|
Dolejska M, Matulova M, Kohoutova L, Literak I, Bardon J, Cizek A. Extended-spectrum beta-lactamase-producing Escherichia coli in turkey meat production farms in the Czech Republic: national survey reveals widespread isolates with bla(SHV-12) genes on IncFII plasmids. Lett Appl Microbiol 2011; 53:271-7. [PMID: 21671965 DOI: 10.1111/j.1472-765x.2011.03099.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM The occurrence and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in the environment of turkey farms in the Czech Republic were studied. METHODS AND RESULTS Extended-spectrum beta-lactamase-producing E. coli isolates were found on 8 (20%) of 40 turkey farms surveyed. A total of 200 environmental smears were examined, and a total of 25 ESBL-producing E. coli were isolated. These isolates were analysed using XbaI pulsed-field gel electrophoresis and divided into nine pulsotypes. Most of the isolates harboured the gene bla(SHV-12) on a 40-kb plasmid of the IncFII group with an identical EcoRV restriction profile. Indistinguishable or clonally related SHV-12-producing isolates belonging to the same pulsotypes were found at some unrelated farms. CONCLUSIONS Widespread occurrence of ESBL-producing E. coli isolates with bla(SHV-12) carried on IncFII plasmids in meat production flocks in the Czech Republic was demonstrated. SIGNIFICANCE AND IMPACT OF THE STUDY Results indicate vertical transmission of ESBL-producing E. coli within the turkey production pyramid. The study shows the risk of multiresistant ESBL-producing bacteria and antibiotic-resistance genes being transmitted to humans via the food chain.
Collapse
Affiliation(s)
- M Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Palackecho, Czech Republic.
| | | | | | | | | | | |
Collapse
|
47
|
Hammerum A, Lester C, Jakobsen L, Porsbo L. Faecal carriage of extended-spectrum β-lactamase-producing and AmpC β-lactamase-producing bacteria among Danish army recruits. Clin Microbiol Infect 2011; 17:566-8. [DOI: 10.1111/j.1469-0691.2010.03340.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Mollenkopf DF, Kleinhenz KE, Funk JA, Gebreyes WA, Wittum TE. Salmonella enterica and Escherichia coli Harboring blaCMY in Retail Beef and Pork Products. Foodborne Pathog Dis 2011; 8:333-6. [DOI: 10.1089/fpd.2010.0701] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Katie E. Kleinhenz
- Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Julie A. Funk
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan
| | | | - Thomas E. Wittum
- Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| |
Collapse
|
49
|
Smet A, Rasschaert G, Martel A, Persoons D, Dewulf J, Butaye P, Catry B, Haesebrouck F, Herman L, Heyndrickx M. In situ ESBL conjugation from avian to human Escherichia coli during cefotaxime administration. J Appl Microbiol 2010; 110:541-9. [DOI: 10.1111/j.1365-2672.2010.04907.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
50
|
Baharoglu Z, Bikard D, Mazel D. Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation. PLoS Genet 2010; 6:e1001165. [PMID: 20975940 PMCID: PMC2958807 DOI: 10.1371/journal.pgen.1001165] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 09/17/2010] [Indexed: 11/21/2022] Open
Abstract
Conjugation is one mechanism for intra- and inter-species horizontal gene transfer among bacteria. Conjugative elements have been instrumental in many bacterial species to face the threat of antibiotics, by allowing them to evolve and adapt to these hostile conditions. Conjugative plasmids are transferred to plasmidless recipient cells as single-stranded DNA. We used lacZ and gfp fusions to address whether conjugation induces the SOS response and the integron integrase. The SOS response controls a series of genes responsible for DNA damage repair, which can lead to recombination and mutagenesis. In this manuscript, we show that conjugative transfer of ssDNA induces the bacterial SOS stress response, unless an anti-SOS factor is present to alleviate this response. We also show that integron integrases are up-regulated during this process, resulting in increased cassette rearrangements. Moreover, the data we obtained using broad and narrow host range plasmids strongly suggests that plasmid transfer, even abortive, can trigger chromosomal gene rearrangements and transcriptional switches in the recipient cell. Our results highlight the importance of environments concentrating disparate bacterial communities as reactors for extensive genetic adaptation of bacteria. Bacteria exchange DNA in their natural environments. The process called conjugation consists of DNA transfer by cell contact from one bacterium to another. Conjugative circular plasmids have been identified as shuttles and reservoirs for adaptive genes. It is now established that such lateral gene transfer plays an essential role, especially for the antibiotic resistance development and dissemination among bacteria. Moreover, integrons, platforms of mobile gene cassettes, have been instrumental in this phenomenon, through their successful association with conjugative resistance plasmids. We demonstrate in this study that the conjugative transfer of plasmids triggers a bacterial stress response—the SOS response—in recipient cells and can impact the cassette content of integrons. The SOS response is already known to induce various genome modifications. Human and animal pathogens cohabit with environmental bacteria, in niches which will favor DNA exchange. SOS induction during conjugation is thus most probably able to impact a wide range of genomes. Bacterial SOS response could then be a suitable target for co-treatment of infections in order to prevent exchange of antibiotic resistance/adaptation genes.
Collapse
Affiliation(s)
- Zeynep Baharoglu
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, URA2171, Paris, France
| | - David Bikard
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, URA2171, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, URA2171, Paris, France
- * E-mail:
| |
Collapse
|