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Yarahmadi N, Halimi S, Moradi P, Zamanian MH, Rezaei A, Vaziri S, Akya A, Alvandi A, Yazdani S, Ghadimi D, Moradi J. Prevalence of Antibiotic-Resistant Lactobacilli in Sepsis Patients with Long-Term Antibiotic Therapy. Curr Microbiol 2022; 79:318. [DOI: 10.1007/s00284-022-03010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 08/24/2022] [Indexed: 11/03/2022]
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2
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Excision and integration of unconventional circularizable structures involving the erm(B) gene in enterococci. Vet Microbiol 2022; 273:109542. [PMID: 35969915 DOI: 10.1016/j.vetmic.2022.109542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 08/04/2022] [Accepted: 08/07/2022] [Indexed: 11/22/2022]
Abstract
Traditionally, insertion sequences (ISs) play a major role in disseminating antimicrobial resistance genes (ARGs) in bacteria through transposition and translocation, forming regions that contain multiple ARGs flanked by single or multiple copies of IS. In addition, unconventional circularizable structures (UCSs), lacking recombinase genes but being surrounded by directly repeated sequences (DRs) of various sizes which do not contain transposase genes, were reported to be involved in the dissemination of ARGs. In this study, a novel UCS was identified on plasmid pE508-2 in E. faecalis E508, which carried a 24,411 bp multiresistance gene cluster, consisting of the resistance genes aphA3, lnu(B), lsa(E), spw, aac(A)-aph(D), lnu(B), dfrG, and two copies of aadE flanked by copies of erm(B). PCR assays revealed that three types of UCSs with lengths of 7235, 16,437, and 23,673 bp were formed, each of which contained the respective resistance genes and one copy of erm(B). Using erm(B)-negative and -positive strains, we demonstrated that erm(B)-carrying UCSs failed to transfer into an erm(B)-negative strain, but could integrate into an erm(B)-positive strain in a new site adjacent to a pre-existing erm(B) gene by natural transformation. Database searches revealed that erm(B)-flanked multiresistance gene regions, which might be able to form the respective UCSs, are present among various bacteria from different sources in various countries. In summary, this study experimentally demonstrated the excision and integration of UCS involving structures that include erm(B). The widespread presence of these UCSs in various Gram-positive bacteria highlights its role in the dissemination of ARGs among bacterial pathogens.
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Yu R, Chen Z, Li D, Schwarz S, Wang X, Du XD. Studies on the Transmission of a Tigecycline Resistance-Mediating tet(A) Gene Variant from Enterobacter hormaechei via a Two-Step Recombination Process. Microbiol Spectr 2022; 10:e0049622. [PMID: 35579466 PMCID: PMC9241890 DOI: 10.1128/spectrum.00496-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
To investigate the contribution of a tet(A) variant to tigecycline resistance in Enterobacter hormaechei and the recombination events that occurred during transmission of this variant. MICs were determined by broth microdilution. E. hormaechei G17 was characterized by PCR, transfer assay, S1-PFGE, Southern blot hybridization, and WGS analysis. A tet(A) variant conferring resistance to tigecycline was present in E. hormaechei G17. This strain harbored two resistance plasmids (pG17-1, 264,084 bp and pG17-2, 68,610 bp) and its E. coli transformant Tm-G17TGC one resistance plasmid (pTm-G17, 93,013 bp). The comparative analysis of pG17-1, pG17-2, and pTm-G17 showed that a tet(A) variant-carrying multiresistance gene cluster (~23 kb) originating from pG17-1 had integrated into pG17-2, forming the novel plasmid pTm-G17. In a first step, this multiresistance gene cluster was excised from pG17-1 by recombination of homologous sequences, including △TnAs1 at both termini, thereby generating an unconventional circularizable structure (UCS). In a second step, this UCS integrated into pG17-2 via recombination between homologous sequences, including IS26 present on both, the UCS and pG17-2, thereby giving rise to the new plasmid pTm-G17. In summary, a tet(A) variant conferring resistance to tigecycline was reported in E. hormaechei. Transfer of a tet(A) variant-carrying multiresistance gene cluster between plasmids occurred in a two-step recombination process, in which homologous sequences, including either △TnAs1 or IS26, were involved. IMPORTANCE Tigecycline is an important last-resort broad spectrum antimicrobial agent. This study describes the two-step recombination processes resulting in the transfer of the tet(A) variant gene between different plasmids in E. hormaechei, which depicts the role of recombination processes in the generation of UCSs and new plasmids, both carrying a tet(A) variant conferring resistance to tigecycline. Such processes enhance the dissemination of resistance genes, which is of particular relevance for resistance genes, such as the tet(A) variant. The presence and transmission of a tet(A) variant in E. hormaechei will compromise the efficacy of tigecycline treatment for E. hormaechei associated infection.
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Affiliation(s)
- Runhao Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Zheng Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Danyang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Xinwei Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
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4
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Moradi J, Fathollahi M, Halimi S, Alvandi A, Abiri R, Vaziri S, Rezaei A. Characterization of resistome in Lactobacillus genomic sequences from the human gut. J Glob Antimicrob Resist 2022; 30:451-458. [DOI: 10.1016/j.jgar.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/20/2022] [Indexed: 10/18/2022] Open
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Nunziata L, Brasca M, Morandi S, Silvetti T. Antibiotic resistance in wild and commercial non-enterococcal Lactic Acid Bacteria and Bifidobacteria strains of dairy origin: An update. Food Microbiol 2022; 104:103999. [DOI: 10.1016/j.fm.2022.103999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 12/19/2022]
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6
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Fatahi-Bafghi M, Naseri S, Alizehi A. Genome analysis of probiotic bacteria for antibiotic resistance genes. Antonie van Leeuwenhoek 2022; 115:375-389. [PMID: 34989942 DOI: 10.1007/s10482-021-01703-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/21/2021] [Indexed: 12/30/2022]
Abstract
To date, probiotic bacteria are used in the diet and have various clinical applications. There are reports of antibiotic resistance genes in these bacteria that can transfer to other commensal and pathogenic bacteria. The aim of this study was to use whole-genome sequence analysis to identify antibiotic resistance genes in a group of bacterial with probiotic properties. Also, this study followed existing issues about the importance and presence of antibiotic resistance genes in these bacteria and the dangers that may affect human health in the future. In the current study, a collection of 126 complete probiotic bacterial genomes was analyzed for antibiotic resistance genes. The results of the current study showed that there are various resistance genes in these bacteria that some of them are transferable to other bacteria. The tet(W) tetracycline resistance gene was more than other antibiotic resistance genes in these bacteria and this gene was found in Bifidobacterium and Lactobacillus. In our study, the most numbers of antibiotic resistance genes were transferred with mobile genetic elements. We propose that probiotic companies before the use of a micro-organism as a probiotic, perform an antibiotic susceptibility testing for a large number of antibiotics. Also, they perform analysis of complete genome sequence for prediction of antibiotic resistance genes.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran. .,Zoonotic Diseases Research Center, Department of Food Hygiene and Safety, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| | - Sara Naseri
- Zoonotic Diseases Research Center, Department of Food Hygiene and Safety, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Alizehi
- International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Chung The H, Nguyen Ngoc Minh C, Tran Thi Hong C, Nguyen Thi Nguyen T, Pike LJ, Zellmer C, Pham Duc T, Tran TA, Ha Thanh T, Van MP, Thwaites GE, Rabaa MA, Hall LJ, Baker S. Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population. Microbiol Spectr 2021; 9:e0052621. [PMID: 34523984 PMCID: PMC8557894 DOI: 10.1128/spectrum.00526-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/13/2021] [Indexed: 01/29/2023] Open
Abstract
Bifidobacterium pseudocatenulatum is a member of the human gut microbiota, and specific variants of B. pseudocatenulatum have been associated with health benefits such as improving gut integrity and reducing inflammatory responses. Here, we aimed to assess the genomic diversity and predicted metabolic profiles of B. pseudocatenulatum cells found colonizing the gut of healthy Vietnamese adults and children. We found that the population of B. pseudocatenulatum from each individual was distinct and highly diverse, with intraclonal variation attributed largely to a gain or loss of carbohydrate-utilizing enzymes. The B. pseudocatenulatum genomes were enriched with glycosyl hydrolases predicted to target plant-based nondigestible carbohydrates (GH13, GH43) but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed extensive genetic diversity and was subject to a high degree of genetic modification. Antimicrobial susceptibility profiling revealed that the Vietnamese B. pseudocatenulatum cells were uniformly susceptible to beta-lactams but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin, and metronidazole. The genomic presence of ermX and tet variants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with a mutation(s) in the quinolone resistance-determining region (GyrA, S115, and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization of B. pseudocatenulatum found in the Vietnamese population, which can be exploited for the rational design of probiotics. IMPORTANCE Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features. Population-specific beneficial microbes represent a promising avenue for the development of potential probiotics, as they may exhibit a more suitable profile in the target population. This study investigates the underexplored diversity of B. pseudocatenulatum in Vietnam and provides more understanding of its genomic diversity, metabolic potential, and antimicrobial susceptibility. Such data from indigenous populations are essential for selecting probiotic candidates that can be accelerated into further preclinical and clinical investigations.
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Affiliation(s)
- Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | - Lindsay J. Pike
- The Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Caroline Zellmer
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Trung Pham Duc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuan-Anh Tran
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Minh Pham Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Maia A. Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Lindsay J. Hall
- Quadram Institute Biosciences, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
- Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Stephen Baker
- The Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
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Watanabe Y, Saito Y, Hara T, Tsukuda N, Aiyama-Suzuki Y, Tanigawa-Yahagi K, Kurakawa T, Moriyama-Ohara K, Matsumoto S, Matsuki T. Xylan utilisation promotes adaptation of Bifidobacterium pseudocatenulatum to the human gastrointestinal tract. ISME COMMUNICATIONS 2021; 1:62. [PMID: 37938239 PMCID: PMC9723692 DOI: 10.1038/s43705-021-00066-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 05/27/2023]
Abstract
Dietary carbohydrates impact the composition of the human gut microbiota. However, the relationship between carbohydrate availability for individual bacteria and their growth in the intestinal environment remains unclear. Here, we show that the availability of long-chain xylans (LCX), one of the most abundant dietary fibres in the human diet, promotes the growth of Bifidobacterium pseudocatenulatum in the adult human gut. Genomic and phenotypic analyses revealed that the availability of LCX-derived oligosaccharides is a fundamental feature of B. pseudocatenulatum, and that some but not all strains possessing the endo-1,4-β-xylanase (BpXyn10A) gene grow on LCX by cleaving the xylose backbone. The BpXyn10A gene, likely acquired by horizontal transfer, was incorporated into the gene cluster for LCX-derived oligosaccharide utilisation. Co-culturing with xylanolytic Bacteroides spp. demonstrated that LCX-utilising strains are more competitive than LCX non-utilising strains even when LCX-derived oligosaccharides were supplied. In LCX-rich dietary interventions in adult humans, levels of endogenous B. pseudocatenulatum increased only when BpXyn10A was detected, indicating that LCX availability is a fitness determinant in the human gut. Our findings highlight the enhanced intestinal adaptability of bifidobacteria via polysaccharide utilisation, and provide a cornerstone for systematic manipulation of the intestinal microbiota through dietary intervention using key enzymes that degrade polysaccharide as biomarkers.
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Affiliation(s)
| | - Yuki Saito
- Yakult Central Institute, Kunitachi, Tokyo, Japan
| | - Taeko Hara
- Yakult Central Institute, Kunitachi, Tokyo, Japan
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9
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Tóth AG, Csabai I, Judge MF, Maróti G, Becsei Á, Spisák S, Solymosi N. Mobile Antimicrobial Resistance Genes in Probiotics. Antibiotics (Basel) 2021; 10:antibiotics10111287. [PMID: 34827225 PMCID: PMC8614787 DOI: 10.3390/antibiotics10111287] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 01/19/2023] Open
Abstract
Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.
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Affiliation(s)
- Adrienn Gréta Tóth
- Health Services Management Training Centre, Semmelweis University, 1125 Budapest, Hungary;
| | - István Csabai
- Department of Phyisics of Complex Systems, Eötvös Loránd University, 1117 Budapest, Hungary; (I.C.); (Á.B.)
| | - Maura Fiona Judge
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, 6726 Szeged, Hungary;
- Faculty of Water Sciences, University of Public Service, 6500 Baja, Hungary
| | - Ágnes Becsei
- Department of Phyisics of Complex Systems, Eötvös Loránd University, 1117 Budapest, Hungary; (I.C.); (Á.B.)
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA;
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
- Correspondence: ; Tel.: +36-30-9347-069
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Lobb B, Tremblay BJM, Moreno-Hagelsieb G, Doxey AC. PathFams: statistical detection of pathogen-associated protein domains. BMC Genomics 2021; 22:663. [PMID: 34521345 PMCID: PMC8442362 DOI: 10.1186/s12864-021-07982-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulence determinants, is a challenging but important goal. Results To facilitate virulence factor discovery, we performed a comprehensive analysis of 17,929 protein domain families within the Pfam database, and scored them based on their overrepresentation in pathogenic versus non-pathogenic species, taxonomic distribution, relative abundance in metagenomic datasets, and other factors. Conclusions We identify pathogen-associated domain families, candidate virulence factors in the human gut, and eukaryotic-like mimicry domains with likely roles in virulence. Furthermore, we provide an interactive database called PathFams to allow users to explore pathogen-associated domains as well as identify pathogen-associated domains and domain architectures in user-uploaded sequences of interest. PathFams is freely available at https://pathfams.uwaterloo.ca. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07982-8.
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Affiliation(s)
- Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | | | | | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
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Nøhr-Meldgaard K, Struve C, Ingmer H, Agersø Y. The Tetracycline Resistance Gene, tet(W) in Bifidobacterium animalis subsp. lactis Follows Phylogeny and Differs From tet(W) in Other Species. Front Microbiol 2021; 12:658943. [PMID: 34335493 PMCID: PMC8319848 DOI: 10.3389/fmicb.2021.658943] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022] Open
Abstract
The tetracycline resistance gene tet(W) encodes a ribosomal protection protein that confers a low level of tetracycline resistance in the probiotic bacterium Bifidobacterium animalis subsp. lactis. With the aim of assessing its phylogenetic origin and potential mobility, we have performed phylogenetic and in silico genome analysis of tet(W) and its flanking genes. tet(W) was found in 41 out of 44 examined B. animalis subsp. lactis strains. In 38 strains, tet(W) was flanked by an IS5-like element and an open reading frame encoding a hypothetical protein, which exhibited a similar GC content (51–53%). These genes were positioned in the same genomic context within the examined genomes. Phylogenetically, the B. animalis subsp. lactis tet(W) cluster in a clade separate from tet(W) of other species and genera. This is not the case for tet(W) encoded by other bifidobacteria and other species where tet(W) is often found in association with transferable elements or in different genomic regions. An IS5-like element identical to the one flanking the B. animalis subsp. lactis tet(W) has been found in a human gut related bacterium, but it was not associated with any tet(W) genes. This suggests that the IS5-like element is not associated with genetic mobility. tet(W) and the IS5 element have previously been shown to be co-transcribed, indicating that co-localization may be associated with tet(W) expression. Here, we present a method where phylogenetic and in silico genome analysis can be used to determine whether antibiotic resistance genes should be considered innate (intrinsic) or acquired. We find that B. animalis subsp. lactis encoded tet(W) is part of the ancient resistome and thereby possess a negligible risk of transfer.
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Affiliation(s)
- Katrine Nøhr-Meldgaard
- Chr. Hansen A/S, Hørsholm, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yvonne Agersø
- Chr. Hansen A/S, Hørsholm, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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12
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Kwiecień E, Stefańska I, Chrobak-Chmiel D, Kizerwetter-Świda M, Moroz A, Olech W, Spinu M, Binek M, Rzewuska M. Trueperella pyogenes Isolates from Livestock and European Bison ( Bison bonasus) as a Reservoir of Tetracycline Resistance Determinants. Antibiotics (Basel) 2021; 10:380. [PMID: 33916765 PMCID: PMC8065510 DOI: 10.3390/antibiotics10040380] [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: 02/15/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
Determinants of tetracycline resistance in Trueperella pyogenes are still poorly known. In this study, resistance to tetracycline was investigated in 114 T. pyogenes isolates from livestock and European bison. Tetracycline minimum inhibitory concentration (MIC) was evaluated by a microdilution method, and tetracycline resistance genes were detected by PCR. To determine variants of tetW and their linkage with mobile elements, sequencing analysis was performed. Among the studied isolates, 43.0% were tetracycline resistant (MIC ≥ 8 µg/mL). The highest MIC90 of tetracycline (32 µg/mL) was noted in bovine and European bison isolates. The most prevalent determinant of tetracycline resistance was tetW (in 40.4% of isolates), while tetA(33) was detected only in 8.8% of isolates. Four variants of tetW (tetW-1, tetW-2, tetW-3, tetW-4) were recognized. The tetW-3 variant was the most frequent and was linked to the ATE-1 transposon. The tetW-2 variant, found in a swine isolate, was not previously reported in T. pyogenes. This is the first report on determinants of tetracycline resistance in T. pyogenes isolates from European bison. These findings highlight that wild animals, including wild ruminants not treated with antimicrobials, can be a reservoir of tetracycline-resistant bacteria carrying resistance determinants, which may be easily spread among pathogenic and environmental microorganisms.
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Affiliation(s)
- Ewelina Kwiecień
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (I.S.); (D.C.-C.); (M.K.-Ś.); (M.B.)
| | - Ilona Stefańska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (I.S.); (D.C.-C.); (M.K.-Ś.); (M.B.)
| | - Dorota Chrobak-Chmiel
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (I.S.); (D.C.-C.); (M.K.-Ś.); (M.B.)
| | - Magdalena Kizerwetter-Świda
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (I.S.); (D.C.-C.); (M.K.-Ś.); (M.B.)
| | - Agata Moroz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c St., 02-786 Warsaw, Poland;
| | - Wanda Olech
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland;
| | - Marina Spinu
- Department of Infectious Diseases and Preventive Medicine, Law and Ethics, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăștur 3-5, 400372 Cluj-Napoca, Romania;
| | - Marian Binek
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (I.S.); (D.C.-C.); (M.K.-Ś.); (M.B.)
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8 St., 02-786 Warsaw, Poland; (I.S.); (D.C.-C.); (M.K.-Ś.); (M.B.)
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13
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Yoo K, Lee G. Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis. Antibiotics (Basel) 2021; 10:antibiotics10020188. [PMID: 33671905 PMCID: PMC7918964 DOI: 10.3390/antibiotics10020188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/03/2021] [Accepted: 02/11/2021] [Indexed: 12/30/2022] Open
Abstract
Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide–lincosamide–streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5–2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems.
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Juricova H, Matiasovicova J, Kubasova T, Cejkova D, Rychlik I. The distribution of antibiotic resistance genes in chicken gut microbiota commensals. Sci Rep 2021; 11:3290. [PMID: 33558560 PMCID: PMC7870933 DOI: 10.1038/s41598-021-82640-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.
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Affiliation(s)
| | | | | | - Darina Cejkova
- Veterinary Research Institute, Brno, Czech Republic.,Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
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15
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Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective. Biotechnol Adv 2020; 45:107654. [DOI: 10.1016/j.biotechadv.2020.107654] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/14/2020] [Accepted: 11/01/2020] [Indexed: 12/15/2022]
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16
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Literature-Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacterium. Curr Microbiol 2020; 77:4104-4113. [PMID: 33057753 DOI: 10.1007/s00284-020-02230-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/29/2020] [Indexed: 01/05/2023]
Abstract
Bifidobacteria are typical commensals inhabiting the human intestine and are beneficial to the host because of their probiotic properties. One of the risks concerning probiotics is the potential of introducing antibiotic resistance genes (ARGs) to the host gut pathogens. This study was aimed to depict the general antibiotic resistance characteristics of the genus Bifidobacterium by combining the reported phenotype dataset and in silico genotype prediction. Bifidobacteria were mostly reported to be sensitive to beta-lactams, glycopeptides, chloramphenicol, and rifampicin, but resistant to aminoglycosides, polypeptides, quinolones, and mupirocin. Generally, the resistance phenotypes to erythromycin, tetracycline, fusidic acid, metronidazole, clindamycin, and trimethoprim were variable. Besides cmX and tetQ, characterized in bifidobacterial resident plasmids, 3520 putative ARGs were identified from 831 bifidobacterial genomes through BLASTP search. The identified ARGs matched thirty-eight reference ARGs, four of which seemed to be mutant housekeeping genes. The two high-abundant ARGs, tetW and ermX, were found to have different distribution traits. The predicted ARGs reasonably explained most of the corresponding resistant phenotypes in the published literature.
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17
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Daniali M, Nikfar S, Abdollahi M. Antibiotic resistance propagation through probiotics. Expert Opin Drug Metab Toxicol 2020; 16:1207-1215. [PMID: 32938241 DOI: 10.1080/17425255.2020.1825682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The widespread use of probiotics globally has established an argument against their safety profile. Recent studies investigated the gastrointestinal tract (GIT) as a reservoir for antibiotic resistance genes and horizontal gene transfer (HGT) amongst opportunistic pathogens, probiotics, and the normal microbiota which might cause severe clinical implications. AREAS COVERED In this review, we aimed to discuss the potential role of probiotics in spreading antibiotic resistance. All relevant data were found through online/updated databases such as PubMed, Google Scholar, and Clinicaltrials.gov. This review is based on the studies undertaken over the past two decades (2000-2020). EXPERT OPINION Microorganisms are capable of transferring resistance genes to survive against antimicrobial medications. Transference of resistance genes among pathogens, probiotics, and gut microbiota in the GIT through HGT endow probiotics as a possible source for antimicrobial resistance genes, which is responsible for the development of the antibiotic resistance crisis. According to the expression of genes in mechanisms of antibiotics resistance and probiotics HGT, the hypothesis of the role of these microorganisms in personalized medicine and gene therapy could also be considered.
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Affiliation(s)
- Marzieh Daniali
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences , Tehran, Iran.,Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences , Tehran, Iran
| | - Shekoufeh Nikfar
- Personalized Medicine Research Center (PMRC), the Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences , Tehran, Iran.,Evidence-Based Evaluation of Cost-Effectiveness and Clinical Outcomes Group, Pharmaceutical Sciences Research Center (PSRC), and the Pharmaceutical Management and Economics Research Center (PMERC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences , Tehran, Iran.,Department of Pharmacoeconomics and Pharmaceutical Administration, School of Pharmacy, Tehran University of Medical Sciences , Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), the Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences , Tehran, Iran.,Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences , Tehran, Iran.,Personalized Medicine Research Center (PMRC), the Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences , Tehran, Iran
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Paul TK, Hasan MM, Haque MA, Talukder S, Sarker YA, Sikder MH, Khan MAHNA, Sakib MN, Kumar A. Dietary supplementation of Neem ( Azadirachta indica) leaf extracts improved growth performance and reduced production cost in broilers. Vet World 2020; 13:1050-1055. [PMID: 32801554 PMCID: PMC7396339 DOI: 10.14202/vetworld.2020.1050-1055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Global trend to remove the antibiotic growth promoter (AGP) from animals contributes to the exploration of successful measures to sustain production and reduces the intestinal diseases in the post-AGP era. Plant extracts, therefore, have been used to improve performance and intestinal health. Here, we conducted a study to evaluate the effects of neem (Azadirachta indica) leaf extracts (NLE) as alternatives to AGPs in broiler chickens. Materials and Methods Sixty day-old broiler chicks were assigned to 12-floor pens, each stocked with five birds and divided into three treatment groups of four pens per treatment. The groups were: Negative control, basal diet without additives; positive control, basal diet with antibiotics and vitamins; and NLE treated group, basal diet supplemented with 0.1% aqua extract of neem leaves. Results Overall feed intake was significantly (p≤0.05) highest in the positive control. Higher body weight, higher dressing percentage, and lower feed conversion ratio were observed in birds treated with NLE compared to the negative control group (p≤0.05) but not the positive control group (p>0.05). There was no significant variation in hematology between different groups. Furthermore, the economic evaluation indicated that the NLE treatment was found cheaper than control and antibiotic treatment in cost-benefit analysis. Conclusion We suggest NLE might be a cheaper alternative to antibiotics in broiler production as indicated by improved body weight and feed efficiency.
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Affiliation(s)
- Torun Kumar Paul
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Md Mehedi Hasan
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Md Anowarul Haque
- Department of Surgery and Theriogenology, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Sudipta Talukder
- Population Medicine and AMR Laboratory, Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Yousuf Ali Sarker
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Mahmudul Hasan Sikder
- Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | | | - Mohammed Nazmus Sakib
- Department of Animal Science, Faculty of Animal Husbandry, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Alip Kumar
- Department of Animal Science, School of Environmental and Rural Science, University of New England, Australia
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Transferable Resistance Gene optrA in Enterococcus faecalis from Swine in Brazil. Antimicrob Agents Chemother 2020; 64:AAC.00142-20. [PMID: 32253215 DOI: 10.1128/aac.00142-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
OptrA is an ATP-binding cassette (ABC)-F protein that confers resistance to oxazolidinones and phenicols and can be either plasmid-encoded or chromosomally encoded. Here, we isolated 13 Enterococcus faecalis strains possessing a linezolid MIC of ≥4 mg/liter from nursery pigs in swine herds located across Brazil. Genome sequence comparison showed that these strains possess optrA in different genetic contexts occurring in 5 different E. faecalis sequence type backgrounds. The optrA gene invariably occurred in association with an araC regulator and a gene encoding a hypothetical protein. In some contexts, this genetic island was able to excise and form a covalently closed circle within the cell; this circle appeared to occur in high abundance and to be transmissible by coresident plasmids.
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Seidlerova Z, Kubasova T, Faldynova M, Crhanova M, Karasova D, Babak V, Rychlik I. Environmental Impact on Differential Composition of Gut Microbiota in Indoor Chickens in Commercial Production and Outdoor, Backyard Chickens. Microorganisms 2020; 8:microorganisms8050767. [PMID: 32443788 PMCID: PMC7285315 DOI: 10.3390/microorganisms8050767] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022] Open
Abstract
In this study, we compared the caecal microbiota composition of egg-laying hens from commercial production that are kept indoors throughout their whole life with microbiota of hens kept outdoors. The microbiota of outdoor hens consisted of lower numbers of bacterial species than the microbiota of indoor hens. At the phylum level, microbiota of outdoor hens was enriched for Bacteroidetes (62.41 ± 4.47% of total microbiota in outdoor hens and 52.01 ± 6.27% in indoor hens) and Proteobacteria (9.33 ± 4.99% in outdoor and 5.47 ± 2.24% in indoor hens). On the other hand, Firmicutes were more abundant in the microbiota of indoor hens (33.28 ± 5.11% in indoor and 20.66 ± 4.41% in outdoor hens). Horizontally transferrable antibiotic resistance genes tetO, tet(32), tet(44), and tetW were also less abundant in the microbiota of outdoor hens than indoor hens. A comparison of the microbiota composition at the genus and species levels pointed toward isolates specifically adapted to the two extreme environments. However, genera and species recorded as being similarly abundant in the microbiota of indoor and outdoor hens are equally as noteworthy because these represent microbiota members that are highly adapted to chickens, irrespective of their genetics, feed composition, and living environment.
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21
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Kim Y, Leung MHY, Kwok W, Fournié G, Li J, Lee PKH, Pfeiffer DU. Antibiotic resistance gene sharing networks and the effect of dietary nutritional content on the canine and feline gut resistome. Anim Microbiome 2020; 2:4. [PMID: 33500005 PMCID: PMC7807453 DOI: 10.1186/s42523-020-0022-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we investigated the association of dietary nutritional content with gut ARG diversity and composition, using publicly available shotgun metagenomic sequence data generated from canine and feline fecal samples. Also, based on network theory, we explored ARG-sharing patterns between gut bacterial genera by identifying the linkage structure between metagenomic assemblies and their functional genes obtained from the same data. RESULTS In both canine and feline gut microbiota, an increase in protein and a reduction in carbohydrate in the diet were associated with increased ARG diversity. ARG diversity of the canine gut microbiota also increased, but less strongly, after a reduction in protein and an increase in carbohydrate in the diet. The association between ARG and taxonomic composition suggests that diet-induced changes in the gut microbiota may be responsible for changes in ARG composition, supporting the links between protein metabolism and antibiotic resistance in gut microbes. In the analysis of the ARG-sharing patterns, 22 ARGs were shared among 46 genera in the canine gut microbiota, and 11 ARGs among 28 genera in the feline gut microbiota. Of these ARGs, the tetracycline resistance gene tet(W) was shared among the largest number of genera, predominantly among Firmicutes genera. Bifidobacterium, a genus extensively used in the fermentation of dairy products and as probiotics, shared tet(W) with a wide variety of other genera. Finally, genera from the same phylum were more likely to share ARGs than with those from different phyla. CONCLUSIONS Our findings show that dietary nutritional content, especially protein content, is associated with the gut resistome and suggest future research to explore the impact of dietary intervention on the development of antibiotic resistance in clinically-relevant gut microbes. Our network analysis also reveals that the genetic composition of bacteria acts as an important barrier to the horizontal transfer of ARGs. By capturing the underlying gene-sharing relationships between different bacterial taxa from metagenomes, our network approach improves our understanding of horizontal gene transfer dynamics.
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Affiliation(s)
- Younjung Kim
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Wendy Kwok
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Guillaume Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Dirk U Pfeiffer
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.,Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
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22
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Rozman V, Mohar Lorbeg P, Accetto T, Bogovič Matijašić B. Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data. Int J Food Microbiol 2020; 314:108388. [DOI: 10.1016/j.ijfoodmicro.2019.108388] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 10/02/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022]
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Tetracycline Resistant Campylobacter jejuni Subtypes Emanating from Beef Cattle Administered Non-Therapeutic Chlortetracycline are Longitudinally Transmitted within the Production Continuum but are Not Detected in Ground Beef. Microorganisms 2019; 8:microorganisms8010023. [PMID: 31877744 PMCID: PMC7022225 DOI: 10.3390/microorganisms8010023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 11/17/2022] Open
Abstract
The impacts of the antimicrobial growth promoter (AGP), chlortetracycline with sulfamethazine (AS700), on the development of antimicrobial resistance and longitudinal transmission of Campylobacter jejuni within the beef production continuum were empirically determined. Carriage of tetracycline resistance determinants in the enteric bacterial community increased at a greater rate for AS700-treatment cattle. The majority of the bacteria from animals administered AS700 carried tetW. Densities of C. jejuni shed in feces increased over the confined feeding period, and the administration of AS700 did not conspicuously reduce C. jejuni densities in feces or within the intestine. The majority of C. jejuni isolates recovered were resistant to tetracycline, but the resistance rates to other antibiotics was low (≤20.1%). The richness of C. jejuni subtypes recovered from AS700-treated animals that were either resistant or susceptible to tetracycline was reduced, indicating selection pressure due to AGP administration. Moreover, a degree of subtype-specific resistance to tetracycline was observed. tetO was the primary tetracycline resistance determinant conferring resistance in C. jejuni isolates recovered from cattle and people. Clinically-relevant C. jejuni subtypes (subtypes that represent a risk to human health) that were resistant to tetracycline were isolated from cattle feces, digesta, hides, the abattoir environment, and carcasses, but not from ground beef. Thus, study findings indicate that clinically-relevant C. jejuni subtypes associated with beef cattle, including those resistant to antibiotics, do not represent a significant foodborne risk.
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Zuo F, Zeng Z, Hammarström L, Marcotte H. Inducible Plasmid Self-Destruction (IPSD) Assisted Genome Engineering in Lactobacilli and Bifidobacteria. ACS Synth Biol 2019; 8:1723-1729. [PMID: 31277549 DOI: 10.1021/acssynbio.9b00114] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genome engineering is essential for application of synthetic biology in probiotics including lactobacilli and bifidobacteria. Several homologous recombination system-based mutagenesis tools have been developed for these bacteria, but still have many limitations in different species or strains. Here we developed a genome engineering method based on an inducible self-destruction plasmid delivering homologous DNA into bacteria. Excision of the replicon by induced recombinase facilitates selection of homologous recombination events. This new genome editing tool called inducible plasmid self-destruction (IPSD) was successfully used to perform gene knockout and knock-in in lactobacilli and bifidobacteria. Due to its simplicity and universality, the IPSD strategy may provide a general approach for genetic engineering of various bacterial species.
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Affiliation(s)
- Fanglei Zuo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
| | - Zhu Zeng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
| | - Lennart Hammarström
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
| | - Harold Marcotte
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
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Pérez-Valera E, Kyselková M, Ahmed E, Sladecek FXJ, Goberna M, Elhottová D. Native soil microorganisms hinder the soil enrichment with antibiotic resistance genes following manure applications. Sci Rep 2019; 9:6760. [PMID: 31043618 PMCID: PMC6494816 DOI: 10.1038/s41598-019-42734-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/05/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial genes responsible for resistance to antibiotic agents (ARG) are spread from livestock to soil through application of manure, threatening environmental and human health. We investigated the mechanisms of ARG dissemination and persistence to disentangle i) the influence of nutrients and microorganisms on the soil tetracycline (TET) resistome, and ii) the role of indigenous soil microbiota in preventing ARG spread. We analysed short-term (7 days) and persistent (84 days) effects of manure on the resistome of three antibiotic-free pasture soils. Four microcosm treatments were evaluated: control, mineral nutrient fertilization, and deposition of a layer of fresh manure onto soil or γ-irradiated soil. We quantified five TET-resistance genes, isolated 135 TET-resistant bacteria and sequenced both culturable TET-resistant and whole bacterial communities. Manure amendments, but not nutrient addition, increased the abundance of TET-r genes such as tet(Y). Such changes persisted with time, in contrast with the TET-resistant bacterial composition, which partially recovered after manure amendments. Manured γ-irradiated soils showed significantly lower nutrient content and higher TET-r gene abundance than non-irradiated soils, suggesting that native soil bacteria are essential for the fertilization effect of manure on soil as well as control the dissemination of potentially risky TET-r genes.
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Affiliation(s)
- Eduardo Pérez-Valera
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.
| | - Martina Kyselková
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Engy Ahmed
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Frantisek Xaver Jiri Sladecek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Marta Goberna
- Department of Environment, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA). Carretera de la Coruña, Km 7.5, E-28040, Madrid, Spain
| | - Dana Elhottová
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
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A Preliminary Study on Probiotic Characteristics of Sporosarcina spp. for Poultry Applications. Curr Microbiol 2019; 76:448-461. [DOI: 10.1007/s00284-019-01647-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/06/2019] [Indexed: 11/28/2022]
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27
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Antimicrobial susceptibility of bifidobacteria from probiotic milk products and determination of the genetic basis of tetracycline resistance in Enterococcus species after in vitro conjugation with Bifidobacterium animalis subsp. lactis. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Morovic W, Roos P, Zabel B, Hidalgo-Cantabrana C, Kiefer A, Barrangou R. Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline. Appl Environ Microbiol 2018; 84:e01999-18. [PMID: 30266728 PMCID: PMC6238047 DOI: 10.1128/aem.01999-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/25/2018] [Indexed: 12/11/2022] Open
Abstract
Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority recommends testing resistance using microdilution culture techniques previously used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes show various inhibition levels, suggesting that other genetic elements also contribute to observed differences. Here, we adapted several molecular assays to confirm the inhibition of B. animalis subsp. lactis strains Bl-04 and HN019 and employed RNA sequencing to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to number of viable genome copies from droplet digital PCR and found that the bacteria were still metabolically active in high drug concentrations. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multidrug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was upregulated only during subinhibitory tetracycline concentrations, while two novel tetracycline resistance genes were upregulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were upregulated, while genes for complex carbohydrate utilization, protein metabolism, and clustered regularly interspaced short palindromic repeat(s) (CRISPR)-Cas systems were downregulated. These results provide high-throughput means for assessing antibiotic resistances of two highly related probiotic strains and determine the genetic network that contributes to the global tetracycline response.IMPORTANCEBifidobacterium animalis subsp. lactis is widely used in human food and dietary supplements. Although well documented to be safe, B. animalis subsp. lactis strains must not contain transferable antibiotic resistance elements. Many B. animalis subsp. lactis strains have different resistance measurements despite being genetically similar, and the reasons for this are not well understood. In the current study, we sought to examine how genomic differences between two closely related industrial B. animalis subsp. lactis strains contribute to different resistance levels. This will lead to a better understanding of resistance, identify future targets for analysis of transferability, and expand our understanding of tetracycline resistance in bacteria.
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Affiliation(s)
- Wesley Morovic
- Genomics & Microbiome Science, DuPont Nutrition & Health, Madison, Wisconsin, USA
| | - Paige Roos
- Genomics Laboratory, DuPont Pioneer, Johnston, Iowa, USA
| | - Bryan Zabel
- Genomics & Microbiome Science, DuPont Nutrition & Health, Madison, Wisconsin, USA
| | - Claudio Hidalgo-Cantabrana
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Anthony Kiefer
- Probiotic Development, DuPont Nutrition & Health, Madison, Wisconsin, USA
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
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Lokesh D, Parkesh R, Kammara R. Bifidobacterium adolescentis is intrinsically resistant to antitubercular drugs. Sci Rep 2018; 8:11897. [PMID: 30093677 PMCID: PMC6085307 DOI: 10.1038/s41598-018-30429-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
Multiple mutations in the β subunit of the RNA polymerase (rpoβ) of Mycobacterium tuberculosis (Mtb) are the primary cause of resistance to rifamycin (RIF). In the present study, bifidobacterial rpoβ sequences were analyzed to characterize the mutations that contribute to the development of intrinsic resistance to RIF, isoniazid, streptomycin and pyrazinamide. Sequence variations, which mapped to cassettes 1 and 2 of the rpoβ pocket, are also found in multidrug-resistant Mtb (MDR Mtb). Growth curves in the presence of osmolytes and different concentrations of RIF showed that the bacteria adapted rapidly by shortening the growth curve lag time. Insight into the adapted rpoβ DNA sequences revealed that B. adolescentis harbored mutations both in the RIF pocket and in regions outside the pocket. The minimum inhibitory concentrations (MICs) and mutant prevention concentrations (MPCs) indicated that B. longum, B. adolescentis and B. animalis are resistant to antitubercular drugs. 3D-homology modeling and binding interaction studies using computational docking suggested that mutants had reduced binding affinity towards RIF. RIF-exposed/resistant bacteria exhibited variant protein profiles along with morphological differences, such as elongated and branched cells, surface conversion from rough to smooth, and formation of a concentrating ring.
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Affiliation(s)
- Dhanashree Lokesh
- Senior Research Fellow, Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysore, 20, India
| | - Raman Parkesh
- Principal Scientist, Protein Science Center, Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Rajagopal Kammara
- Senior Research Fellow, Department of Protein Chemistry and Technology, CSIR-CFTRI, Mysore, 20, India.
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Polit A, Yang H, Amund D. Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2018; 37:39-43. [PMID: 29662736 PMCID: PMC5897239 DOI: 10.12938/bmfh.17-017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/09/2017] [Indexed: 11/08/2022]
Abstract
Transfer of antibiotic resistance genes from probiotic bacteria to pathogens poses a safety concern. Orally administered probiotics are exposed to stressful conditions during gastrointestinal transit. In this study,
filter mating experiments were performed to investigate the potential role of exposure of Bifidobacterium isolates to acid and bile stress on the transfer of a tetracycline resistance gene,
tet(W), to Enterococcus faecalis ATCC 51299. No E. faecalis transconjugants were obtained after mating with either stressed or unstressed
Bifidobacterium, thereby suggesting that tet(W) could not be transferred as a result of exposure to gastrointestinal stresses.
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Affiliation(s)
- Agnieszka Polit
- School of Life Sciences, Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry CV1 5FB, United Kingdom
| | - Huiying Yang
- School of Life Sciences, Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry CV1 5FB, United Kingdom
| | - Daniel Amund
- School of Life Sciences, Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry CV1 5FB, United Kingdom
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31
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Morovic W, Roper JM, Smith AB, Mukerji P, Stahl B, Rae JC, Ouwehand AC. Safety evaluation of HOWARU ® Restore ( Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, Bifidobacterium animalis subsp. lactis Bl-04 and B. lactis Bi-07) for antibiotic resistance, genomic risk factors, and acute toxicity. Food Chem Toxicol 2017; 110:316-324. [DOI: 10.1016/j.fct.2017.10.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 12/30/2022]
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Tamanai-Shacoori Z, Smida I, Bousarghin L, Loreal O, Meuric V, Fong SB, Bonnaure-Mallet M, Jolivet-Gougeon A. Roseburia spp.: a marker of health? Future Microbiol 2017; 12:157-170. [PMID: 28139139 DOI: 10.2217/fmb-2016-0130] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The genus Roseburia consists of obligate Gram-positive anaerobic bacteria that are slightly curved, rod-shaped and motile by means of multiple subterminal flagella. It includes five species: Roseburia intestinalis, R. hominis, R. inulinivorans, R. faecis and R. cecicola. Gut Roseburia spp. metabolize dietary components that stimulate their proliferation and metabolic activities. They are part of commensal bacteria producing short-chain fatty acids, especially butyrate, affecting colonic motility, immunity maintenance and anti-inflammatory properties. Modification in Roseburia spp. representation may affect various metabolic pathways and is associated with several diseases (including irritable bowel syndrome, obesity, Type 2 diabetes, nervous system conditions and allergies). Roseburia spp. could also serve as biomarkers for symptomatic pathologies (e.g., gallstone formation) or as probiotics for restoration of beneficial flora.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Imen Smida
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Latifa Bousarghin
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Olivier Loreal
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France
| | - Vincent Meuric
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France.,CHU Rennes, 2 rue Henri Le Guilloux, 35000 Rennes, France.,Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Shao Bing Fong
- Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Martine Bonnaure-Mallet
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France.,CHU Rennes, 2 rue Henri Le Guilloux, 35000 Rennes, France.,Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Anne Jolivet-Gougeon
- INSERM 1241/NUtrition MEtabolism CANcer/CIMIAD, 2 avenue du Professeur Léon Bernard, Rennes, France.,CHU Rennes, 2 rue Henri Le Guilloux, 35000 Rennes, France.,Université de Rennes 1, 2 avenue du Professeur Léon Bernard, 35043 Rennes, France
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Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria. Sci Rep 2017; 7:6267. [PMID: 28740169 PMCID: PMC5524971 DOI: 10.1038/s41598-017-06595-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/13/2017] [Indexed: 11/22/2022] Open
Abstract
Due to tetracycline abuse, the safe bifidobacteria in the human gastrointestinal intestinal tract (GIT) may serve as a reservoir of tetracycline resistance genes. In the present investigation of 92 bifidobacterial strains originating from the human GIT, tetracycline resistance in 29 strains was mediated by the tet(W), tet(O) or tet(S) gene, and this is the first report of tet(O)- and tet(S)-mediated tetracycline resistance in bifidobacteria. Antibiotic resistance genes harbored by bifidobacteria are transferred from other bacteria. However, the characteristics of the spread and integration of tetracycline resistance genes into the human intestinal bifidobacteria chromosome are poorly understood. Here, conserved sequences were identified in bifidobacterial strains positive for tet(W), tet(O), or tet(S), including the tet(W), tet(O), or tet(S) and their partial flanking sequences, which exhibited identity with the sequences in multiple human intestinal pathogens, and genes encoding 23 S rRNA, an ATP transporter, a Cpp protein, and a membrane-spanning protein were flanking by the 1920-bp tet(W), 1920-bp tet(O), 1800-bp tet(O) and 252-bp tet(S) in bifidobacteria, respectively. These findings suggest that tetracycline resistance genes harbored by human intestinal bifidobacteria might initially be transferred from pathogens and that each kind of tetracycline resistance gene might tend to insert in the vicinity of specific bifidobacteria genes.
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Probiotic Characteristics of Lactobacillus curvatus DN317, a Strain Isolated from Chicken Ceca. Probiotics Antimicrob Proteins 2017; 9:415-424. [DOI: 10.1007/s12602-017-9301-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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35
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Leclercq SO, Wang C, Zhu Y, Wu H, Du X, Liu Z, Feng J. Diversity of the Tetracycline Mobilome within a Chinese Pig Manure Sample. Appl Environ Microbiol 2016; 82:6454-6462. [PMID: 27565618 PMCID: PMC5066362 DOI: 10.1128/aem.01754-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/20/2016] [Indexed: 11/20/2022] Open
Abstract
Tetracycline antibiotics are widely used in livestock, and tetracycline resistance genes (TRG) are frequently reported in the manure of farmed animals. However, the diversity of TRG-carrying transposons in manure has still been rarely investigated. Using a culture-free functional metagenomic procedure, combined with large-insert library construction and sequencing, bioinformatic analyses, and functional experiments, we identified 17 distinct TRGs in a single pig manure sample, including two new tet genes: tet(59), encoding a tetracycline efflux pump, and tet(W/N/W), encoding mosaic ribosomal protection. Our study also revealed six new TRG-carrying putative nonconjugative transposons: Tn5706-like transposon Tn6298, IS200/605-related transposon Tn6303, Tn3 family transposon Tn6299, and three ISCR2-related transposons, Tn62300, Tn62301, and Tn62302 IMPORTANCE: Fertilization of agricultural fields with animal manure is believed to play a major role in antibiotic resistance dissemination in the environment. There is growing concern for the possible spread of antibiotic resistance from the environment to humans since genetic resistance determinants may be located in transposons and other mobile genetic elements potentially transferable to pathogens. Among the various antibiotic resistance genes found in manure, tetracycline resistance genes (TRGs) are some of the most common. The present study provides a detailed snapshot of the tetracycline mobilome in a single pig manure sample, revealing an unappreciated diversity of TRGs and potential TRG mobility vectors. Our precise identification of the TRG-carrying units will enable us to investigate in more details their mobility effectiveness.
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Affiliation(s)
- Sébastien Olivier Leclercq
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hai Wu
- College of Life Sciences, Hebei University, Baoding, China
| | - Xiaochen Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhipei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Leclercq SO, Wang C, Sui Z, Wu H, Zhu B, Deng Y, Feng J. A multiplayer game: species of Clostridium, Acinetobacter, and Pseudomonas are responsible for the persistence of antibiotic resistance genes in manure-treated soils. Environ Microbiol 2016; 18:3494-3508. [PMID: 27120080 DOI: 10.1111/1462-2920.13337] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/28/2016] [Accepted: 04/06/2016] [Indexed: 12/01/2022]
Abstract
Antibiotics are routinely used in modern livestock farming. The manure from medicated animals is used for the fertilization of arable crops, which in turn leads to the accumulation of antibiotic resistance genes (ARGs) in the environment. This is a potentially serious public health issue, yet the identities of the bacterial taxa involved in ARG persistence are as yet undetermined. Using soil-manure microcosm experiments, we investigated the relationship between (i) the persistence of diverse ARGs and (ii) the dynamics of bacterial community members. We were able to identify, for the first time, the bacterial taxa involved in ARG enrichment in manured soils. They were gut-associated Clostridium species, and environmental species of Acinetobacter and Pseudomonas genera, all of them closely related to important nosocomial pathogens. Our data provide new clues on the routes by which ARGs may spread from farms to medical clinics.
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Affiliation(s)
- Sebastien Olivier Leclercq
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhihai Sui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hai Wu
- College of Life Sciences, Hebei University, Baoding, China
| | - Baoli Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Lab of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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37
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Couvigny B, Thérial C, Gautier C, Renault P, Briandet R, Guédon E. Streptococcus thermophilus Biofilm Formation: A Remnant Trait of Ancestral Commensal Life? PLoS One 2015; 10:e0128099. [PMID: 26035177 PMCID: PMC4452758 DOI: 10.1371/journal.pone.0128099] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 04/23/2015] [Indexed: 12/27/2022] Open
Abstract
Microorganisms have a long history of use in food production and preservation. Their adaptation to food environments has profoundly modified their features, mainly through genomic flux. Streptococcus thermophilus, one of the most frequent starter culture organisms consumed daily by humans emerged recently from a commensal ancestor. As such, it is a useful model for genomic studies of bacterial domestication processes. Many streptococcal species form biofilms, a key feature of the major lifestyle of these bacteria in nature. However, few descriptions of S. thermophilus biofilms have been reported. An analysis of the ability of a representative collection of natural isolates to form biofilms revealed that S. thermophilus was a poor biofilm producer and that this characteristic was associated with an inability to attach firmly to surfaces. The identification of three biofilm-associated genes in the strain producing the most biofilms shed light on the reasons for the rarity of this trait in this species. These genes encode proteins involved in crucial stages of biofilm formation and are heterogeneously distributed between strains. One of the biofilm genes appears to have been acquired by horizontal transfer. The other two are located in loci presenting features of reductive evolution, and are absent from most of the strains analyzed. Their orthologs in commensal bacteria are involved in adhesion to host cells, suggesting that they are remnants of ancestral functions. The biofilm phenotype appears to be a commensal trait that has been lost during the genetic domestication of S. thermophilus, consistent with its adaptation to the milk environment and the selection of starter strains for dairy fermentations.
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Affiliation(s)
- Benoit Couvigny
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Claire Thérial
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Céline Gautier
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Pierre Renault
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Romain Briandet
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
| | - Eric Guédon
- INRA, UMR 1319 Micalis, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
- AgroParisTech, UMR MICALIS, Jouy-en-Josas, France
- * E-mail:
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38
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Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG. The microbiome of uncontacted Amerindians. SCIENCE ADVANCES 2015; 1:e1500183. [PMID: 26229982 PMCID: PMC4517851 DOI: 10.1126/sciadv.1500183] [Citation(s) in RCA: 510] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.
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Affiliation(s)
- Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erica C. Pehrsson
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Martin J. Blaser
- Laboratory Service, VA Medical Center, New York, NY 10010, USA
- New York University School of Medicine, New York, NY 10016, USA
| | - Kuldip Sandhu
- New York University School of Medicine, New York, NY 10016, USA
| | - Zhan Gao
- New York University School of Medicine, New York, NY 10016, USA
| | - Bin Wang
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Magda Magris
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Glida Hidalgo
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Monica Contreras
- Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela
| | - Óscar Noya-Alarcón
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Orlana Lander
- Sección de Ecología Parasitaria, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | | | - Mike Cox
- Anaerobe Systems, Morgan Hill, CA 95037, USA
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
| | - Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
| | - Jean F. Ruiz
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
| | - Selena Rodriguez
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
| | - Nan Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Se Jin Song
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Jessica Metcalf
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Gautam Dantas
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - M. Gloria Dominguez-Bello
- New York University School of Medicine, New York, NY 10016, USA
- Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
- Corresponding author. E-mail:
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Amund O, Ouoba L, Sutherland J, Ghoddusi H. Assessing the effects of exposure to environmental stress on some functional properties of Bifidobacterium animalis ssp. lactis. Benef Microbes 2014; 5:461-9. [DOI: 10.3920/bm2013.0099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This study assessed the effects of exposing a strain of Bifidobacterium animalis ssp. lactis to acid, bile and osmotic stresses on antagonistic properties, biofilm formation and antibiotic susceptibility/resistance profile. Exposure to each stress factor appeared to have no significant effect on the antagonism against Escherichia coli NCTC 12900 and Salmonella enterica serovar Enteritidis PT4. No suppression in biofilm formation due to exposure to stress was observed. Bile and osmotic stresses resulted in significantly higher biofilm formation. Expression of an exopolysaccharide synthesis gene, gtf 01207, was significantly higher when the B. animalis ssp. lactis strain was exposed to osmotic stress. Susceptibility of the B. animalis ssp. lactis strain to chloramphenicol, erythromycin, ampicillin and vancomycin, and resistance to tetracycline remained unchanged when exposed to each stress. The expression of a tetracycline resistance gene, tet(W), was significantly higher when exposed to each stress. These results may suggest that the potential for the B. animalis ssp. lactis strain to provide probiotic benefit, after exposure to the stressful conditions of the gastrointestinal tract, remains intact.
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Affiliation(s)
- O.D. Amund
- Microbiology Research Unit, Faculty of Life Sciences and Computing, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - L.I.I. Ouoba
- Microbiology Research Unit, Faculty of Life Sciences and Computing, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - J.P. Sutherland
- Microbiology Research Unit, Faculty of Life Sciences and Computing, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
| | - H.B. Ghoddusi
- Microbiology Research Unit, Faculty of Life Sciences and Computing, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK
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Wang FH, Qiao M, Su JQ, Chen Z, Zhou X, Zhu YG. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9079-85. [PMID: 25057898 DOI: 10.1021/es502615e] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Reclaimed water irrigation (RWI) in urban environments is becoming popular, due to rapid urbanization and water shortage. The continuous release of residual antibiotics and antibiotic resistance genes (ARGs) from reclaimed water could result in the dissemination of ARGs in the downstream environment. This study provides a comprehensive profile of ARGs in park soils exposed to RWI through a high-throughput quantitative PCR approach. 147 ARGs encoding for resistance to a broad-spectrum of antibiotics were detected among all park soil samples. Aminoglycoside and beta-lactam were the two most dominant types of ARGs, and antibiotic deactivation and efflux pump were the two most dominant mechanisms in these RWI samples. The total enrichment of ARGs varied from 99.3-fold to 8655.3-fold compared to respective controls. Six to 60 ARGs were statistically enriched among these RWI samples. Four transposase genes were detected in RWI samples. TnpA-04 was the most enriched transposase gene with an enrichment was up to 2501.3-fold in Urumqi RWI samples compared with control soil samples. Furthermore, significantly positive correlation was found between ARGs and transposase abundances, indicating that transposase might be involved in the propagation of ARGs. This study demonstrated that RWI resulted in the enrichment of ARGs in urban park soils.
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Affiliation(s)
- Feng-Hua Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, People's Republic of China
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Redondo LM, Chacana PA, Dominguez JE, Fernandez Miyakawa ME. Perspectives in the use of tannins as alternative to antimicrobial growth promoter factors in poultry. Front Microbiol 2014; 5:118. [PMID: 24723916 PMCID: PMC3973907 DOI: 10.3389/fmicb.2014.00118] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 03/08/2014] [Indexed: 12/17/2022] Open
Abstract
Antibiotics have been included in the formulation of feed for livestock production for more than 40 years as a strategy to improve feed conversion rates and to reduce costs. The use of antimicrobials as growth-promoting factors (AGP) in sub-therapeutic doses for long periods is particularly favorable for the selection of antimicrobial resistant microorganisms. In the last years, global concern about development of antimicrobial resistance and transference of resistance genes from animal to human strains has been rising. Removal of AGP from animal diets involves tremendous pressure on the livestock and poultry farmers, one of the main consequences being a substantial increase in the incidence of infectious diseases with the associated increase in the use of antibiotics for therapy, and concomitantly, economic cost. Therefore, alternatives to AGP are urgently needed. The challenge is to implement new alternatives without affecting the production performances of livestock and avoiding the increase of antimicrobial resistant microorganisms. Plant extracts and purified derived substances are showing promising results for animal nutrition, either from their efficacy as well as from an economical point of view. Tannins are plant derived compounds that are being successfully used as additives in poultry feed to control diseases and to improve animal performance. Successful use of any of these extracts as feed additives must ensure a product of consistent quality in enough quantity to fulfill the actual requirements of the poultry industry. Chestnut (hydrolysable) and Quebracho (condensed) tannins are probably the most readily available commercial products that are covering those needs. The present report intends to analyze the available data supporting their use.
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Affiliation(s)
- Leandro M Redondo
- Instituto de Patobiología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Buenos Aires, Argentina ; Consejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires, Argentina
| | - Pablo A Chacana
- Instituto de Patobiología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Buenos Aires, Argentina
| | - Johana E Dominguez
- Instituto de Patobiología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Buenos Aires, Argentina
| | - Mariano E Fernandez Miyakawa
- Instituto de Patobiología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria Buenos Aires, Argentina ; Consejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires, Argentina
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Ciric L, Brouwer MSM, Mullany P, Roberts AP. Minocycline resistance in an oral Streptococcus infantis isolate is encoded by tet(S) on a novel small, low copy number plasmid. FEMS Microbiol Lett 2014; 353:106-15. [PMID: 24605990 PMCID: PMC4237122 DOI: 10.1111/1574-6968.12410] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 11/29/2022] Open
Abstract
We have determined the genetic basis of minocycline resistance in a strain of Streptococcus infantis isolated from a healthy human oral cavity. We demonstrate that tet(S), identical to tet(S) found on the enterococcal conjugative transposon Tn6000, is responsible for the observed resistance. The gene is located on a small, low copy number plasmid and is flanked by IS1216 elements. The tet(S) gene is capable of excising from the plasmid together with one of the IS1216 elements. The plasmid contains a putative toxin/antitoxin system related to relBE. Deletion of the toxin, relE, did not result in plasmid instability but did increase the fitness of the mutant compared to the wild-type strain.
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Affiliation(s)
- Lena Ciric
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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Sharma P, Tomar SK, Goswami P, Sangwan V, Singh R. Antibiotic resistance among commercially available probiotics. Food Res Int 2014. [DOI: 10.1016/j.foodres.2014.01.025] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Kyselková M, Jirout J, Chroňáková A, Vrchotová N, Bradley R, Schmitt H, Elhottová D. Cow excrements enhance the occurrence of tetracycline resistance genes in soil regardless of their oxytetracycline content. CHEMOSPHERE 2013; 93:2413-2418. [PMID: 24053942 DOI: 10.1016/j.chemosphere.2013.08.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 07/22/2013] [Accepted: 08/19/2013] [Indexed: 06/02/2023]
Abstract
Fertilizing soils with animal excrements from farms with common antibiotic use represents a risk of disseminating antibiotic resistance genes into the environment. In the case of tetracycline antibiotics, it is not clear, however, whether the presence of antibiotic residues further enhances the gene occurrence in manured soils. We established a microcosm experiment in which 3 farm soils that had no recent history of fertilization with animal excrements were amended on a weekly basis (9 times) with excrements from either an oxytetracycline-treated or an untreated cow. Throughout the study, the concentration of oxytetracycline in excrements from the treated cow was above 500 μg g(-1)dw, whereas no oxytetracycline was detected in excrements from the healthy cow. Both excrements contained tetracycline resistance (TC-r) genes tet(L), tet(M), tet(V), tet(Z), tet(Q) and tet(W). The excrements from the treated cow also contained the tet(B) gene, and a higher abundance of tet(Z), tet(Q) and tet(W). Three weeks after the last excrement addition, the individual TC-r genes differed in their persistence in soil: tet(Q) and tet(B) were not detectable while tet(L), tet(M), tet(Z) and tet(W) were found in all 3 soils. There were, however, no significant differences in the total number, nor in the abundance, of TC-r genes between soil samples amended with each excrement type. The oxytetracycline-rich and the oxytetracycline-free excrement therefore contributed equally to the increase of tetracycline resistome in soil. Our results indicate that other mechanisms than OTC-selection pressure may be involved in the maintenance of TC-r genes in manured soils.
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Affiliation(s)
- Martina Kyselková
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology, 370 05 České Budějovice, Czech Republic.
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Unconventional circularizable bacterial genetic structures carrying antibiotic resistance determinants. Antimicrob Agents Chemother 2013; 57:2440-1. [PMID: 23580584 DOI: 10.1128/aac.02548-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Devirgiliis C, Zinno P, Perozzi G. Update on antibiotic resistance in foodborne Lactobacillus and Lactococcus species. Front Microbiol 2013; 4:301. [PMID: 24115946 PMCID: PMC3792357 DOI: 10.3389/fmicb.2013.00301] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 09/19/2013] [Indexed: 12/21/2022] Open
Abstract
Lactobacilli represent a major Lactic Acid Bacteria (LAB) component within the complex microbiota of fermented foods obtained from meat, dairy, and vegetable sources. Lactococci, on the other hand, are typical of milk and fermented dairy products, which in turn represent the vast majority of fermented foods. As is the case for all species originating from the environment, foodborne lactobacilli and lactococci consist of natural, uncharacterized strains, whose biodiversity depends on geographical origin, seasonality, animal feeding/plant growth conditions. Although a few species of opportunistic pathogens have been described, lactobacilli and lactococci are mostly non-pathogenic, Gram-positive bacteria displaying probiotic features. Since antibiotic resistant (AR) strains do not constitute an immediate threat to human health, scientific interest for detailed studies on AR genes in these species has been greatly hindered. However, increasing evidence points at a crucial role for foodborne LAB as reservoir of potentially transmissible AR genes, underlining the need for further, more detailed studies aimed at identifying possible strategies to avoid AR spread to pathogens through fermented food consumption. The availability of a growing number of sequenced bacterial genomes has been very helpful in identifying the presence/distribution of mobile elements associated with AR genes, but open questions and knowledge gaps still need to be filled, highlighting the need for systematic and datasharing approaches to implement both surveillance and mechanistic studies on transferability of AR genes. In the present review we report an update of the recent literature on AR in lactobacilli and lactococci following the 2006 EU-wide ban of the use of antibiotics as feed additives in animal farming, and we discuss the limits of the present knowledge in evaluating possible risks for human health.
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Affiliation(s)
- Chiara Devirgiliis
- CRA-NUT, Food and Nutrition Research Center, Agricultural Research Council Roma, Italy
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Guglielmetti S, Mayo B, Álvarez-Martín P. Mobilome and genetic modification of bifidobacteria. Benef Microbes 2013; 4:143-66. [PMID: 23271067 DOI: 10.3920/bm2012.0031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Until recently, proper development of molecular studies in Bifidobacterium species has been hampered by growth difficulties, because of their exigent nutritive requirements, oxygen sensitivity and lack of efficient genetic tools. These studies, however, are critical to uncover the cross-talk between bifidobacteria and their hosts' cells and to prove unequivocally the supposed beneficial effects provided through the endogenous bifidobacterial populations or after ingestion as probiotics. The genome sequencing projects of different bifidobacterial strains have provided a wealth of genetic data that will be of much help in deciphering the molecular basis of the physiological properties of bifidobacteria. To this end, the purposeful development of stable cloning and expression vectors based on robust replicons - either from temperate phages or resident plasmids - is still needed. This review addresses the current knowledge on the mobile genetic elements of bifidobacteria (prophages, plasmids and transposons) and summarises the different types of vectors already available, together with the transformation procedures for introducing DNA into the cells. It also covers recent molecular studies performed with such vectors and incipient results on the genetic modification of these organisms, establishing the basis that would allow the use of bifidobacteria for future biotechnological applications.
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Affiliation(s)
- S Guglielmetti
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Sezione di Microbiologia Industriale, Università degli studi di Milano, Via Celoria 2, 20133 Milan, Italy
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Gueimonde M, Sánchez B, G. de los Reyes-Gavilán C, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol 2013; 4:202. [PMID: 23882264 PMCID: PMC3714544 DOI: 10.3389/fmicb.2013.00202] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/28/2013] [Indexed: 11/17/2022] Open
Abstract
Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. The main probiotic bacteria are strains belonging to the genera Lactobacillus and Bifidobacterium, although other representatives, such as Bacillus or Escherichia coli strains, have also been used. Lactobacillus and Bifidobacterium are two common inhabitants of the human intestinal microbiota. Also, some species are used in food fermentation processes as starters, or as adjunct cultures in the food industry. With some exceptions, antibiotic resistance in these beneficial microbes does not constitute a safety concern in itself, when mutations or intrinsic resistance mechanisms are responsible for the resistance phenotype. In fact, some probiotic strains with intrinsic antibiotic resistance could be useful for restoring the gut microbiota after antibiotic treatment. However, specific antibiotic resistance determinants carried on mobile genetic elements, such as tetracycline resistance genes, are often detected in the typical probiotic genera, and constitute a reservoir of resistance for potential food or gut pathogens, thus representing a serious safety issue.
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Affiliation(s)
| | | | | | - Abelardo Margolles
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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Chen H, Zhang M. Occurrence and removal of antibiotic resistance genes in municipal wastewater and rural domestic sewage treatment systems in eastern China. ENVIRONMENT INTERNATIONAL 2013; 55:9-14. [PMID: 23454279 DOI: 10.1016/j.envint.2013.01.019] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/23/2013] [Accepted: 01/29/2013] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging environmental contaminants and pose a threat to public health. In this study, four tetracycline resistance genes (tetM, tetO, tetQ and tetW) and two sulfonamide resistance genes (sulI and sulII) were evaluated in 4 municipal wastewater and 8 rural domestic sewage treatment systems with different wastewater handling abilities and treatment processes using quantitative polymerase chain reaction (qPCR). In the influents, the relative abundance of different ARGs showed significant variations among the sampling sites. In addition, significant correlations (tetQ: R(2)=0.712, P<0.05; tetO: R(2)=0.394, P<0.05) between the gene copy numbers and wastewater-receiving capacity were observed. Statistical analysis revealed a positive correlation (R(2)=0.756, P<0.05) between the gene copy numbers of sulI and intI1, whereas the gene numbers of tetM and sulI were strongly correlated with 16S rDNA. Significant reductions (1-3 orders of magnitude) in ARGs were observed in municipal wastewater treatment systems, but a smaller reduction was found in the rural domestic sewage treatment systems. These results provide insights into the occurrence and removal of ARGs in wastewater treatment systems in both rural and urban areas in eastern China.
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Affiliation(s)
- Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
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