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Gião J, Leão C, Albuquerque T, Clemente L, Amaro A. Antimicrobial Susceptibility of Enterococcus Isolates from Cattle and Pigs in Portugal: Linezolid Resistance Genes optrA and poxtA. Antibiotics (Basel) 2022; 11:antibiotics11050615. [PMID: 35625259 PMCID: PMC9137492 DOI: 10.3390/antibiotics11050615] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Enterococci are part of the commensal gut microbiota of mammals, with Enterococcus faecalis and Enterococcus faecium being the most clinically relevant species. This study assesses the prevalence and diversity of enterococcal species in cattle (n = 201) and pig (n = 249) cecal samples collected in 2017. Antimicrobial susceptibility profiles of E. faecium (n = 48) and E. faecalis (n = 84) were assessed by agar and microdilution methods. Resistance genes were screened through PCR and nine strains were analyzed by Whole Genome Sequencing. A wide range of enterococci species was found colonizing the intestines of pigs and cattle. Overall, the prevalence of resistance to critically important antibiotics was low (except for erythromycin), and no glycopeptide-resistant isolates were identified. Two daptomycin-resistant E. faecalis ST58 and ST93 were found. Linezolid-resistant strains of E. faecalis (n = 3) and E. faecium (n = 1) were detected. Moreover, oxazolidinone resistance determinants optrA (n = 8) and poxtA (n = 2) were found in E. faecalis (ST16, ST58, ST207, ST474, ST1178) and E. faecium (ST22, ST2138). Multiple variants of optrA were found in different genetic contexts, either in the chromosome or plasmids. We highlight the importance of animals as reservoirs of resistance genes to critically important antibiotics.
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Affiliation(s)
- Joana Gião
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- Department of Veterinary Medicine, University of Évora, 7002-554 Évora, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, University of Lisbon, 1300-477 Lisboa, Portugal
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal; (J.G.); (C.L.); (T.A.); (L.C.)
- Correspondence:
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Antibiotic Treatment during Pregnancy Alters Offspring Gut Microbiota in a Sex-Dependent Manner. Biomedicines 2022; 10:biomedicines10051042. [PMID: 35625778 PMCID: PMC9138679 DOI: 10.3390/biomedicines10051042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
This study investigated the effect of antibiotics administered to pregnant dams on offspring gut microbiome composition and metabolic capabilities, and how these changes in the microbiota may influence their immune responses in both the periphery and the brain. We orally administered a broad-spectrum antibiotic (ABX) cocktail consisting of vancomycin 0.5 mg/mL, ampicillin 1 mg/mL, and neomycin 1 mg/mL to pregnant dams during late gestation through birth. Bacterial DNA was extracted from offspring fecal samples, and 16S ribosomal RNA gene was sequenced by Illumina, followed by analysis of gut microbiota composition and PICRUSt prediction. Serum and brain tissue cytokine levels were analyzed by Luminex. Our results indicate that the ABX-cocktail led to significant diversity and taxonomic changes to the offspring's gut microbiome. In addition, the predicted KEGG and MetaCyc pathways were significantly altered in the offspring. Finally, there were decreased innate inflammatory cytokines and chemokines and interleukin (IL)-17 seen in the brains of ABX-cocktail offspring in response to lipopolysaccharide (LPS) immune challenge. Our results suggest that maternal ABX can produce long-lasting effects on the gut microbiome and neuroimmune responses of offspring. These findings support the role of the early microbiome in the development of offspring gastrointestinal and immune systems.
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Tolonen AC, Beauchemin N, Bayne C, Li L, Tan J, Lee J, Meehan BM, Meisner J, Millet Y, LeBlanc G, Kottler R, Rapp E, Murphy C, Turnbaugh PJ, von Maltzahn G, Liu CM, van Hylckama Vlieg JET. Synthetic glycans control gut microbiome structure and mitigate colitis in mice. Nat Commun 2022; 13:1244. [PMID: 35273143 PMCID: PMC8913648 DOI: 10.1038/s41467-022-28856-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
Relative abundances of bacterial species in the gut microbiome have been linked to many diseases. Species of gut bacteria are ecologically differentiated by their abilities to metabolize different glycans, making glycan delivery a powerful way to alter the microbiome to promote health. Here, we study the properties and therapeutic potential of chemically diverse synthetic glycans (SGs). Fermentation of SGs by gut microbiome cultures results in compound-specific shifts in taxonomic and metabolite profiles not observed with reference glycans, including prebiotics. Model enteric pathogens grow poorly on most SGs, potentially increasing their safety for at-risk populations. SGs increase survival, reduce weight loss, and improve clinical scores in mouse models of colitis. Synthetic glycans are thus a promising modality to improve health through selective changes to the gut microbiome.
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Affiliation(s)
| | - Nicholas Beauchemin
- Kaleido Biosciences, Lexington, MA, 02421, USA.,Seres Therapeutics, Cambridge, MA, 02139, USA
| | | | - Lingyao Li
- Kaleido Biosciences, Lexington, MA, 02421, USA
| | - Jie Tan
- Kaleido Biosciences, Lexington, MA, 02421, USA
| | - Jackson Lee
- Kaleido Biosciences, Lexington, MA, 02421, USA
| | - Brian M Meehan
- Kaleido Biosciences, Lexington, MA, 02421, USA.,Pareto Bio, Cambridge, MA, 02140, USA
| | | | - Yves Millet
- Kaleido Biosciences, Lexington, MA, 02421, USA
| | | | | | - Erdmann Rapp
- glyXera GmbH, 39120, Magdeburg, Germany.,Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | - Chris Murphy
- Kaleido Biosciences, Lexington, MA, 02421, USA.,Bacainn Therapeutics, Inc and Morningside BioPharma Advisory, Concord, MA, 01742, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Geoffrey von Maltzahn
- Kaleido Biosciences, Lexington, MA, 02421, USA.,Flagship Pioneering, Cambridge, MA, 02142, USA
| | - Christopher M Liu
- Kaleido Biosciences, Lexington, MA, 02421, USA.,Exo Therapeutics, Watertown, MA, 02472, USA
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Lee HJ, Cho JH, Cho WJ, Gang SH, Park SH, Jung BJ, Kim HB, Song KH. Effects of Synbiotic Preparation Containing Lactobacillus gasseri BNR17 on Body Fat in Obese Dogs: A Pilot Study. Animals (Basel) 2022; 12:ani12050642. [PMID: 35268209 PMCID: PMC8909091 DOI: 10.3390/ani12050642] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The present study evaluated the effectiveness of a synbiotic preparation containing L. gasseri BNR17 on body fat in obese dogs. Body weight and the body condition score showed a significant reduction after 10 weeks of synbiotic preparation administration compared with those at baseline (0-week). The subcutaneous fat mass at the level of the third lumbar vertebra and its proportion, compared with the body mass, reduced significantly after 10 weeks of synbiotic preparation administration, compared with those at baseline. Following synbiotic supplementation, microbiome analysis revealed increased microbial diversity, and functional analysis of the microbiota showed an increased abundance of carbohydrate and lipid metabolism. Based on these results, we consider that synbiotic preparation containing L. gasseri BNR17 may play a role in reducing body fat and resolving obesity. Abstract Obesity is an important health concern in humans and dogs. It can cause a variety of secondary problems, including low bacterial diversity. Several approaches have been tried to solve this problem; one of them is probiotic supplementation. Lactobacillus gasseri BNR17 is derived from breast milk and has been proven to be effective for obesity in humans. However, there have been no studies using a synbiotic preparation containing L. gasseri BNR17 for obesity management in dogs. Therefore, the present study evaluated the effectiveness of a synbiotic preparation containing L. gasseri BNR17 in reducing body fat in obese dogs. A group of obese dogs were fed a synbiotic preparation for 10 weeks. Obesity variables included body weight, body condition score, subcutaneous fat thickness, subcutaneous fat mass and proportion of the fat mass. In addition, feces collected at 0-week and 10-week time points were analyzed for the intestinal microbiome. Results showed a significant decrease in body weight, body condition score, and subcutaneous fat mass and proportion at the level of the third lumbar vertebra. Diversity and functional analysis of the microbiota in obese dogs showed increased microbial diversity, and increased abundance of metabolism of carbohydrate, and lipid after supplementation with a synbiotic preparation. This study was conducted as a pilot study, and the results demonstrated that a synbiotic preparation containing L. gasseri BNR17 may play a role in reducing body fat and resolving the obesity in dogs.
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Affiliation(s)
- Han-Joon Lee
- College of Veterinary Medicine, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea;
| | - Jae Hyoung Cho
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea;
| | - Woo-Jae Cho
- Veterinary Nutrition Laboratory, JEIL Feed Co., Ltd., Daejeon 34029, Korea;
| | - Seong-Ho Gang
- SNH Biotech Co., Ltd., Daejeon 34015, Korea; (S.-H.G.); (S.-H.P.)
| | - Seung-Hwan Park
- SNH Biotech Co., Ltd., Daejeon 34015, Korea; (S.-H.G.); (S.-H.P.)
| | | | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Korea;
- Correspondence: (H.B.K.); (K.H.S.)
| | - Kun Ho Song
- College of Veterinary Medicine, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea;
- Correspondence: (H.B.K.); (K.H.S.)
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. Nat Commun 2022; 13:586. [PMID: 35102136 PMCID: PMC8803835 DOI: 10.1038/s41467-022-28048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT. Here, Siranosian et al. provide evidence for rare transmission of commensal and pathogenic bacteria between the microbiomes of hospitalized adults, with important factors being roommate overlap and exposure to broad-spectrum antibiotics.
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Prasad R, Asare-Bediko B, Harbour A, Floyd JL, Chakraborty D, Duan Y, Lamendella R, Wright J, Grant MB. Microbial Signatures in The Rodent Eyes With Retinal Dysfunction and Diabetic Retinopathy. Invest Ophthalmol Vis Sci 2022; 63:5. [PMID: 34985498 PMCID: PMC8742510 DOI: 10.1167/iovs.63.1.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose The gut microbiome has been linked to disease pathogenesis through their interaction in metabolic, endocrine, and immune functions. The goal of this study was to determine whether the gut and plasma microbiota could transfer microbes to the retina in type 1 diabetic mice with retinopathy. Methods We analyzed the fecal, plasma, whole globe, and retina microbiome in Akita mice and compared with age-matched wild-type (WT) mice using 16S rRNA sequencing and metatranscriptomic analysis. To eliminate the contribution of the ocular surface and plasma microbiome, mice were perfused with sterile saline solution, the whole globes were extracted, and the neural retina was removed under sterile conditions for retinal microbiome. Results Our microbiome analysis revealed that Akita mice demonstrated a distinct pattern of microbes within each source: feces, plasma, whole globes, and retina. WT mice and Akita mice experienced transient bacteremia in the plasma and retina. Bacteria were identified in the retina of the Akita mice, specifically Corynebacterium, Pseudomonas, Lactobacillus, Staphylococcus, Enterococcus, and Bacillus. Significantly increased levels of peptidoglycan (0.036 ± 0.001 vs. 0.023 ± 0.002; P < 0.002) and TLR2 (3.47 ± 0.15 vs. 1.99 ± 0.07; P < 0.0001) were observed in the retina of Akita mice compared to WT. Increased IBA+ cells in the retina, reduced a- and b-waves on electroretinography, and increased acellular capillary formation demonstrated the presence of retinopathy in the Akita cohort compared to WT mice. Conclusions Together, our findings suggest that transient bacteremia exists in the plasma and retina of both cohorts. The bacteria found in Akita mice are distinct from WT mice and may contribute to development of retinal inflammation and barrier dysfunction in retinopathy.
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Affiliation(s)
- Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Bright Asare-Bediko
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Angela Harbour
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Jason L Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Dibyendu Chakraborty
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Yaqian Duan
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana, United States.,Department of Endocrinology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | | | - Justin Wright
- Wright Labs, LLC, Huntingdon, Pennsylvania, United States
| | - Maria B Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States
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Reissier S, Le Neindre K, Bordeau V, Dejoies L, Le Bot A, Felden B, Cattoir V, Revest M. The Regulatory RNA ern0160 Confers a Potential Selective Advantage to Enterococcus faecium for Intestinal Colonization. Front Microbiol 2021; 12:757227. [PMID: 34858368 PMCID: PMC8631354 DOI: 10.3389/fmicb.2021.757227] [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: 08/11/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to evaluate the role of the regulatory small RNA (sRNA) Ern0160 in gastrointestinal tract (GIT) colonization by Enterococcus faecium. For this purpose, four strains of E. faecium were used, Aus0004 (WT), an ern0160-deleted Aus0004 mutant (Δ0160), a trans-complemented Δ0160 strain overexpressing ern0160 (Δ0160_0160), and a strain Δ0160 with an empty pAT29 vector (Δ0160_pAT29). Strains were studied both in vitro and in vivo, alone and in competitive assays. In in vitro experiments, no difference was observed between WT and Δ0160 strains cultured single while Δ0160_0160 strain grew more slowly than Δ0160_pAT29. In competitive assays, the WT strain was predominant compared to the deleted strain Δ0160 at the end of the experiment. Then, in vivo experiments were performed using a GIT colonization mouse model. Several existing models of GIT colonization were compared while a novel one, combining ceftriaxone and amoxicillin, was developed. A GIT colonization was performed with each strain alone, and no significant difference was noticed. By contrast, significant results were obtained with co-colonization experiments. With WT + Δ0160 suspension, a significant advantage for the WT strain was observed from day 5 to the end of the protocol, suggesting the involvement of ern0160 in GIT colonization. With Δ0160_0160 + Δ0160_pAT29 suspension, the strain with the empty vector took the advantage from day 3 to the end of the protocol, suggesting a deleterious effect of ern0160 overexpression. Altogether, these findings demonstrate the potential implication of Ern0160 in GIT colonization of E. faecium. Further investigations are needed for the identification of sRNA target(s) in order to decipher underlying molecular mechanisms.
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Affiliation(s)
| | - Killian Le Neindre
- Unité Inserm U1230, Université de Rennes 1, Rennes, France.,Service de Bactériologie-Hygiène Hospitalière & CNR de la Résistance aux Antibiotiques (Laboratoire Associé 'Entérocoques'), CHU de Rennes, Rennes, France
| | | | - Loren Dejoies
- Unité Inserm U1230, Université de Rennes 1, Rennes, France.,Service de Bactériologie-Hygiène Hospitalière & CNR de la Résistance aux Antibiotiques (Laboratoire Associé 'Entérocoques'), CHU de Rennes, Rennes, France
| | - Audrey Le Bot
- Unité Inserm U1230, Université de Rennes 1, Rennes, France.,Service de Maladies Infectieuses et Réanimation Médicale, CHU de Rennes, Rennes, France
| | - Brice Felden
- Unité Inserm U1230, Université de Rennes 1, Rennes, France
| | - Vincent Cattoir
- Unité Inserm U1230, Université de Rennes 1, Rennes, France.,Service de Bactériologie-Hygiène Hospitalière & CNR de la Résistance aux Antibiotiques (Laboratoire Associé 'Entérocoques'), CHU de Rennes, Rennes, France
| | - Matthieu Revest
- Unité Inserm U1230, Université de Rennes 1, Rennes, France.,Service de Maladies Infectieuses et Réanimation Médicale, CHU de Rennes, Rennes, France
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Greenwood MP, Hull KL, Brink-Hull M, Lloyd M, Rhode C. Feed and Host Genetics Drive Microbiome Diversity with Resultant Consequences for Production Traits in Mass-Reared Black Soldier Fly ( Hermetia illucens) Larvae. INSECTS 2021; 12:1082. [PMID: 34940170 PMCID: PMC8706267 DOI: 10.3390/insects12121082] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/25/2023]
Abstract
Mass rearing the black soldier fly, Hermetia illucens, for waste bioremediation and valorisation is gaining traction on a global scale. While the health and productivity of this species are underpinned by associations with microbial taxa, little is known about the factors that govern gut microbiome assembly, function, and contributions towards host phenotypic development in actively feeding larvae. In the present study, a 16S rDNA gene sequencing approach applied to a study system incorporating both feed substrate and genetic variation is used to address this knowledge gap. It is determined that the alpha diversity of larval gut bacterial communities is driven primarily by features of the larval feed substrate, including the diversity of exogenous bacterial populations. Microbiome beta diversity, however, demonstrated patterns of differentiation consistent with an influence of diet, larval genetic background, and a potential interaction between these factors. Moreover, evidence for an association between microbiome structure and the rate of larval fat accumulation was uncovered. Taxonomic enrichment analysis and clustering of putative functional gut profiles further suggested that feed-dependent turnover in microbiome communities is most likely to impact larval characteristics. Taken together, these findings indicate that host-microbiome interactions in this species are complex yet relevant to larval trait emergence.
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Affiliation(s)
- Matthew P. Greenwood
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
| | - Kelvin L. Hull
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
| | - Marissa Brink-Hull
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
| | - Melissa Lloyd
- Insect Technology Group Holdings UK Ltd., 1 Farnham Road, Guildford, Surrey GU2 4RG, UK;
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
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Identification of Enterococcus faecalis in Different Clonal Lineages with the Pulsed-Field Gel Electrophoresis Method in Imam Khomeini Hospital, Ilam, Iran. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.118955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Due to the importance of identifying the source of infectious agents, different typing methods have been developed, among which the pulsed-field gel electrophoresis (PFGE) method is known as the gold standard for bacteria. Also, Enterococcus faecalis is classified as a nosocomial infection. Objectives: The current study aimed to identify the source of E. faecalis by the PFGE method. Methods: Bacteria were collected from all cases of urinary tract infections. Then, the identification process was performed. All isolates were evaluated for vancomycin resistance, and then PFGE was carried out. Results: The results of disk diffusion showed that 54% of the isolates showed resistance to vancomycin. Also, 4% of the isolates were intermediate, and 42% showed sensitivity to vancomycin. Afterwards, the PCR of the VanA gene was performed to confirm the results of disk diffusion. Thus, 48 out of 54 (88.8%) isolates had the VanA gene, and none of the four intermediate isolates had the VanA gene. Our results demonstrated that 54 isolates were vancomycin-resistant, and 50 different pulsotypes groups were identified. Conclusions: Our findings showed the isolates of E. faecalis were from different clonal lineages.
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Zarzecka U, Zadernowska A, Chajęcka-Wierzchowska W. Effects of osmotic and high pressure stress on expression of virulence factors among Enterococcus spp. isolated from food of animal origin. Food Microbiol 2021; 102:103900. [PMID: 34809932 DOI: 10.1016/j.fm.2021.103900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/22/2021] [Accepted: 09/09/2021] [Indexed: 01/01/2023]
Abstract
The aim of study was to determine the occurrence of virulence factors and virulence-related genes among enterococci isolated from food of animal origin and effects of osmotic and high pressure stress on expression of virulence-related genes. The number of 78 isolates were analyzed. None of them showed a strong ability to form biofilm, 38.5% (n = 30) had the slime production ability, 41% (n = 32) had gelatinase activity, γ -type hemolysis was observed in 55% of isolates, and α-type hemolysis in 45%. All of the isolates carried 1-13 virulence-related genes. The most common genes were gelE (85.9%), sprE (78.2%) and asa1 (75.6%). There were also observed changes in the expression of the gelE, esp, asa1 and cylL genes in response to various NaCl concentration and high pressure processing. Results obtained in this study indicate that enterococci isolated from food may act as reservoirs of virulence genes. The presence of virulence factors among enterococci, especially the ability to biofilm formation is important for food safety and the protection of public health. The results presented in our work demonstrate that stress that can occur during food preservation and food processing can induce the changes in the virulence-related genes expression.
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Affiliation(s)
- Urszula Zarzecka
- Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, Plac Cieszyński 1, 10-726, Olsztyn, Poland.
| | - Anna Zadernowska
- Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, Plac Cieszyński 1, 10-726, Olsztyn, Poland
| | - Wioleta Chajęcka-Wierzchowska
- Chair of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury, Plac Cieszyński 1, 10-726, Olsztyn, Poland
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Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review. Processes (Basel) 2021. [DOI: 10.3390/pr9112058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.
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Masuda S, Koizumi K, Uojima H, Kimura K, Nishino T, Tasaki J, Ichita C, Sasaki A. Effect of Antibiotic Resistance of Pathogens on Initial Antibiotic Therapy for Patients With Cholangitis. Cureus 2021; 13:e18449. [PMID: 34650837 PMCID: PMC8487445 DOI: 10.7759/cureus.18449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 12/24/2022] Open
Abstract
Objectives Considering that pathogens resistant to initial antibiotic therapies for cholangitis can affect mortality rates, appropriate initial empiric antibiotic therapy is important. However, evidence regarding the influence of pathogens resistant to initial antibiotics in patients with cholangitis who have undergone early endoscopic retrograde cholangiopancreatography (ERCP) is limited, and the conditions in several cases can improve with early ERCP even when pathogens resistant to initial antibiotics are detected on time. Therefore, this study aimed to assess the influence of pathogens resistant to initial antibiotics on the course of cholangitis in patients undergoing early ERCP. Materials and methods Patients (n=266) with positive blood or bile culture results treated with early ERCP were divided into those with cultures that were resistant to the initial antibiotics (antibiotic-resistant group; n=66; 24.8%) and those with cultures that were sensitive to the initial antibiotics (antibiotic-sensitive group; n=200; 75.2%). The duration of hospitalization, in-hospital mortality rates due to cholangitis, rates of increased disease severity, and complications during hospitalization were studied. Results Enterococcus, Enterobacter, Citrobacter, and Pseudomonas species showed high resistance to several antibiotics. No significant between-group differences were found in the duration of hospitalization, in-hospital mortality rates due to cholangitis, and rates of increased disease severity. However, the rate of post-ERCP cholecystitis was significantly higher in the antibiotic-resistant group than in the antibiotic-sensitive group (p=0.0245). Conclusions Even if the initial antibiotics were ineffective, the rate of fatal outcomes did not increase among patients with cholangitis who had undergone early ERCP. However, when initial antibiotics were ineffective, the frequency of post-ERCP cholecystitis increased even after early bile duct decompression.
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Affiliation(s)
- Sakue Masuda
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Kazuya Koizumi
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Haruki Uojima
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Karen Kimura
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Takashi Nishino
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Junichi Tasaki
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Chikamasa Ichita
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
| | - Akiko Sasaki
- Gastroenterology Medicine Center, Shonan Kamakura General Hospital, Kanagawa, JPN
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Almeida-Santos AC, Novais C, Peixe L, Freitas AR. Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context. Antibiotics (Basel) 2021; 10:antibiotics10101215. [PMID: 34680796 PMCID: PMC8532689 DOI: 10.3390/antibiotics10101215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/10/2023] Open
Abstract
Enterococcus spp. are one of the most frequent producers of bacteriocins (enterocins), which provides them with an advantage to compete in their natural environment, which is the gut of humans and many animals. The enterocins’ activity against microorganisms from different phylogenetic groups has raised interest in Enterococcus spp. in different contexts throughout the last decades, especially in the food industry. Nevertheless, some species can also cause opportunistic life-threatening infections and are frequently multidrug-resistant (MDR). Vancomycin-resistant Enterococcus (VRE), in particular, are an ongoing global challenge given the lack of therapeutic options. In this scenario, bacteriocins can offer a potential solution to this persistent threat, either alone or in combination with other antimicrobials. There are a handful of studies that demonstrate the advantages and applications of bacteriocins, especially against VRE. The purpose of this review is to present a current standpoint about the dual role of Enterococcus spp., from important producers to targets needed to be controlled, and the crucial role that enterocins may have in the expansion of enterococcal populations. Classification and distribution of enterocins, the current knowledge about the bacteriocinome of clinical enterococci, and the challenges of bacteriocin use in the fight against VRE infections are particularly detailed.
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Affiliation(s)
- Ana C. Almeida-Santos
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Carla Novais
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
| | - Ana R. Freitas
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN–Toxicology Research Unit, Department of Sciences, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
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The Many Faces of Enterococcus spp.-Commensal, Probiotic and Opportunistic Pathogen. Microorganisms 2021; 9:microorganisms9091900. [PMID: 34576796 PMCID: PMC8470767 DOI: 10.3390/microorganisms9091900] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023] Open
Abstract
Enterococcus spp. are Gram-positive, facultative, anaerobic cocci, which are found in the intestinal flora and, less frequently, in the vagina or mouth. Enterococcus faecalis and Enterococcus faecium are the most common species found in humans. As commensals, enterococci colonize the digestive system and participate in the modulation of the immune system in humans and animals. For many years reference enterococcal strains have been used as probiotic food additives or have been recommended as supplements for the treatment of intestinal dysbiosis and other conditions. The use of Enterococcus strains as probiotics has recently become controversial due to the ease of acquiring different virulence factors and resistance to various classes of antibiotics. Enterococci are also seen as opportunistic pathogens. This problem is especially relevant in hospital environments, where enterococcal outbreaks often occur. Their ability to translocate from the gastro-intestinal tract to various tissues and organs as well as their virulence and antibiotic resistance are risk factors that hinder eradication. Due to numerous reports on the plasticity of the enterococcal genome and the acquisition of pathogenic microbial features, we ask ourselves, how far is this commensal genus from acquiring pathogenicity? This paper discusses both the beneficial properties of these microorganisms and the risk factors related to their evolution towards pathogenicity.
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Barnes AMT, Frank KL, Dunny GM. Enterococcal Endocarditis: Hiding in Plain Sight. Front Cell Infect Microbiol 2021; 11:722482. [PMID: 34527603 PMCID: PMC8435889 DOI: 10.3389/fcimb.2021.722482] [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: 06/08/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Enterococcus faecalis is a major opportunistic bacterial pathogen of increasing clinical relevance. A substantial body of experimental evidence suggests that early biofilm formation plays a critical role in these infections, as well as in colonization and persistence in the GI tract as a commensal member of the microbiome in most terrestrial animals. Animal models of experimental endocarditis generally involve inducing mechanical valve damage by cardiac catheterization prior to infection, and it has long been presumed that endocarditis vegetation formation resulting from bacterial attachment to the endocardial endothelium requires some pre-existing tissue damage. Here we review both historical and contemporary animal model studies demonstrating the robust ability of E. faecalis to directly attach and form stable microcolony biofilms encased within a bacterially-derived extracellular matrix on the undamaged endovascular endothelial surface. We also discuss the morphological similarities when these biofilms form on other host tissues, including when E. faecalis colonizes the GI epithelium as a commensal member of the normal vertebrate microbiome - hiding in plain sight where it can serve as a source for systemic infection via translocation. We propose that these phenotypes may allow the organism to persist as an undetected infection in asymptomatic individuals and thus provide an infectious reservoir for later clinical endocarditis.
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Affiliation(s)
- Aaron M. T. Barnes
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN, United States
- Department of Laboratory Medicine and Pathology, University of Minnesota School of Medicine, Minneapolis, MN, United States
| | - Kristi L. Frank
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN, United States
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gary M. Dunny
- Department of Microbiology and Immunology, University of Minnesota School of Medicine, Minneapolis, MN, United States
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Aresti-Sanz J, Schwalbe M, Pereira RR, Permentier H, El Aidy S. Stability of Methylphenidate under Various pH Conditions in the Presence or Absence of Gut Microbiota. Pharmaceuticals (Basel) 2021; 14:ph14080733. [PMID: 34451830 PMCID: PMC8398889 DOI: 10.3390/ph14080733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 01/06/2023] Open
Abstract
Methylphenidate is one of the most widely used oral treatments for attention-deficit/hyperactivity disorder (ADHD). The drug is mainly absorbed in the small intestine and has low bioavailability. Accordingly, a high interindividual variability in terms of response to the treatment is known among ADHD patients treated with methylphenidate. Nonetheless, very little is known about the factors that influence the drug's absorption and bioavailability. Gut microbiota has been shown to reduce the bioavailability of a wide variety of orally administered drugs. Here, we tested the ability of small intestinal bacteria to metabolize methylphenidate. In silico analysis identified several small intestinal bacteria to harbor homologues of the human carboxylesterase 1 enzyme responsible for the hydrolysis of methylphenidate in the liver into the inactive form, ritalinic acid. Despite our initial results hinting towards possible bacterial hydrolysis of the drug, up to 60% of methylphenidate is spontaneously hydrolyzed in the absence of bacteria and this hydrolysis is pH-dependent. Overall, our results indicate that the stability of methylphenidate is compromised under certain pH conditions in the presence or absence of gut microbiota.
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Affiliation(s)
- Julia Aresti-Sanz
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands; (J.A.-S.); (M.S.)
| | - Markus Schwalbe
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands; (J.A.-S.); (M.S.)
| | | | - Hjalmar Permentier
- Interfaculty Mass Spectrometry Center, Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy (GRIP), 9713 AV Groningen, The Netherlands;
| | - Sahar El Aidy
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands; (J.A.-S.); (M.S.)
- Correspondence: ; Tel.: +31-(0)503-632201
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Mariam SH. A sampling survey of enterococci within pasteurized, fermented dairy products and their virulence and antibiotic resistance properties. PLoS One 2021; 16:e0254390. [PMID: 34264984 PMCID: PMC8282027 DOI: 10.1371/journal.pone.0254390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/28/2021] [Indexed: 01/17/2023] Open
Abstract
Globally, fermented foods (FFs), which may be traditional or industrially-produced, are major sources of nutrition. In the traditional practice, the fermentation process is driven by communities of virtually uncharacterized microflora indigenous to the food substrate. Some of these flora can have virulent or antibiotic resistance properties, posing risk to consumers. Others, such as Enterococcus faecalis and Enterococcus faecium, may also be found in such foods. Enterococci that harbor antibiotic resistance or virulence factors can cycle among animals, food, humans and the environment, thereby transferring these harmful properties at the gene level to harmless commensals in the food matrix, animals and humans. In this work, several microbial isolates obtained from different FF sources were analyzed for their identity and virulence and/or antibiotic resistance properties. For identification aiming at enterococci, isolates that were Gram-positive and catalase- and oxidase-negative were subjected to multiple tests including for growth in broth containing 6.5% NaCl, growth and hydrolytic activity on medium containing bile-esculin, hemolytic activity on blood agar, and growth at 45°C and survival after incubation at 60°C for 30 min. Furthermore, the isolates were tested for susceptibility/resistance to a select group of antibiotics. Finally, the isolates were molecularly-characterized with respect to species identity and presence of virulence-encoding genes by amplification of target genes. Most sources contained enterococci, in addition to most of them also containing Gram-negative flora. Most of these also harbored virulence factors. Several isolates were also antibiotic-resistant. These results strongly suggest attention should be given to better control presence of such potentially pathogenic species.
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Affiliation(s)
- Solomon H. Mariam
- Aklilu Lemma Institute of Pathobiology, Armauer Hansen Research Institute, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
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Iorizzo M, Albanese G, Testa B, Ianiro M, Letizia F, Succi M, Tremonte P, D’Andrea M, Iaffaldano N, Coppola R. Presence of Lactic Acid Bacteria in the Intestinal Tract of the Mediterranean Trout ( Salmo macrostigma) in Its Natural Environment. Life (Basel) 2021; 11:667. [PMID: 34357039 PMCID: PMC8306010 DOI: 10.3390/life11070667] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 12/19/2022] Open
Abstract
Knowledge of the composition of the gut microbiota in freshwater fish living in their natural habitat has taxonomic and ecological importance. Few reports have been produced on the composition of the gut microbiota and on the presence of LAB in the intestines of freshwater fish that inhabit river environments. In this study, we investigated the LAB community that was present in the gastrointestinal tract (GIT) of Mediterranean trout (Salmo macrostigma) that colonized the Biferno and Volturno rivers of the Molise region (Italy). The partial 16S rRNA gene sequences of these strains were determined for the species-level taxonomic placement. The phylogenetic analysis revealed that the isolated LABs belonged to seven genera (Carnobacterium, Enterococcus, Lactobacillus, Lactiplantibacillus, Vagococcus, Lactococcus, and Weissella). The study of the enzymatic activities showed that these LABs could contribute to the breakdown of polysaccharides, proteins, and lipids. In future studies, a greater understanding of how the LABs act against pathogens and trigger the fish immune response may provide practical means to engineer the indigenous fish microbiome and enhance disease control and fish health.
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Affiliation(s)
| | | | - Bruno Testa
- Department of Agriculture, Environmental and Food Sciences, University of Molise, Via De Sanctis, 86100 Campobasso, Italy; (M.I.); (G.A.); (M.I.); (F.L.); (M.S.); (P.T.); (M.D.); (N.I.); (R.C.)
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Catarino MD, Marçal C, Bonifácio-Lopes T, Campos D, Mateus N, Silva AMS, Pintado MM, Cardoso SM. Impact of Phlorotannin Extracts from Fucus vesiculosus on Human Gut Microbiota. Mar Drugs 2021; 19:375. [PMID: 34209623 PMCID: PMC8306378 DOI: 10.3390/md19070375] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/17/2022] Open
Abstract
Recent studies indicate that plant polyphenols could be pointed as potential prebiotic candidates since they may interact with the gut microbiota, stimulating its growth and the production of metabolites. However, little is known about the fate of brown seaweeds' phlorotannins during their passage throughout the gastrointestinal tract. This work aimed to evaluate the stability and bioaccessibility of Fucus vesiculosus phlorotannins after being submitted to a simulated digestive process, as well as their possible modulatory effects on gut microbiota and short-chain fatty acids production following a fermentation procedure using fecal inoculates to mimic the conditions of the large intestine. The stability of phlorotannins throughout the gastrointestinal tract was reduced, with a bioaccessibility index between 2 and 14%. Moreover, slight alterations in the growth of certain commensal bacteria were noticed, with Enterococcus spp. being the most enhanced group. Likewise, F. vesiculosus phlorotannins displayed striking capacity to enhance the levels of propionate and butyrate, which are two important short-chain fatty acids known for their role in intestinal homeostasis. In summary, this work provides valuable information regarding the behavior of F. vesiculosus phlorotannins along the gastrointestinal tract, presenting clear evidence that these compounds can positively contribute to the maintenance of a healthy gastrointestinal condition.
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Affiliation(s)
- Marcelo D. Catarino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.D.C.); (C.M.); (A.M.S.S.)
| | - Catarina Marçal
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.D.C.); (C.M.); (A.M.S.S.)
| | - Teresa Bonifácio-Lopes
- CBQF-Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (T.B.-L.); (D.C.); (M.M.P.)
| | - Débora Campos
- CBQF-Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (T.B.-L.); (D.C.); (M.M.P.)
| | - Nuno Mateus
- REQUIMTE/LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal;
| | - Artur M. S. Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.D.C.); (C.M.); (A.M.S.S.)
| | - Maria Manuela Pintado
- CBQF-Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (T.B.-L.); (D.C.); (M.M.P.)
| | - Susana M. Cardoso
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.D.C.); (C.M.); (A.M.S.S.)
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Comparative Biofilm Assays Using Enterococcus faecalis OG1RF Identify New Determinants of Biofilm Formation. mBio 2021; 12:e0101121. [PMID: 34126766 PMCID: PMC8262879 DOI: 10.1128/mbio.01011-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enterococcus faecalis is a common commensal organism and a prolific nosocomial pathogen that causes biofilm-associated infections. Numerous E. faecalis OG1RF genes required for biofilm formation have been identified, but few studies have compared genetic determinants of biofilm formation and biofilm morphology across multiple conditions. Here, we cultured transposon (Tn) libraries in CDC biofilm reactors in two different media and used Tn sequencing (TnSeq) to identify core and accessory biofilm determinants, including many genes that are poorly characterized or annotated as hypothetical. Multiple secondary assays (96-well plates, submerged Aclar discs, and MultiRep biofilm reactors) were used to validate phenotypes of new biofilm determinants. We quantified biofilm cells and used fluorescence microscopy to visualize biofilms formed by six Tn mutants identified using TnSeq and found that disrupting these genes (OG1RF_10350, prsA, tig, OG1RF_10576, OG1RF_11288, and OG1RF_11456) leads to significant time- and medium-dependent changes in biofilm architecture. Structural predictions revealed potential roles in cell wall homeostasis for OG1RF_10350 and OG1RF_11288 and signaling for OG1RF_11456. Additionally, we identified growth medium-specific hallmarks of OG1RF biofilm morphology. This study demonstrates how E. faecalis biofilm architecture is modulated by growth medium and experimental conditions and identifies multiple new genetic determinants of biofilm formation.
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Aggarwal S, Ranjha R, Paul J. Neuroimmunomodulation by gut bacteria: Focus on inflammatory bowel diseases. World J Gastrointest Pathophysiol 2021; 12:25-39. [PMID: 34084590 PMCID: PMC8160600 DOI: 10.4291/wjgp.v12.i3.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/01/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Microbes colonize the gastrointestinal tract are considered as highest complex ecosystem because of having diverse bacterial species and 150 times more genes as compared to the human genome. Imbalance or dysbiosis in gut bacteria can cause dysregulation in gut homeostasis that subsequently activates the immune system, which leads to the development of inflammatory bowel disease (IBD). Neuromediators, including both neurotransmitters and neuropeptides, may contribute to the development of aberrant immune response. They are emerging as a regulator of inflammatory processes and play a key role in various autoimmune and inflammatory diseases. Neuromediators may influence immune cell’s function via the receptors present on these cells. The cytokines secreted by the immune cells, in turn, regulate the neuronal functions by binding with their receptors present on sensory neurons. This bidirectional communication of the enteric nervous system and the enteric immune system is involved in regulating the magnitude of inflammatory pathways. Alterations in gut bacteria influence the level of neuromediators in the colon, which may affect the gastrointestinal inflammation in a disease condition. Changed neuromediators concentration via dysbiosis in gut microbiota is one of the novel approaches to understand the pathogenesis of IBD. In this article, we reviewed the existing knowledge on the role of neuromediators governing the pathogenesis of IBD, focusing on the reciprocal relationship among the gut microbiota, neuromediators, and host immunity. Understanding the neuromediators and host-microbiota interactions would give a better insight in to the disease pathophysiology and help in developing the new therapeutic approaches for the disease.
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Affiliation(s)
- Surbhi Aggarwal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi 110016, India
- School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India
| | - Raju Ranjha
- School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India
- Field Unit Raipur, ICMR-National Institute of Malaria Research, Raipur 492015, Chhattisgarh, India
| | - Jaishree Paul
- School of Life Sciences, Jawaharlal Nehru University, Delhi 110067, India
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Kaczmarczyk M, Löber U, Adamek K, Węgrzyn D, Skonieczna-Żydecka K, Malinowski D, Łoniewski I, Markó L, Ulas T, Forslund SK, Łoniewska B. The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. J Transl Med 2021; 19:177. [PMID: 33910577 PMCID: PMC8082808 DOI: 10.1186/s12967-021-02839-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The intestinal barrier plays an important role in the defense against infections, and nutritional, endocrine, and immune functions. The gut microbiota playing an important role in development of the gastrointestinal tract can impact intestinal permeability and immunity during early life, but data concerning this problem are scarce. METHODS We analyzed the microbiota in fecal samples (101 samples in total) collected longitudinally over 24 months from 21 newborns to investigate whether the markers of small intestinal paracellular permeability (zonulin) and immune system development (calprotectin) are linked to the gut microbiota. The results were validated using data from an independent cohort that included the calprotectin and gut microbiota in children during the first year of life. RESULTS Zonulin levels tended to increase for up to 6 months after childbirth and stabilize thereafter remaining at a high level while calprotectin concentration was high after childbirth and began to decline from 6 months of life. The gut microbiota composition and the related metabolic potentials changed during the first 2 years of life and were correlated with zonulin and calprotectin levels. Faecal calprotectin correlated inversely with alpha diversity (Shannon index, r = - 0.30, FDR P (Q) = 0.039). It also correlated with seven taxa; i.a. negatively with Ruminococcaceae (r = - 0.34, Q = 0.046), and Clostridiales (r = - 0.34, Q = 0.048) and positively with Staphylococcus (r = 0.38, Q = 0.023) and Staphylococcaceae (r = 0.35, Q = 0.04), whereas zonulin correlated with 19 taxa; i.a. with Bacillales (r = - 0.52, Q = 0.0004), Clostridiales (r = 0.48, Q = 0.001) and the Ruminococcus (torques group) (r = 0.40, Q = 0.026). When time intervals were considered only changes in abundance of the Ruminococcus (torques group) were associated with changes in calprotectin (β = 2.94, SE = 0.8, Q = 0.015). The dynamics of stool calprotectin was negatively associated with changes in two MetaCyc pathways: pyruvate fermentation to butanoate (β = - 4.54, SE = 1.08, Q = 0.028) and Clostridium acetobutylicum fermentation (β = - 4.48, SE = 1.16, Q = 0.026). CONCLUSIONS The small intestinal paracellular permeability, immune system-related markers and gut microbiota change dynamically during the first 2 years of life. The Ruminococcus (torques group) seems to be especially involved in controlling paracellular permeability. Staphylococcus, Staphylococcaceae, Ruminococcaceae, and Clostridiales, may be potential biomarkers of the immune system. Despite observed correlations their clear causation and health consequences were not proven. Mechanistic studies are required.
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Affiliation(s)
- Mariusz Kaczmarczyk
- Department of Clinical Biochemistry, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Ulrike Löber
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Karolina Adamek
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Dagmara Węgrzyn
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | | | - Damian Malinowski
- Department of Pharmacology, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Igor Łoniewski
- Department of Biochemical Sciences, Pomeranian Medical University in Szczecin, 71-460, Szczecin, Poland.
- Department of Human Nutrition and Metabolomics, Broniewskiego 24, 71-460, Szczecin, Poland.
| | - Lajos Markó
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127, Bonn, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Beata Łoniewska
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
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73
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Jahan D, Peile E, Sheikh MA, Islam S, Parasnath S, Sharma P, Iskandar K, Dhingra S, Charan J, Hardcastle TC, Samad N, Chowdhury TS, Dutta S, Haque M. Is it time to reconsider prophylactic antimicrobial use for hematopoietic stem cell transplantation? a narrative review of antimicrobials in stem cell transplantation. Expert Rev Anti Infect Ther 2021; 19:1259-1280. [PMID: 33711240 DOI: 10.1080/14787210.2021.1902304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Hematopoietic Stem Cell Transplantation (HSCT) is a life-saving procedure for multiple types of hematological cancer, autoimmune diseases, and genetic-linked metabolic diseases in humans. Recipients of HSCT transplant are at high risk of microbial infections that significantly correlate with the presence of graft-versus-host disease (GVHD) and the degree of immunosuppression. Infection in HSCT patients is a leading cause of life-threatening complications and mortality. AREAS COVERED This review covers issues pertinent to infection in the HSCT patient, including bacterial and viral infection; strategies to reduce GVHD; infection patterns; resistance and treatment options; adverse drug reactions to antimicrobials, problems of antimicrobial resistance; perturbation of the microbiome; the role of prebiotics, probiotics, and antimicrobial peptides. We highlight potential strategies to minimize the use of antimicrobials. EXPERT OPINION Measures to control infection and its transmission remain significant HSCT management policy and planning issues. Transplant centers need to consider carefully prophylactic use of antimicrobials for neutropenic patients. The judicious use of appropriate antimicrobials remains a crucial part of the treatment protocol. However, antimicrobials' adverse effects cause microbiome diversity and dysbiosis and have been shown to increase morbidity and mortality.
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Affiliation(s)
- Dilshad Jahan
- Department of Hematology, Asgar Ali Hospital, 111/1/A Distillery Road, Gandaria Beside Dhupkhola, Dhaka 1204, Bangladesh
| | - Ed Peile
- Department of Medical Education, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sharlene Parasnath
- Department of Clinical Hematology, Inkosi Albert Luthuli Central Hospital, 800 Vusi Mzimela Road, Cato Manor, Durban, South Africa
| | - Paras Sharma
- Department of Pharmacognosy, BVM College of Pharmacy, Gwalior, India
| | - Katia Iskandar
- Lebanese University, School of Pharmacy, Beirut, Lebanon.,INSPECT-LB: Institute National de Sante Publique, Epidemiologie Clinique et Toxicologie, Beirut, Lebanon.,Universite Paul Sabatier UT3, INSERM, UMR1027, Toulouse, France
| | - Sameer Dhingra
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India
| | - Jaykaran Charan
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Timothy Craig Hardcastle
- Trauma Service, Inkosi Albert Luthuli Central Hospital, Mayville, South Africa.,Department of Surgery, Nelson R Mandela School of Clinical Medicine, UKZN, South Africa
| | - Nandeeta Samad
- Department of Public Health, North South University, Bangladesh
| | | | - Siddhartha Dutta
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kem Perdana Sungai Besi, Kuala Lumpur, Malaysia
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74
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Kabwe M, Meehan-Andrews T, Ku H, Petrovski S, Batinovic S, Chan HT, Tucci J. Lytic Bacteriophage EFA1 Modulates HCT116 Colon Cancer Cell Growth and Upregulates ROS Production in an Enterococcus faecalis Co-culture System. Front Microbiol 2021; 12:650849. [PMID: 33868210 PMCID: PMC8044584 DOI: 10.3389/fmicb.2021.650849] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/08/2021] [Indexed: 12/12/2022] Open
Abstract
Enterococcus faecalis is an opportunistic pathogen in the gut microbiota that’s associated with a range of difficult to treat nosocomial infections. It is also known to be associated with some colorectal cancers. Its resistance to a range of antibiotics and capacity to form biofilms increase its virulence. Unlike antibiotics, bacteriophages are capable of disrupting biofilms which are key in the pathogenesis of diseases such as UTIs and some cancers. In this study, bacteriophage EFA1, lytic against E. faecalis, was isolated and its genome fully sequenced and analyzed in silico. Electron microscopy images revealed EFA1 to be a Siphovirus. The bacteriophage was functionally assessed and shown to disrupt E. faecalis biofilms as well as modulate the growth stimulatory effects of E. faecalis in a HCT116 colon cancer cell co-culture system, possibly via the effects of ROS. The potential exists for further testing of bacteriophage EFA1 in these systems as well as in vivo models.
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Affiliation(s)
- Mwila Kabwe
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Terri Meehan-Andrews
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Heng Ku
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Steven Batinovic
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Hiu Tat Chan
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia.,Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Joseph Tucci
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
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75
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Aun E, Kisand V, Laht M, Telling K, Kalmus P, Väli Ü, Brauer A, Remm M, Tenson T. Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs. Front Microbiol 2021; 12:601490. [PMID: 33841342 PMCID: PMC8032980 DOI: 10.3389/fmicb.2021.601490] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
In this study, we aimed to characterize the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. Sixty-one Enterococcus faecalis and 34 Enterococcus faecium isolates were collected between 2012 and 2014 across the country from various sites and sources, including farm animals and poultry (n = 53), humans (n = 12), environment (n = 24), and wild birds (n = 44). Clonal relationships of the strains were determined by whole-genome sequencing and analyzed by multi-locus sequence typing. We determined the presence of acquired antimicrobial resistance genes and 23S rRNA mutations, virulence genes, and also the plasmid or chromosomal origin of the genes using dedicated DNA sequence analysis tools available and/or homology search against an ad hoc compiled database of relevant sequences. Two E. faecalis isolates from human with vanB genes were highly resistant to vancomycin. Closely related E. faecalis strains were isolated from different host species. This indicates interspecies spread of strains and potential transfer of antibiotic resistance. Genomic context analysis of the resistance genes indicated frequent association with plasmids and mobile genetic elements. Resistance genes are often present in the identical genetic context in strains with diverse origins, suggesting the occurrence of transfer events.
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Affiliation(s)
- Erki Aun
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mailis Laht
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kaidi Telling
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Piret Kalmus
- Department of Clinical Veterinary Medicine, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Ülo Väli
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Age Brauer
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
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76
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Weiss S, Taggart D, Smith I, Helgen KM, Eisenhofer R. Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons). Anim Microbiome 2021; 3:13. [PMID: 33500001 PMCID: PMC7836174 DOI: 10.1186/s42523-021-00074-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 01/08/2021] [Indexed: 01/17/2023] Open
Abstract
Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00074-8.
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Affiliation(s)
- Sesilje Weiss
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - David Taggart
- School of Animal and Veterinary Sciences (Waite), University of Adelaide, Adelaide, South Australia, Australia.,FAUNA Research Alliance, Ltd, PO Box 98, Callaghan, NSW, 2308, Australia
| | - Ian Smith
- School of Animal and Veterinary Sciences (Waite), University of Adelaide, Adelaide, South Australia, Australia.,Zoos South Australia, Frome Rd, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, 1 William St, Sydney, New South Wales, Australia.,Australian Research Council Centre for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. .,Australian Research Council Centre for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia.
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77
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Rasheed MA, Iqbal MN, Saddick S, Ali I, Khan FS, Kanwal S, Ahmed D, Ibrahim M, Afzal U, Awais M. Identification of Lead Compounds against Scm (fms10) in Enterococcus faecium Using Computer Aided Drug Designing. Life (Basel) 2021; 11:life11020077. [PMID: 33494233 PMCID: PMC7909823 DOI: 10.3390/life11020077] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/29/2020] [Accepted: 01/09/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: Enterococcus faecium DO is an environmental microbe, which is a mesophilic, facultative, Gram-positive, and multiple habitat microorganism. Enterococcus faecium DO is responsible for many diseases in human. The fight against infectious diseases is confronted by the development of multiple drug resistance in E. faecium. The focus of this research work is to identify a novel compound against this pathogen by using bioinformatics tools and technology. (2) Methods: We screened the proteome (accession No. PRJNA55353) information from the genome database of the National Centre for Biotechnology Information (NCBI) and suggested a potential drug target. I-TASSER was used to predict the three-dimensional structure of the protein, and the structure was optimized and minimized by different tools. PubChem and ChEBI were used to retrieve the inhibitors. Pharmacophore modeling and virtual screening were performed to identify novel compounds. Binding interactions of compounds with target protein were checked using LigPlot. pkCSM, SwissADME, and ProTox-II were used for adsorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. (3) Results: Novel selected compounds have improved absorption and have better ADMET properties. Based on our results, the chemically identified inhibitor ZINC48942 targeted the receptor that can inhibit the activity of infection in E. faecium. This research work will be beneficial for the scientific community and could aid in the design of a new drug against E. faecium infections. (4) Conclusions: It was observed that novel compounds are potential inhibitors with more efficacy and fewer side effects. This research work will help researchers in testing and identification of these chemicals useful against E. faecium.
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Affiliation(s)
- Muhammad Asif Rasheed
- Department of Biosciences, Sahiwal Campus, COMSATS University Islamabad, Sahiwal 57000, Pakistan; (M.A.R.); (M.N.I.); (I.A.); (S.K.); (M.I.)
| | - Muhammad Nasir Iqbal
- Department of Biosciences, Sahiwal Campus, COMSATS University Islamabad, Sahiwal 57000, Pakistan; (M.A.R.); (M.N.I.); (I.A.); (S.K.); (M.I.)
| | - Salina Saddick
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia;
| | - Iqra Ali
- Department of Biosciences, Sahiwal Campus, COMSATS University Islamabad, Sahiwal 57000, Pakistan; (M.A.R.); (M.N.I.); (I.A.); (S.K.); (M.I.)
| | - Falak Sher Khan
- Department of Biotechnology, University of Sialkot, Sialkot 51040, Pakistan;
| | - Sumaira Kanwal
- Department of Biosciences, Sahiwal Campus, COMSATS University Islamabad, Sahiwal 57000, Pakistan; (M.A.R.); (M.N.I.); (I.A.); (S.K.); (M.I.)
| | - Dawood Ahmed
- Department of Medical Lab Technology, University of Haripur, Haripur 22620, Pakistan;
| | - Muhammad Ibrahim
- Department of Biosciences, Sahiwal Campus, COMSATS University Islamabad, Sahiwal 57000, Pakistan; (M.A.R.); (M.N.I.); (I.A.); (S.K.); (M.I.)
| | - Umara Afzal
- Department of Chemistry, Rawalpindi Women University, Satellite Town, Rawalpindi 43600, Pakistan;
| | - Muhammad Awais
- Department of Biosciences, Sahiwal Campus, COMSATS University Islamabad, Sahiwal 57000, Pakistan; (M.A.R.); (M.N.I.); (I.A.); (S.K.); (M.I.)
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 43600, Pakistan
- Correspondence: or
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78
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Zhang H, Wang M, Jia J, Zhao J, Radebe SM, Yu Q. The Protective Effect of E. faecium on S. typhimurium Infection Induced Damage to Intestinal Mucosa. Front Vet Sci 2021; 8:740424. [PMID: 34722703 PMCID: PMC8554125 DOI: 10.3389/fvets.2021.740424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 01/17/2023] Open
Abstract
Intensive farming is prone to induce large-scale outbreaks of infectious diseases, with increasing use of antibiotics, which deviate from the demand of organic farming. The high mortality rate of chickens infected with Salmonella caused huge economic losses; therefore, the promising safe prevention and treatment measures of Salmonella are in urgent need, such as probiotics. Probiotics are becoming an ideal alternative treatment option besides antibiotics, but the effective chicken probiotic strains with clear protective mechanism against Salmonella remain unclear. In this study, we found Enterococcus faecium YQH2 was effective in preventing Salmonella typhimurium infection in chickens. Salmonella typhimurium induced the loss of body weight, and liver and intestinal morphology damage. The inflammatory factor levels increased and intestinal proliferation inhibited. However, after treatment with Enterococcus faecium YQH2, broilers grew normally, the pathological changes of liver and intestine were reduced, and the colonization of Salmonella in the intestine was improved. Not only that, the length of villi and the depth of crypts were relatively normal, and the levels of inflammatory factors such as IL-1β, TNF-α, and IL-8 were reduced. The number of PCNA cells of Enterococcus faecium YQH2 returned to normal under the action of Salmonella typhimurium infection, which was conducive to the normal proliferation of intestinal epithelial cells. The protective effect of Enterococcus faecium YQH2 may be due to the attribution to the activation of hypoxia and then induced the proliferation of intestinal stem cells to repair the damage of intestinal mucosa under Salmonella typhimurium infection. This study demonstrated that Enterococcus faecium YQH2 was effective in preventing Salmonella typhimurium infection, which could be further used in the chicken health breeding.
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79
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Orababa OQ, Soriwei JD, Akinsuyi SO, Essiet UU, Solesi OM. A systematic review and meta-analysis on the prevalence of vancomycin-resistant enterococci (VRE) among Nigerians. Porto Biomed J 2021; 6:e125. [PMID: 33884321 PMCID: PMC8055482 DOI: 10.1097/j.pbj.0000000000000125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Enterococci are opportunistic pathogens and are one of the most important bacteria in hospital-acquired infections. Their resistance to antibiotics such as vancomycin has led to life-threatening and difficult-to-treat nosocomial infections. The true prevalence in clinical settings in Nigeria is not well known due to the lack of a comprehensive antibiotic surveillance system. This study aims to estimate the prevalence of vancomycin-resistant enterococci (VRE) in clinical infections in Nigeria. METHODS Databases (PubMed, African Journal Online, and Google scholar) were searched following the Preferred Reporting Items for Systematic review and meta-analysis protocols (PRISMA-P) 2015 statements for articles reporting VRE prevalence, and were published before August 5, 2020. Data from the studies were extracted and analyzed using Microsoft Excel and Comprehensive Meta-Analysis (CMA 3.0), respectively. The pooled prevalence of VRE was estimated with the random-effects model and the 95% confidence interval (CI). The heterogeneity level was assessed using Cochran Q and I 2 tests. RESULTS A total of 35 articles were scanned for eligibility, among which 7 were included in the study after fulfilling the eligibility criteria. The studies analyzed a total of 832 enterococci isolates and 90 VRE strains. The prevalence of Enterococcus faecium and E faecalis in this study are 361 (59.3%) and 248 (40.7%), respectively, among which 41 (63.1%) of the E faecium and 24 (36.9%) of the E faecalis were vancomycin resistant. The pooled prevalence of VRE was estimated at (95% CI; 10.0-53.9%; I 2 = 93.50%; P < .001). The highest prevalence of VRE was reported from western Nigeria, 14.6% (95% CI; I 2 = 97.27; P < .001). CONCLUSION The prevalence of VRE in Nigeria according to the reports from this study is relatively high. The report of this study should help policymakers to put in place measures that will help curb the spread of VRE and associated resistant genes to other important clinical pathogens like Staphylococcus aureus.
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Affiliation(s)
| | - Jeffry Difiye Soriwei
- Department of Microbiology in Public Health, University of Bedfordshire, Luton, Bedfordshire, United Kingdom
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80
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Taco-Masias AA, Fernandez-Aristi AR, Cornejo-Tapia A, Aguilar-Luis MA, Del Valle LJ, Silva-Caso W, Zavaleta-Gavidia V, Weilg P, Cornejo-Pacherres H, Bazán-Mayra J, Puyen ZM, Del Valle-Mendoza J. Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital. PeerJ 2020; 8:e9964. [PMID: 33194370 PMCID: PMC7646295 DOI: 10.7717/peerj.9964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
Background Acute infective gastroenteritis (AIG) is a leading cause of mortality in children worldwide. In Peru, more than 40% of cases of AIG occurring in children under 5 years old. The disruption of the gut microbiota can increase risk for several health complications especially in patients with gastric infections caused by viruses or bacteria. Objective The main objective of this study was to describe the prevalence of 13 representative bacteria from the gut microbiota (GM) in stools samples from children under 5 years of age with acute infective gastroenteritis. Results The most commonly isolated bacteria from the GM were Firmicutes (63.2% 74/117) Bacteriodetes (62.4%; 73/117), Lactobacillus (59.8%; 70/117), Prevotella (57.2%; 67/117), Proteobacterium (53.8%; 63/117), regardless of the etiological agent responsible for the AIG. Interestingly, despite the high prevalence of Firmicutes, Bacteroidetes, Lactobacillus and Prevotella across all samples, a visible reduction of these agents was observed especially among patients with a single bacterial infection or even bacteria-bacteria coinfections when compared to viral etiologies. Patients with exclusive or mixed breastfeeding registered the highest amount of gut microbiota bacteria, in contrast to infants who received formula or were not breastfed.
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Affiliation(s)
- Andre Alonso Taco-Masias
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Augusto R Fernandez-Aristi
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Angela Cornejo-Tapia
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Miguel Angel Aguilar-Luis
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | - Luis J Del Valle
- Barcelona Research Center for Multiscale Science and Engineering, Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Wilmer Silva-Caso
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
| | | | - Pablo Weilg
- Mercy One North Iowa Medical Center, Mason City, USA
| | | | | | - Zully M Puyen
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Juana Del Valle-Mendoza
- School of Medicine, Research and Innovation Centre of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru.,Laboratorio de Biologia Molecular, Instituto de Investigación Nutricional, Lima, Peru
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81
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Mull RW, Brennan AA, Russ BR, Tal-Gan Y. Attenuating the Selection of Vancomycin Resistance Among Enterococci through the Development of Peptide-Based Vancomycin Antagonists. ACS Infect Dis 2020; 6:2913-2925. [PMID: 32946213 DOI: 10.1021/acsinfecdis.0c00319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The emergence and spread of multidrug resistant (MDR) pathogens with acquired resistance to almost all available antimicrobial agents has severely threatened the international healthcare community over the last two decades. The last resort antibiotic vancomycin is critical for treatment of several of these pathogens; howeverc vancomycin resistance is spreading due to the undesired accumulation of IV vancomycin in the colon post-treatment. This accumulation exerts selective pressure upon members of the colonic microflora, including Enterococci, which possess vancomycin resistance genes. To ensure the continual effectiveness of vancomycin in the clinical setting by preventing the spread of antibiotic resistance, it is crucial to develop strategies that reduce selective pressure on the colonic microflora while allowing vancomycin to maintain its desired activity at the site of infection. Herein we report that modification of the native l-Lys-d-Ala-d-Ala vancomycin binding site can be used to produce peptides with the ability to competitively bind vancomycin, reducing its activity against susceptible Enterococci. Moreover, several modifications to the N-termini of the native tripeptide have produced compounds with enhanced vancomycin binding activity, including several analogs that were designed to covalently bind vancomycin, thereby acting as suicide inhibitors. Finally, in a mixed culture of susceptible and resistant bacteria, a single lead compound was found to protect high ratios of susceptible bacteria from vancomycin over the course of a week-long period, preventing the selection for vancomycin-resistant Enterococci. These findings demonstrate the ability of these peptides as potential therapeutic adjuvants for counteracting the undesired accumulation of colonic vancomycin, allowing for protection of the colonic microflora.
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Affiliation(s)
- Ryan W. Mull
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Alec A. Brennan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Brittany R. Russ
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, United States
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Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium. mSystems 2020; 5:5/4/e00452-20. [PMID: 32817384 PMCID: PMC7438022 DOI: 10.1128/msystems.00452-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vancomycin-resistant Enterococcus faecium (VREfm) is an emerging antibiotic-resistant pathogen. Strain-level investigations are beginning to reveal the molecular mechanisms used by VREfm to colonize regions of the human bowel. However, the role of commensal bacteria during VREfm colonization, in particular following antibiotic treatment, remains largely unknown. We employed amplicon 16S rRNA gene sequencing and metabolomics in a murine model system to try and investigate functional roles of the gut microbiome during VREfm colonization. First-order taxonomic shifts between Bacteroidetes and Tenericutes within the gut microbial community composition were detected both in response to pretreatment using ceftriaxone and to subsequent VREfm challenge. Using neural networking approaches to find cooccurrence profiles of bacteria and metabolites, we detected key metabolome features associated with butyric acid during and after VREfm colonization. These metabolite features were associated with Bacteroides, indicative of a transition toward a preantibiotic naive microbiome. This study shows the impacts of antibiotics on the gut ecosystem and the progression of the microbiome in response to colonization with VREfm. Our results offer insights toward identifying potential nonantibiotic alternatives to eliminate VREfm through metabolic reengineering to preferentially select for Bacteroides IMPORTANCE This study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.
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83
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Enterococci, from Harmless Bacteria to a Pathogen. Microorganisms 2020; 8:microorganisms8081118. [PMID: 32722391 PMCID: PMC7463792 DOI: 10.3390/microorganisms8081118] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Enterococci are gastrointestinal commensals whose hardiness allowed them to colonize very diverse environments, including soils, water, food, and feed. This ability to overcome adverse conditions makes enterococci problematic once they colonize hospital niches. Together with the malleability of their genomes, the capacity to acquire and disseminate determinants of antibiotic resistance has contributed to converting what was once just another opportunistic pathogen into a first-class clinical problem. This review discusses the dimension of the emergence of enterococcal resistance to key antimicrobial agents, the dissemination of this resistance, and its significance in terms of public health, with the aim of raising awareness of the need to devise and implement surveillance programs and more effective antibiotic stewardship.
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84
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Weber A, Maechler F, Schwab F, Gastmeier P, Kola A. Increase of vancomycin-resistant Enterococcus faecium strain type ST117 CT71 at Charité - Universitätsmedizin Berlin, 2008 to 2018. Antimicrob Resist Infect Control 2020; 9:109. [PMID: 32678047 PMCID: PMC7364619 DOI: 10.1186/s13756-020-00754-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In addition to an overall rise in vancomycin-resistant Enterococcus faecium (VREfm), an increase in certain strain types marked by sequence type (ST) and cluster type (CT) has been reported in Germany over the past few years. Outbreak analyses at Charité - Universitätsmedizin Berlin revealed the frequent occurrence of VREfm ST117 CT71 isolates in 2017 and 2018. To investigate whether ST117 CT71 have emerged in recent years or whether these strains have been circulating for a longer time, we retrospectively analyzed non-outbreak strains that occurred between 2008 and 2018 to identify frequent STs and CTs. METHODS In total, 120 VREfm isolates obtained from clinical and surveillance cultures from the years 2008, 2013, 2015, and 2018 were analyzed. Thirty isolates per year comprising the first 7-8 non-outbreak isolates of each quarter of the respective year were sequenced using whole genome sequencing. MLST and cgMLST were determined as well as resistance genes and virulence factors. Risk factors for VREfm ST117 were analyzed in a multivariable analysis with patient characteristics as possible confounders. RESULTS The percentage of VREfm of type ST117 increased from 17% in 2008 to 57% in 2018 (p = 0.012). In 2008, vanA genotype accounted for 80% of all ST117 isolates compared to 6% in 2018. VanB CT71 first appeared in 2018 and predominated over all other ST117 at 43% (p < 0.0001). The set of resistance genes (msrC, efmA, erm(B), dfrG, aac(6')-Ii, gyrA, parC and pbp5) and virulence factors (acm, esp, hylEfm, ecbA and sgrA) in CT71 was also found in other ST117 non-CT71 strains, mainly in CT36. The study population did not differ among the different calendar years analyzed in terms of age, gender, length of stay, or ward type (each p > 0.2). CONCLUSION This study revealed an increase in ST117 strains from 2008 to 2018, accompanied by a shift toward CT71 strains with the vanB genotype in 2018. We did not detect resistance or virulence traits in CT71 that could confer survival advantage compared to other CTs among ST117 strains. To date, it is not clear why ST117 and in particular strain type ST117 CT71 predominates over other strains.
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Affiliation(s)
- Anna Weber
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany.
| | - Friederike Maechler
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Frank Schwab
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Hindenburgdamm 27, 12203, Berlin, Germany
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85
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Chong R, Cheng Y, Hogg CJ, Belov K. Marsupial Gut Microbiome. Front Microbiol 2020; 11:1058. [PMID: 32547513 PMCID: PMC7272691 DOI: 10.3389/fmicb.2020.01058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.
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Affiliation(s)
- Rowena Chong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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86
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Klammsteiner T, Walter A, Bogataj T, Heussler CD, Stres B, Steiner FM, Schlick-Steiner BC, Arthofer W, Insam H. The Core Gut Microbiome of Black Soldier Fly ( Hermetia illucens) Larvae Raised on Low-Bioburden Diets. Front Microbiol 2020; 11:993. [PMID: 32508795 PMCID: PMC7253588 DOI: 10.3389/fmicb.2020.00993] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/23/2020] [Indexed: 12/23/2022] Open
Abstract
An organism’s gut microbiome handles most of the metabolic processes associated with food intake and digestion but can also strongly affect health and behavior. A stable microbial core community in the gut provides general metabolic competences for substrate degradation and is robust against extrinsic disturbances like changing diets or pathogens. Black Soldier Fly larvae (BSFL; Hermetia illucens) are well known for their ability to efficiently degrade a wide spectrum of organic materials. The ingested substrates build up the high fat and protein content in their bodies that make the larvae interesting for the animal feedstuff industry. In this study, we subjected BSFL to three distinct types of diets carrying a low bioburden and assessed the diets’ impact on larval development and on the composition of the bacterial and archaeal gut community. No significant impact on the gut microbiome across treatments pointed us to the presence of a predominant core community backed by a diverse spectrum of low-abundance taxa. Actinomyces spp., Dysgonomonas spp., and Enterococcus spp. as main members of this community provide various functional and metabolic skills that could be crucial for the thriving of BSFL in various environments. This indicates that the type of diet could play a lesser role in guts of BSFL than previously assumed and that instead a stable autochthonous collection of bacteria provides the tools for degrading of a broad range of substrates. Characterizing the interplay between the core gut microbiome and BSFL helps to understand the involved degradation processes and could contribute to further improving large-scale BSFL rearing.
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Affiliation(s)
- Thomas Klammsteiner
- Department of Microbiology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria.,Department of Environmental, Process and Energy Engineering, MCI - The Entrepreneurial School, Innsbruck, Austria
| | - Andreas Walter
- Department of Biotechnology and Food Engineering, MCI - The Entrepreneurial School, Innsbruck, Austria
| | - Tajda Bogataj
- Department of Microbiology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria
| | - Carina D Heussler
- Department of Microbiology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria.,Department of Ecology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Institute of Sanitary Engineering, Faculty of Geodetic and Civil Engineering, University of Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Florian M Steiner
- Department of Ecology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria
| | | | - Wolfgang Arthofer
- Department of Ecology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria
| | - Heribert Insam
- Department of Microbiology, Faculty of Biology, University of Innsbruck, Innsbruck, Austria
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87
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Enterococcus faecalis Manganese Exporter MntE Alleviates Manganese Toxicity and Is Required for Mouse Gastrointestinal Colonization. Infect Immun 2020; 88:IAI.00058-20. [PMID: 32229614 DOI: 10.1128/iai.00058-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/21/2020] [Indexed: 01/13/2023] Open
Abstract
Bacterial pathogens encounter a variety of nutritional environments in the human host, including nutrient metal restriction and overload. Uptake of manganese (Mn) is essential for Enterococcus faecalis growth and virulence; however, it is not known how this organism prevents Mn toxicity. In this study, we examine the role of the highly conserved MntE transporter in E. faecalis Mn homeostasis and virulence. We show that inactivation of mntE results in growth restriction in the presence of excess Mn, but not other metals, demonstrating its specific role in Mn detoxification. Upon growth in the presence of excess Mn, an mntE mutant accumulates intracellular Mn, iron (Fe), and magnesium (Mg), supporting a role for MntE in Mn and Fe export and a role for Mg in offsetting Mn toxicity. Growth of the mntE mutant in excess Fe also results in increased levels of intracellular Fe, but not Mn or Mg, providing further support for MntE in Fe efflux. Inactivation of mntE in the presence of excess iron also results in the upregulation of glycerol catabolic genes and enhanced biofilm growth, and addition of glycerol is sufficient to augment biofilm growth for both the mntE mutant and its wild-type parental strain, demonstrating that glycerol availability significantly enhances biofilm formation. Finally, we show that mntE contributes to colonization of the antibiotic-treated mouse gastrointestinal (GI) tract, suggesting that E. faecalis encounters excess Mn in this niche. Collectively, these findings demonstrate that the manganese exporter MntE plays a crucial role in E. faecalis metal homeostasis and virulence.
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88
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Antibiotic Resistance and Virulence Traits in Vancomycin-Resistant Enterococci (VRE) and Extended-Spectrum β-Lactamase/AmpC-producing (ESBL/AmpC) Enterobacteriaceae from Humans and Pets. Antibiotics (Basel) 2020; 9:antibiotics9040152. [PMID: 32244399 PMCID: PMC7235867 DOI: 10.3390/antibiotics9040152] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 01/01/2023] Open
Abstract
Background: We investigated the virulence factors, genes, antibiotic resistance patterns, and genotypes (VRE and ESBL/AmpC) production in Enterococci and Enterobacteriaceae strains isolated from fecal samples of humans, dogs, and cats. Methods: A total of 100 fecal samples from 50 humans, 25 dogs, and 25 cats were used in the study. MICs of nine antimicrobials were determined using the broth microdilution method. Polymerase chain reaction was used for the detection of genes responsible for antibiotic resistance (VRE and ESBL/AmpC) and virulence genes both in Enterococcus species, such as cytolysin (cylA, cylB, cylM), aggregation substance (agg), gelatinase (gelE), enterococcal surface protein (esp), cell wall adhesins (efaAfs and efaAfm), and in Enterobacteriaceae, such as cytolysin (hemolysin) and gelatinase production (afa, cdt, cnf1, hlyA, iutA, papC, sfa). Results: Enterococcus faecium was the most prevalent species in humans and cats, whereas Enterococcus faecalis was the species isolated in the remaining samples. A total of 200 Enterobacteriaceae strains were also detected, mainly from humans, and Escherichia coli was the most frequently isolated species in all types of samples. In the Enterococcus spp, the highest percentages of resistance for ampicillin, amoxicillin/clavulanate, erythromycin, tetracycline, ciprofloxacin, teicoplanin, and vancomycin were detected in cat isolates (41.6%, 52.8%, 38.9%, 23.6%, 62.5%, 20.8%, and 23.6% respectively), and in E. coli, a higher rate of resistance to cefotaxime and ceftazidime emerged in cat and dog samples, if compared with humans (75.4% and 66.0%, 80.0% and 71.4%, and 32.0% and 27.2%, respectively). Regarding the total number of enterococci, 5% and 3.4% of the strains were vancomycin and teicoplanin resistant, and the vancomycin resistance (van A) gene has been detected in all samples by PCR amplification. All the Enterobacteriaceae strains were confirmed as ESBL producers by PCR and sequencing, and the most frequent ESBL genes in E. coli strains from humans and pet samples were blaCTX-M-1 and blaCTX-M-15. Conclusions: Our results provide evidence that one or more virulence factors were present in both genera, underlining again the ability of pet strains to act as pathogens.
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89
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Stein-Thoeringer CK, Nichols KB, Lazrak A, Docampo MD, Slingerland AE, Slingerland JB, Clurman AG, Armijo G, Gomes ALC, Shono Y, Staffas A, Burgos da Silva M, Devlin SM, Markey KA, Bajic D, Pinedo R, Tsakmaklis A, Littmann ER, Pastore A, Taur Y, Monette S, Arcila ME, Pickard AJ, Maloy M, Wright RJ, Amoretti LA, Fontana E, Pham D, Jamal MA, Weber D, Sung AD, Hashimoto D, Scheid C, Xavier JB, Messina JA, Romero K, Lew M, Bush A, Bohannon L, Hayasaka K, Hasegawa Y, Vehreschild MJGT, Cross JR, Ponce DM, Perales MA, Giralt SA, Jenq RR, Teshima T, Holler E, Chao NJ, Pamer EG, Peled JU, van den Brink MRM. Lactose drives Enterococcus expansion to promote graft-versus-host disease. Science 2019; 366:1143-1149. [PMID: 31780560 PMCID: PMC7003985 DOI: 10.1126/science.aax3760] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022]
Abstract
Disruption of intestinal microbial communities appears to underlie many human illnesses, but the mechanisms that promote this dysbiosis and its adverse consequences are poorly understood. In patients who received allogeneic hematopoietic cell transplantation (allo-HCT), we describe a high incidence of enterococcal expansion, which was associated with graft-versus-host disease (GVHD) and mortality. We found that Enterococcus also expands in the mouse gastrointestinal tract after allo-HCT and exacerbates disease severity in gnotobiotic models. Enterococcus growth is dependent on the disaccharide lactose, and dietary lactose depletion attenuates Enterococcus outgrowth and reduces the severity of GVHD in mice. Allo-HCT patients carrying lactose-nonabsorber genotypes showed compromised clearance of postantibiotic Enterococcus domination. We report lactose as a common nutrient that drives expansion of a commensal bacterium that exacerbates an intestinal and systemic inflammatory disease.
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Affiliation(s)
- C K Stein-Thoeringer
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - K B Nichols
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - A Lazrak
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - M D Docampo
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - A E Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - J B Slingerland
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - A G Clurman
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Armijo
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - A L C Gomes
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Y Shono
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - A Staffas
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - M Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - S M Devlin
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - K A Markey
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Bajic
- Department of Internal Medicine II, Technical University of Munich, Munich, Germany
| | - R Pinedo
- Gnotobiotic Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Tsakmaklis
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - E R Littmann
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Section of Infectious Medicine and Global Health, University of Chicago, Chicago, IL, USA
| | - A Pastore
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Taur
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, USA
| | - M E Arcila
- Diagnostic Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A J Pickard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Maloy
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - R J Wright
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - L A Amoretti
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Fontana
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M A Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - D Weber
- Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - A D Sung
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - D Hashimoto
- Department of Hematology, Hokkaido University, Faculty of Medicine, Sapporo, Japan
| | - C Scheid
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - J B Xavier
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J A Messina
- Division of Infectious Diseases, Department of Medicine, Duke University, Durham, NC, USA
| | - K Romero
- Office of Clinical Research, Duke University School of Medicine, Durham, NC, USA
| | - M Lew
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - A Bush
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - L Bohannon
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - K Hayasaka
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Y Hasegawa
- Department of Hematology, Hokkaido University, Faculty of Medicine, Sapporo, Japan
| | - M J G T Vehreschild
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- German Center for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - J R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D M Ponce
- Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M A Perales
- Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S A Giralt
- Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - R R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - T Teshima
- Department of Hematology, Hokkaido University, Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - E Holler
- Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - N J Chao
- Division of Hematologic Malignancies and Cellular Therapy, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - E G Pamer
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Section of Infectious Medicine and Global Health, University of Chicago, Chicago, IL, USA
| | - J U Peled
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M R M van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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90
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Delaplain PT, Bell BA, Wang J, Isani M, Zhang E, Gayer CP, Grishin AV, Ford HR. Effects of artificially introduced Enterococcus faecalis strains in experimental necrotizing enterocolitis. PLoS One 2019; 14:e0216762. [PMID: 31675374 PMCID: PMC6824573 DOI: 10.1371/journal.pone.0216762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 10/20/2019] [Indexed: 01/07/2023] Open
Abstract
Enterococcus faecalis is a ubiquitous intestinal symbiont and common early colonizer of the neonatal gut. Although colonization with E. faecalis has been previously associated with decreased pathology of necrotizing enterocolitis (NEC), these bacteria have been also implicated as opportunistic pathogens. Here we characterized 21 strains of E. faecalis, naturally occurring in 4-day-old rats, for potentially pathogenic properties and ability to colonize the neonatal gut. The strains differed in hemolysis, gelatin liquefaction, antibiotic resistance, biofilm formation, and ability to activate the pro-inflammatory transcription factor NF-κB in cultured enterocytes. Only 3 strains, BB70, 224, and BB24 appreciably colonized the neonatal intestine on day 4 after artificial introduction with the first feeding. The best colonizer, strain BB70, effectively displaced E. faecalis of maternal origin. Whereas BB70 and BB24 significantly increased NEC pathology, strain 224 significantly protected from NEC. Our results show that different strains of E. faecalis may be pathogenic or protective in experimental NEC.
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Affiliation(s)
- Patrick T. Delaplain
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Brandon A. Bell
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Jin Wang
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Mubina Isani
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Emily Zhang
- Shady Side Academy, Pittsburgh, PA, United States of America
| | - Christopher P. Gayer
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Anatoly V. Grishin
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- * E-mail:
| | - Henri R. Ford
- Division of Pediatric Surgery, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
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91
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Leite GGS, Morales W, Weitsman S, Celly S, Parodi G, Mathur R, Sedighi R, Barlow GM, Rezaie A, Pimentel M. Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study. BMC Microbiol 2019; 19:239. [PMID: 31675917 PMCID: PMC6824053 DOI: 10.1186/s12866-019-1617-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 10/20/2019] [Indexed: 12/16/2022] Open
Abstract
Background The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associated methodologies are ill-suited for the viscosity and low microbial biomass of small intestine samples. As part of the REIMAGINE study to examine the specific roles of the small bowel microbiome in human health and disease, this study aimed to develop and validate methodologies to optimize microbial analysis of the small intestine. Results Subjects undergoing esophagogastroduodenoscopy without colon preparation for standard of care were prospectively recruited, and ~ 2 ml samples of luminal fluid were obtained from the duodenum using a custom sterile aspiration catheter. Samples of duodenal aspirates were either untreated (DA-U, N = 127) or pretreated with dithiothreitol (DA-DTT, N = 101), then cultured on MacConkey agar for quantitation of aerobic gram-negative bacteria, typically from the class Gammaproteobacteria, and on blood agar for quantitation of anaerobic microorganisms. DA-DTT exhibited 2.86-fold greater anaerobic bacterial counts compared to DA-U (P = 0.0101), but were not statistically different on MacConkey agar. DNA isolation from DA-U (N = 112) and DA-DTT (N = 43) samples and library preparation for 16S rRNA gene sequencing were also performed using modified protocols. DA-DTT samples exhibited 3.81-fold higher DNA concentrations (P = 0.0014) and 4.18-fold higher 16S library concentrations (P < 0.0001) then DA-U samples. 16S rRNA gene sequencing revealed increases in the detected relative abundances of obligate and facultative anaerobes in DA-DTT samples, including increases in the genera Clostridium (false discovery rate (FDR) P = 4.38E-6), Enterococcus (FDR P = 2.57E-8), Fusobacterium (FDR P = 0.02) and Bacteroides (FDR P = 5.43E-9). Detected levels of Gram-negative enteropathogens from the phylum Proteobacteria, such as Klebsiella (FDR P = 2.73E-6) and Providencia (FDR P < 0.0001) (family Enterobacteriaceae) and Pseudomonas (family Pseudomonadaceae) (FDR P = 0.04), were also increased in DA-DTT samples. Conclusions This study validates novel DTT-based methodology which optimizes microbial culture and 16S rRNA gene sequencing for the study of the small bowel microbiome. The microbial analyses indicate increased isolation of facultative and obligate anaerobes from the mucus layer using these novel techniques.
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Affiliation(s)
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA. .,Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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92
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Exploiting biofilm phenotypes for functional characterization of hypothetical genes in Enterococcus faecalis. NPJ Biofilms Microbiomes 2019; 5:23. [PMID: 31552139 PMCID: PMC6753144 DOI: 10.1038/s41522-019-0099-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/21/2019] [Indexed: 12/12/2022] Open
Abstract
Enterococcus faecalis is a commensal organism as well as an important nosocomial pathogen, and its infections are typically linked to biofilm formation. Nearly 25% of the E. faecalis OG1RF genome encodes hypothetical genes or genes of unknown function. Elucidating their function and how these gene products influence biofilm formation is critical for understanding E. faecalis biology. To identify uncharacterized early biofilm determinants, we performed a genetic screen using an arrayed transposon (Tn) library containing ~2000 mutants in hypothetical genes/intergenic regions and identified eight uncharacterized predicted protein-coding genes required for biofilm formation. We demonstrate that OG1RF_10435 encodes a phosphatase that modulates global protein expression and arginine catabolism and propose renaming this gene bph (biofilm phosphatase). We present a workflow for combining phenotype-driven experimental and computational evaluation of hypothetical gene products in E. faecalis, which can be used to study hypothetical genes required for biofilm formation and other phenotypes of diverse bacteria.
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93
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Salli K, Anglenius H, Hirvonen J, Hibberd AA, Ahonen I, Saarinen MT, Tiihonen K, Maukonen J, Ouwehand AC. The effect of 2'-fucosyllactose on simulated infant gut microbiome and metabolites; a pilot study in comparison to GOS and lactose. Sci Rep 2019; 9:13232. [PMID: 31520068 PMCID: PMC6744565 DOI: 10.1038/s41598-019-49497-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 08/27/2019] [Indexed: 01/01/2023] Open
Abstract
Human milk oligosaccharides (HMOs) shape gut microbiota during infancy by acting as fermentable energy source. Using a semi-continuous colon simulator, effect of an HMO, 2'-fucosyllactose (2'-FL), on composition of the infant microbiota and microbial metabolites was evaluated in comparison to galacto-oligosaccharide (GOS) and lactose and control without additional carbon source. Data was analysed according to faecal sample donor feeding type: breast-fed (BF) or formula-fed (FF), and to rate of 2'-FL fermentation: fast or slow. Variation was found between the simulations in the ability to utilise 2'-FL. The predominant phyla regulated by 2'-FL, GOS and lactose were significant increase in Firmicutes, numerical in Actinobacteria, and numerical decrease in Proteobacteria compared to control. Verrucomicrobia increased in FF accounted for Akkermansia, whereas in fast-fermenting simulations Actinobacteria increased with trend for higher Bifidobacterium, and Proteobacteria decrease accounted for Enterobacteriaceae. Short-chain fatty acids and lactic acid with 2'-FL were produced in intermediate levels being between ones generated by the control and GOS or lactose. In 2'-FL fast-fermenting group, acetic acid specifically increased with 2'-FL, whereas lactose and GOS also increased lactic acid. The results highlight specificity of 2'-FL as energy source for only certain microbes over GOS and lactose in the simulated gut model.
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Affiliation(s)
- Krista Salli
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland.
| | - Heli Anglenius
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland
| | - Johanna Hirvonen
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland
| | - Ashley A Hibberd
- DuPont Nutrition & Biosciences, Genomics & Microbiome Science, Madison, WI, USA
| | | | - Markku T Saarinen
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland
| | - Kirsti Tiihonen
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland
| | - Johanna Maukonen
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland
| | - Arthur C Ouwehand
- DuPont Nutrition & Biosciences, Global Health & Nutrition Science, Kantvik, Finland
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94
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Kerschner H, Cabal A, Hartl R, Machherndl-Spandl S, Allerberger F, Ruppitsch W, Apfalter P. Hospital outbreak caused by linezolid resistant Enterococcus faecium in Upper Austria. Antimicrob Resist Infect Control 2019; 8:150. [PMID: 31516698 PMCID: PMC6732827 DOI: 10.1186/s13756-019-0598-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Enterococcus faecium is part of the human gastrointestinal flora but may act as opportunistic pathogen. Environmental persistence, high colonization capability and diverse intrinsic and acquired resistance mechanisms make it especially successful in nosocomial high-risk settings. In March 2014, an outbreak of Linezolid resistant Enterococcus faecium (LREfm) was observed at the hematooncology department of a tertiary care center in Upper Austria. Methods We report on the outbreak investigation together with the whole genome sequencing (WGS)-based typing results including also non-outbreak LREfm and susceptible isolates. Results The 54 investigated isolates could be divided in six clusters based on cgMLST. Cluster one comprised LREfm isolates of genotype ST117 and CT24, which was identified as the causative clone of the outbreak. In addition, the detection of four other clusters comprising isolates originating from hematooncology patients but also at other hospitals, pointed to LREfm transmission between local healthcare facilities. LREfm patients (n = 36) were typically at risk for acquisition of nosocomial pathogens because of immunosuppression, frequent hospitalization and antibiotic therapies. Seven of these 36 patients developed LREfm infection but were successfully treated. After termination of the initial outbreak, sporadic cases occurred despite a bundle of applied outbreak control interventions. Conclusions WGS proved to be an effective tool to differentiate several LREfm clusters in an outbreak. Active screening for LREfm is important in a high-risk setting such as hematooncology, where multiple introductions are possible and occur despite intensified infection control measures. Electronic supplementary material The online version of this article (10.1186/s13756-019-0598-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Adriana Cabal
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria.,3European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Sigrid Machherndl-Spandl
- Department of Internal Medicine 1, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
| | - Franz Allerberger
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria
| | - Werner Ruppitsch
- AGES - Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Waehringerstrasse 25a, 1090 Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections, Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Fadingerstrasse 1, 4020 Linz, Austria
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95
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Hakkou K, Molina-Pinilla I, Rangel-Núñez C, Suárez-Cruz A, Pajuelo E, Bueno-Martínez M. Synthesis of novel (bio) degradable linear azo polymers conjugated with olsalazine. Polym Degrad Stab 2019. [DOI: 10.1016/j.polymdegradstab.2019.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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96
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Nguyen AH, Miller WR, Arias CA. Shape Follows Function: Gastrointestinal Signals for Enterococcal Colonization. Trends Mol Med 2019; 25:464-466. [PMID: 31109795 DOI: 10.1016/j.molmed.2019.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 01/16/2023]
Abstract
Vancomycin-resistant Enterococcus faecium (VRE) is a major cause of nosocomial infections. A new study by McKenney et al. (Cell Host Microbe 2019;25:695-705.e5) reports that VRE undergo a morphotype switch in response to lithocholic acid (LCA) to facilitate gastrointestinal (GI) tract colonization. This metabolic cue is a potential target to decrease VRE colonization and subsequent transmission of antibiotic resistance.
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Affiliation(s)
- April H Nguyen
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - William R Miller
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Division of Infectious Diseases, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA
| | - Cesar A Arias
- Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Division of Infectious Diseases, University of Texas Health Science Center, McGovern School of Medicine, Houston, TX, USA; Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, TX, USA; Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogotá, Colombia.
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97
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Rehman MA, Yin X, Zaheer R, Goji N, Amoako KK, McAllister T, Pritchard J, Topp E, Diarra MS. Genotypes and Phenotypes of Enterococci Isolated From Broiler Chickens. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00083] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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98
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George F, Daniel C, Thomas M, Singer E, Guilbaud A, Tessier FJ, Revol-Junelles AM, Borges F, Foligné B. Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective. Front Microbiol 2018; 9:2899. [PMID: 30538693 PMCID: PMC6277688 DOI: 10.3389/fmicb.2018.02899] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022] Open
Abstract
Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called "transionts" microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.
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Affiliation(s)
- Fanny George
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Catherine Daniel
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 – UMR 8204 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| | - Muriel Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elisabeth Singer
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Axel Guilbaud
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Frédéric J. Tessier
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
| | - Anne-Marie Revol-Junelles
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Frédéric Borges
- Laboratoire d’Ingénierie des Biomolécules, École Nationale Supérieure d’Agronomie et des Industries Alimentaires – Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Benoît Foligné
- Université de Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International Center, Lille, France
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99
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Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll. Microorganisms 2018; 6:microorganisms6030068. [PMID: 30002322 PMCID: PMC6163277 DOI: 10.3390/microorganisms6030068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/04/2018] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal.
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