scholarly journals Antibiotic treatment at delivery shapes the initial oral microbiome in neonates

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Luisa F. Gomez-Arango ◽  
Helen L. Barrett ◽  
H. David. McIntyre ◽  
Leonie K. Callaway ◽  
Mark Morrison ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Treatment ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Obese Mother ◽  
Health And Disease ◽  
Intrapartum Antibiotic ◽  
Oral Microorganisms

Abstract Oral microorganisms are important determinants of health and disease. The source of the initial neonatal microbiome and the factors dictating initial human oral microbiota development are unknown. This study aimed to investigate this in placental, oral and gut microbiome profiles from 36 overweight or obese mother-baby dyads as determined by 16S rRNA sequencing. Expression of five antibiotic resistance genes of the β-lactamase class was analysed in the infant oral microbiota samples by QPCR. The neonatal oral microbiota was 65.35% of maternal oral, 3.09% of placental, 31.56% of unknown and 0% of maternal gut origin. Two distinct neonatal oral microbiota profiles were observed: one strongly resembling the maternal oral microbiota and one with less similarity. Maternal exposure to intrapartum antibiotics explained the segregation of the profiles. Families belonging to Proteobacteria were abundant after antibiotics exposure while the families Streptococcaceae, Gemellaceae and Lactobacillales dominated in unexposed neonates. 26% of exposed neonates expressed the Vim-1 antibiotic resistance gene. These findings indicate that maternal intrapartum antibiotic treatment is a key regulator of the initial neonatal oral microbiome.

scholarly journals Ontology-Aware Deep Learning Enables Novel Antibiotic Resistance Gene Discovery Towards Comprehensive Profiling of ARGs

2021 ◽  
Author(s):  
Yuguo Zha ◽  
Cheng Chen ◽  
Qihong Jiao ◽  
Xiaomei Zeng ◽  
Xuefeng Cui ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Deep Learning ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Oral Microbiome ◽  
Gram Positive Bacteria ◽  
Wet Lab ◽  
Deep Learning Model

Antibiotic resistance genes (ARGs) have emerged in pathogens and spread faster than expected, arousing a worldwide concern. Current methods are suitable mainly for the discovery of close homologous ARGs and have limited utility for discovery of novel ARGs, thus rendering the profiling of ARGs incomprehensive. Here, an ontology-aware deep learning model, ONN4ARG (http://onn4arg.xfcui.com/), is proposed for the discovery of novel ARGs based on multi-level annotations. Experiments based on billions of candidate microbial genes collected from various environments show the superiority of ONN4ARG in comprehensive ARG profiling. Enrichment analyses show that ARGs are both environment-specific and host-specific. For example, resistance genes for rifamycin, which is an important antibacterial agent active against gram-positive bacteria, are enriched in Actinobacteria and in soil environment. Case studies verified ONN4ARG's ability for novel ARG discovery. For example, a novel streptomycin resistance gene was discovered from oral microbiome samples and validated through wet-lab experiments. ONN4ARG provides a complete picture of the prevalence of ARGs in microbial communities as well as guidance for detection and reduction of the spread of resistance genes.

scholarly journals Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 230
Author(s):  
Shan Wan ◽  
Min Xia ◽  
Jie Tao ◽  
Yanjun Pang ◽  
Fugen Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Pathogen Transmission ◽  
Transmission Risk ◽  
Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

scholarly journals Nitric oxide (NO) elicits aminoglycoside tolerance in Escherichia coli but antibiotic resistance gene carriage and NO sensitivity have not co-evolved

2021 ◽  
Author(s):  
Cláudia A. Ribeiro ◽  
Luke A. Rahman ◽  
Louis G. Holmes ◽  
Ayrianna M. Woody ◽  
Calum M. Webster ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Antibiotic Resistance ◽  
Antibiotic Susceptibility ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Current Work ◽  
E Coli ◽  
Respiratory Inhibitor

AbstractThe spread of multidrug-resistance in Gram-negative bacterial pathogens presents a major clinical challenge, and new approaches are required to combat these organisms. Nitric oxide (NO) is a well-known antimicrobial that is produced by the immune system in response to infection, and numerous studies have demonstrated that NO is a respiratory inhibitor with both bacteriostatic and bactericidal properties. However, given that loss of aerobic respiratory complexes is known to diminish antibiotic efficacy, it was hypothesised that the potent respiratory inhibitor NO would elicit similar effects. Indeed, the current work demonstrates that pre-exposure to NO-releasers elicits a > tenfold increase in IC50 for gentamicin against pathogenic E. coli (i.e. a huge decrease in lethality). It was therefore hypothesised that hyper-sensitivity to NO may have arisen in bacterial pathogens and that this trait could promote the acquisition of antibiotic-resistance mechanisms through enabling cells to persist in the presence of toxic levels of antibiotic. To test this hypothesis, genomics and microbiological approaches were used to screen a collection of E. coli clinical isolates for antibiotic susceptibility and NO tolerance, although the data did not support a correlation between increased carriage of antibiotic resistance genes and NO tolerance. However, the current work has important implications for how antibiotic susceptibility might be measured in future (i.e. ± NO) and underlines the evolutionary advantage for bacterial pathogens to maintain tolerance to toxic levels of NO.

scholarly journals OTUs clustering should be avoided for defining oral microbiome

2021 ◽  
Author(s):  
Alba Regueira-Iglesias ◽  
Lara Vazquez-Gonzalez ◽  
Carlos Balsa-Castro ◽  
Triana Blanco-Pintos ◽  
Victor Manuel Arce ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Operational Taxonomic Unit ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
High Coverage ◽  
Archaeal Species ◽  
Health And Disease ◽  
Similarity Relationships

This in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated. Based on the SC-NASI≥97% values, the best primer pairs were OP_F053-KP_R020 for bacteria (65.05%), KP_F018-KP_R002 for archaea (51.11%), and OP_F114-KP_R031 for bacteria and archaea together (52.02%). Eighty percent of the oral-bacteria and oral-archaea species shared an ASI≥97% with at least one other taxa, including Campylobacter, Rothia, Streptococcus, and Tannerella, which played conflicting roles in the oral microbiota. Moreover, around a quarter and a third of these two-by-two similarity relationships were between species from different bacteria and archaea genera, respectively. Furthermore, even taxa from distinct families, orders, and classes could be grouped in the same cluster. Consequently, irrespective of the primer pair used, OTUs constructed with a 97% similarity provide an inaccurate description of oral-bacterial and oral-archaeal species, greatly affecting microbial diversity parameters. As a result, clustering by OTUs impacts the credibility of the associations between some oral species and certain health and disease conditions. This limits significantly the comparability of the microbial diversity findings reported in oral microbiome literature.

scholarly journals Antimicrobial Resistance and CRISPR Typing Among Salmonella Isolates From Poultry Farms in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Cui Li ◽  
Yulong Wang ◽  
Yufeng Gao ◽  
Chao Li ◽  
Boheng Ma ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Direct Repeat ◽  
Epidemiological Data ◽  
Multidrug Resistant ◽  
Typing Method ◽  
Crispr Locus ◽  
Research Areas

Although knowledge of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been applied in many research areas, comprehensive studies of this system in Salmonella, particularly in analysis of antibiotic resistance, have not been reported. In this work, 75 Salmonella isolates obtained from broilers or broilers products were characterized to determine their antimicrobial susceptibilities, antibiotic resistance gene profiles, and CRISPR array diversities, and genotyping was explored. In total, 80.00% (60/75) of the strains were multidrug resistant, and the main pattern observed in the isolates was CN-AZM-AMP-AMC-CAZ-CIP-ATM-TE-SXT-FOS-C. The resistance genes of streptomycin (aadA), phenicol (floR-like and catB3-like), β-lactams (blaTEM, blaOXA, and blaCTX), tetracycline [tet(A)-like], and sulfonamides (sul1 and sul2) appeared at higher frequencies among the corresponding resistant isolates. Subsequently, we analyzed the CRISPR arrays and found 517 unique spacer sequences and 31 unique direct repeat sequences. Based on the CRISPR spacer sequences, we developed a novel typing method, CRISPR locus three spacer sequences typing (CLTSST), to help identify sources of Salmonella outbreaks especially correlated with epidemiological data. Compared with multi-locus sequence typing (MLST), conventional CRISPR typing (CCT), and CRISPR locus spacer pair typing (CLSPT), discrimination using CLTSST was weaker than that using CCT but stronger than that using MLST and CLSPT. In addition, we also found that there were no close correlations between CRISPR loci and antibiotics but had close correlations between CRISPR loci and antibiotic resistance genes in Salmonella isolates.

scholarly journals Deep analysis and optimization of CARD antibiotic resistance gene discovery models

BMC Genomics ◽  
2019 ◽  
Vol 20 (S10) ◽  
Author(s):  
Haobin Yao ◽  
Siu-Ming Yiu
Keyword(s):  
Antibiotic Resistance ◽  
Human Health ◽  
Resistance Gene ◽  
Decision Model ◽  
Antibiotic Resistance Gene ◽  
Gene Discovery ◽  
Antibiotic Resistance Genes ◽  
Optimization Method ◽  
Depth Analysis ◽  
Card Model

Abstract Background Identification of antibiotic resistance genes from environmental samples has been a critical sub-domain of gene discovery which is directly connected to human health. However, it is drawing extraordinary attention in recent years and regarded as a severe threat to human health by many institutions around the world. To satisfy the needs for efficient ARG discovery, a series of online antibiotic resistance gene databases have been published. This article will conduct an in-depth analysis of CARD, one of the most widely used ARG databases. Results The decision model of CARD is based the alignment score with a single ARG type. We discover the occasions where the model is likely to make false prediction, and then propose an optimization method on top of the current CARD model. The optimization is expected to raise the coherence with BLAST homology relationships and improve the confidence for identification of ARGs using the database. Conclusions The absence of public recognized benchmark makes it challenging to evaluate the performance of ARG identification. However, possible wrong predictions and methods for resolving the problem can be inferred by computational analysis of the identification method and the underlying reference sequences. We hope our work can bring insight to the mission of precise ARG type classifications.

scholarly journals Removal of Antibiotic Resistance Gene-Carrying Plasmids from Lactobacillus reuteri ATCC 55730 and Characterization of the Resulting Daughter Strain, L. reuteri DSM 17938

2008 ◽  
Vol 74 (19) ◽  
pp. 6032-6040 ◽  
Author(s):  
Anna Rosander ◽  
Eamonn Connolly ◽  
Stefan Roos
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Lactobacillus Reuteri ◽  
Antibiotic Resistance Gene ◽  
Genetically Modify ◽  
Antibiotic Resistance Genes ◽  
Probiotic Strain ◽  
Probiotic Properties ◽  
Food Borne

ABSTRACT The spread of antibiotic resistance in pathogens is primarily a consequence of the indiscriminate use of antibiotics, but there is concern that food-borne lactic acid bacteria may act as reservoirs of antibiotic resistance genes when distributed in large doses to the gastrointestinal tract. Lactobacillus reuteri ATCC 55730 is a commercially available probiotic strain which has been found to harbor potentially transferable resistance genes. The aims of this study were to define the location and nature of β-lactam, tetracycline, and lincosamide resistance determinants and, if they were found to be acquired, attempt to remove them from the strain by methods that do not genetically modify the organism before subsequently testing whether the probiotic characteristics were retained. No known β-lactam resistance genes was found, but penicillin-binding proteins from ATCC 55730, two additional resistant strains, and three sensitive strains of L. reuteri were sequenced and comparatively analyzed. The β-lactam resistance in ATCC 55730 is probably caused by a number of alterations in the corresponding genes and can be regarded as not transferable. The strain was found to harbor two plasmids carrying tet(W) tetracycline and lnu(A) lincosamide resistance genes, respectively. A new daughter strain, L. reuteri DSM 17938, was derived from ATCC 55730 by removal of the two plasmids, and it was shown to have lost the resistances associated with them. Direct comparison of the parent and daughter strains for a series of in vitro properties and in a human clinical trial confirmed the retained probiotic properties of the daughter strain.

scholarly journals Genomic and Functional Analyses of SXT, an Integrating Antibiotic Resistance Gene Transfer Element Derived from Vibrio cholerae

2002 ◽  
Vol 184 (15) ◽  
pp. 4259-4269 ◽  
Author(s):  
John W. Beaber ◽  
Bianca Hochhut ◽  
Matthew K. Waldor
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Amino Acid Sequences ◽  
Conjugation System ◽  
Conjugative Transposons ◽  
The One ◽  
Functional Analyses

ABSTRACT SXT is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. In recent years, SXT-related conjugative, self-transmissible integrating elements have become widespread in Asian Vibrio cholerae. We have determined the 100-kb DNA sequence of SXT. This element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many genes from unknown sources. We constructed a nearly comprehensive set of deletions through the use of the one-step chromosomal gene inactivation technique to identify SXT genes involved in conjugative transfer and chromosomal excision. SXT, unlike other conjugative transposons, utilizes a conjugation system related to that encoded by the F plasmid. More than half of the SXT genome, including the composite transposon-like structure that contains its antibiotic resistance genes, was not required for its mobility. Two SXT loci, designated setC and setD, whose predicted amino acid sequences were similar to those of the flagellar regulators FlhC and FlhD, were found to encode regulators that activate the transcription of genes required for SXT excision and transfer. Another locus, designated setR, whose gene product bears similarity to lambdoid phage CI repressors, also appears to regulate SXT gene expression.

scholarly journals Development of a DNA Microarray for Enterococcal Species, Virulence, and Antibiotic Resistance Gene Determinations among Isolates from Poultry

2011 ◽  
Vol 77 (8) ◽  
pp. 2625-2633 ◽  
Author(s):  
J. Champagne ◽  
M. S. Diarra ◽  
H. Rempel ◽  
E. Topp ◽  
C. W. Greer ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Dna Microarray ◽  
Virulence Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Content Type ◽  
Virulence Potential ◽  
Enterococcal Species ◽  
Species Specific ◽  
Simultaneous Identification

ABSTRACTA DNA microarray (Enteroarray) was designed with probes targeting four species-specific taxonomic identifiers to discriminate among 18 different enterococcal species, while other probes were designed to identify 18 virulence factors and 174 antibiotic resistance genes. In total, 262 genes were utilized for rapid species identification of enterococcal isolates, while characterizing their virulence potential through the simultaneous identification of endogenous antibiotic resistance and virulence genes. Enterococcal isolates from broiler chicken farms were initially identified by using the API 20 Strep system, and the results were compared to those obtained with the taxonomic genesatpA,recA,pheS, andddlrepresented on our microarray. Among the 171 isolates studied, five different enterococcal species were identified by using the API 20 Strep system:Enterococcus faecium,E. faecalis,E. durans,E. gallinarum, andE. avium. The Enteroarray detected the same species as API 20 Strep, as well as two more:E. casseliflavusandE. hirae. Species comparisons resulted in 15% (27 isolates) disagreement between the two methods among the five API 20 Strep identifiable species and 24% (42 isolates) disagreement when considering the seven Enteroarray identified species. The species specificity of key antibiotic and virulence genes identified by the Enteroarray were consistent with the literature adding further robustness to the redundant taxonomic probe data. Sequencing of thecpn60gene further confirmed the complete accuracy of the microarray results. The new Enteroarray should prove to be a useful tool to accurately genotype strains of enterococci and assess their virulence potential.

scholarly journals Molecular Analysis of Antibiotic Resistance Gene Clusters in Vibrio cholerae O139 and O1 SXT Constins

2001 ◽  
Vol 45 (11) ◽  
pp. 2991-3000 ◽  
Author(s):  
Bianca Hochhut ◽  
Yasmin Lotfi ◽  
Didier Mazel ◽  
Shah M. Faruque ◽  
Roger Woodgate ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Dna Sequences ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Vibrio Cholerae O139 ◽  
El Tor

ABSTRACT Many recent Asian clinical Vibrio cholerae E1 Tor O1 and O139 isolates are resistant to the antibiotics sulfamethoxazole (Su), trimethoprim (Tm), chloramphenicol (Cm), and streptomycin (Sm). The corresponding resistance genes are located on large conjugative elements (SXT constins) that are integrated into prfC on the V. cholerae chromosome. We determined the DNA sequences of the antibiotic resistance genes in the SXT constin in MO10, an O139 isolate. In SXTMO10, these genes are clustered within a composite transposon-like structure found near the element's 5′ end. The genes conferring resistance to Cm (floR), Su (sulII), and Sm (strA and strB) correspond to previously described genes, whereas the gene conferring resistance to Tm, designated dfr18, is novel. In some other O139 isolates the antibiotic resistance gene cluster was found to be deleted from the SXT-related constin. The El Tor O1 SXT constin, SXTET, does not contain the same resistance genes as SXTMO10. In this constin, the Tm resistance determinant was located nearly 70 kbp away from the other resistance genes and found in a novel type of integron that constitutes a fourth class of resistance integrons. These studies indicate that there is considerable flux in the antibiotic resistance genes found in the SXT family of constins and point to a model for the evolution of these related mobile elements.

Sign in / Sign up

Export Citation Format

Share Document