scholarly journals Analysis of Identification Method for Bacterial Species and Antibiotic Resistance Genes Using Optical Data From DNA Oligomers

2020 ◽  
Vol 11 ◽  
Author(s):  
Ryan L. Wood ◽  
Tanner Jensen ◽  
Cindi Wadsworth ◽  
Mark Clement ◽  
Prashant Nagpal ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Optical Data ◽  
Dna Oligomers ◽  
Identification Method

scholarly journals Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhaoyan Chen ◽  
Hang Cheng ◽  
Zhao Cai ◽  
Qingjun Wei ◽  
Jinlong Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Community ◽  
Pleural Effusion ◽  
Resistance Genes ◽  
Antimicrobial Therapy ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Pleural Empyema ◽  
Sequencing Platform ◽  
Core Species

Identification of the offending organism and appropriate antimicrobial therapy are crucial for treating empyema. Diagnosis of empyema is largely obscured by the conventional bacterial cultivation and PCR process that has relatively low sensitivity, leading to limited understanding of the etiopathogenesis, microbiology, and role of antibiotics in the pleural cavity. To expand our understanding of its pathophysiology, we have carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure. Our results showed that the variation of microbiota in the pleural effusion is generally stratified, not continuous. There are two distinct microbiome clusters observed in the forty-five samples: HA-SA type and LA-SA type. The categorization is mostly driven by species composition: HA-SA type is marked by Staphylococcus aureus as the core species, with other enriched 6 bacteria and 3 fungi, forming a low diversity and highly stable microbial community; whereas the LA-SA type has a more diverse microbial community with a distinct set of bacterial species that are assumed to be the oral origin. The microbial community does not shape the dominant antibiotic resistance classes which were common in the two types, while the increase of microbial diversity was correlated with the increase in antibiotic resistance genes. The existence of well-balanced microbial symbiotic states might respond differently to pathogen colonization and drug intake. This study provides a deeper understanding of the pathobiology of pleural empyema and suggests that potential resistance genes may hinder the antimicrobial therapy of empyema.

scholarly journals Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids

2011 ◽  
Vol 7 (6) ◽  
pp. 902-905 ◽  
Author(s):  
Matti Jalasvuori ◽  
Ville-Petri Friman ◽  
Anne Nieminen ◽  
Jaana K. H. Bamford ◽  
Angus Buckling
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Low Frequency ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Bacterial Cells ◽  
Antibiotic Resistant ◽  
Resistance Plasmids ◽  
Resistant Mutants

Antibiotic-resistance genes are often carried by conjugative plasmids, which spread within and between bacterial species. It has long been recognized that some viruses of bacteria (bacteriophage; phage) have evolved to infect and kill plasmid-harbouring cells. This raises a question: can phages cause the loss of plasmid-associated antibiotic resistance by selecting for plasmid-free bacteria, or can bacteria or plasmids evolve resistance to phages in other ways? Here, we show that multiple antibiotic-resistance genes containing plasmids are stably maintained in both Escherichia coli and Salmonella enterica in the absence of phages, while plasmid-dependent phage PRD1 causes a dramatic reduction in the frequency of antibiotic-resistant bacteria. The loss of antibiotic resistance in cells initially harbouring RP4 plasmid was shown to result from evolution of phage resistance where bacterial cells expelled their plasmid (and hence the suitable receptor for phages). Phages also selected for a low frequency of plasmid-containing, phage-resistant bacteria, presumably as a result of modification of the plasmid-encoded receptor. However, these double-resistant mutants had a growth cost compared with phage-resistant but antibiotic-susceptible mutants and were unable to conjugate. These results suggest that bacteriophages could play a significant role in restricting the spread of plasmid-encoded antibiotic resistance.

scholarly journals Analytical Performance of Multiplexed Screening Test for 10 Antibiotic Resistance Genes from Perianal Swab Samples

2016 ◽  
Vol 62 (2) ◽  
pp. 353-359 ◽  
Author(s):  
G Terrance Walker ◽  
Tony J Rockweiler ◽  
Rossio K Kersey ◽  
Kelly L Frye ◽  
Susan R Mitchner ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Test Performance ◽  
Health Care Systems ◽  
Bacterial Species ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Gene Test

Abstract BACKGROUND Multiantibiotic-resistant bacteria pose a threat to patients and place an economic burden on health care systems. Carbapenem-resistant bacilli and extended-spectrum β-lactamase (ESBL) producers drive the need to screen infected and colonized patients for patient management and infection control. METHODS We describe a multiplex microfluidic PCR test for perianal swab samples (Acuitas® MDRO Gene Test, OpGen) that detects the vancomycin-resistance gene vanA plus hundreds of gene subtypes from the carbapenemase and ESBL families Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), Verona integron-mediated metallo-β-lactamase (VIM), imipenemase metallo-β-lactamase (IMP), OXA-23, OXA-48, OXA-51, CTX-M-1, and CTX-M-2, regardless of the bacterial species harboring the antibiotic resistance. RESULTS Analytical test sensitivity per perianal swab is 11–250 CFU of bacteria harboring the antibiotic resistance genes. Test throughput is 182 samples per test run (1820 antibiotic resistance gene family results). We demonstrate reproducible test performance and 100% gene specificity for 265 clinical bacterial organisms harboring a variety of antibiotic resistance genes. CONCLUSIONS The Acuitas MDRO Gene Test is a sensitive, specific, and high-throughput test to screen colonized patients and diagnose infections for several antibiotic resistance genes directly from perianal swab samples, regardless of the bacterial species harboring the resistance genes.

scholarly journals Class 1 Integrons Potentially Predating the Association with Tn402-Like Transposition Genes Are Present in a Sediment Microbial Community

2006 ◽  
Vol 188 (16) ◽  
pp. 5722-5730 ◽  
Author(s):  
H. W. Stokes ◽  
Camilla L. Nesbø ◽  
Marita Holley ◽  
Martin I. Bahl ◽  
Michael R. Gillings ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Global Scale ◽  
Human Pathogens ◽  
Class 1 Integrons ◽  
Recombination System ◽  
Class 1

ABSTRACT Integrons are genetic elements that contribute to lateral gene transfer in bacteria as a consequence of possessing a site-specific recombination system. This system facilitates the spread of genes when they are part of mobile cassettes. Most integrons are contained within chromosomes and are confined to specific bacterial lineages. However, this is not the case for class 1 integrons, which were the first to be identified and are one of the single biggest contributors to multidrug-resistant nosocomial infections, carrying resistance to many antibiotics in diverse pathogens on a global scale. The rapid spread of class 1 integrons in the last 60 years is partly a result of their association with a specific suite of transposition functions, which has facilitated their recruitment by plasmids and other transposons. The widespread use of antibiotics has acted as a positive selection pressure for bacteria, especially pathogens, which harbor class 1 integrons and their associated antibiotic resistance genes. Here, we have isolated bacteria from soil and sediment in the absence of antibiotic selection. Class 1 integrons were recovered from four different bacterial species not known to be human pathogens or commensals. All four integrons lacked the transposition genes previously considered to be a characteristic of this class. At least two of these integrons were located on a chromosome, and none of them possessed antibiotic resistance genes. We conclude that novel class 1 integrons are present in a sediment environment in various bacteria of the β-proteobacterial class. These data suggest that the dispersal of this class may have begun before the “antibiotic era.”

scholarly journals Increased whiB7 Expression and Antibiotic Resistance in Mycobacterium Chelonae Carrying Two Prophages

2021 ◽  
Author(s):  
Jaycee Cushman ◽  
Emma Freeman ◽  
Sarah McCallister ◽  
Anna Schumann ◽  
Keith Hutchison ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Virulence Gene ◽  
Mycobacterium Chelonae ◽  
Viral Genomes ◽  
Global Increase ◽  
First Time ◽  
Insight Into

Abstract Background: The global increase in the incidence of non-tuberculosis mycobacterial infections is of increasing concern due their high levels of intrinsic antibiotic resistance. Although integrated viral genomes, called prophage, are linked to increased antibiotic resistance in some bacterial species, we know little of their role in mycobacterial drug resistance. Results: We present here for the first time evidence of increased antibiotic resistance and expression of intrinsic antibiotic resistance genes in a strain of Mycobacterium chelonae carrying prophage. Strains carrying the prophage McProf demonstrated increased resistance to amikacin. Resistance in these strains was further enhanced by exposure to sub-inhibitory concentrations of the antibiotic, acivicin, or by the presence of a second prophage, BPs. Increased expression of the virulence gene, whiB7, was observed in strains carrying both prophage, BPs and McProf, relative to strains carrying a single prophage or no prophages. Conclusions: This study provides evidence that prophage alter expression of important mycobacterial intrinsic antibiotic resistance genes and additionally offers insight into the role prophage may play in mycobacterial adaptation to stress.

scholarly journals Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

2018 ◽  
Author(s):  
Bálint Kintses ◽  
Orsolya Méhi ◽  
Eszter Ari ◽  
Mónika Számel ◽  
Ádám Györkei ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Horizontal Transfer ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Genetic Exchange ◽  
Human Gut ◽  
Human Gut Microbiota

AbstractThe human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs) that are ancient components of immune defence. Despite important medical relevance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here we show that AMP- and antibiotic-resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics revealed that AMP resistance genes originating from phylogenetically distant bacteria only have a limited potential to confer resistance inEscherichia coli, an intrinsically susceptible species. Third, the phenotypic impact of acquired AMP resistance genes heavily depends on the genetic background of the recipient bacteria. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota with implications for disease risks.

scholarly journals Detection of antibiotic-resistant bacteria and their resistance genes from houseflies

2020 ◽  
Vol 13 (2) ◽  
pp. 266-274 ◽  
Author(s):  
Sharmin Akter ◽  
Abdullah Al Momen Sabuj ◽  
Zobayda Farzana Haque ◽  
Md. Tanvir Rahman ◽  
Md. Abdul Kafi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Animal Health ◽  
Antibiotic Resistance Genes ◽  
Diffusion Method ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Salmonella Spp ◽  
Antibiotic Resistant

Background and Aim: Houseflies (Musca domestica) are synanthropic insects which serve as biological or mechanical vectors for spreading multidrug-resistant bacteria responsible for many infectious diseases. This study aimed to detect antibiotic-resistant bacteria from houseflies, and to examine their resistance genes. Materials and Methods: A total of 140 houseflies were captured using sterile nylon net from seven places of Mymensingh city, Bangladesh. Immediately after collection, flies were transferred to a sterile zipper bag and brought to microbiology laboratory within 1 h. Three bacterial species were isolated from houseflies, based on cultural and molecular tests. After that, the isolates were subjected to antimicrobial susceptibility testing against commonly used antibiotics, by the disk diffusion method. Finally, the detection of antibiotic resistance genes tetA, tetB, mcr-3, mecA, and mecC was performed by a polymerase chain reaction. Results: The most common isolates were Staphylococcus aureus (78.6%), Salmonella spp., (66.4%), and Escherichia coli (51.4%). These species of bacteria were recovered from 78.3% of isolates from the Mymensingh Medical College Hospital areas. Most of the isolates of the three bacterial species were resistant to erythromycin, tetracycline, penicillin and amoxicillin and were sensitive to ciprofloxacin, ceftriaxone, chloramphenicol, gentamicin, and azithromycin. Five antibiotic resistance genes of three bacteria were detected: tetA, tetB, mcr-3, and mecA were found in 37%, 20%, 20%, and 14% isolates, respectively, and no isolates were positive for mecC gene. Conclusion: S. aureus, Salmonella spp., and E. coli with genetically-mediated multiple antibiotic resistance are carried in houseflies in the Mymensingh region. Flies may, therefore, represent an important means of transmission of these antibiotic-resistant bacteria, with consequent risks to human and animal health.

scholarly journals Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates

2020 ◽  
Vol 8 (10) ◽  
pp. 1522
Author(s):  
Pamela Afouda ◽  
Grégory Dubourg ◽  
Anthony Levasseur ◽  
Pierre-Edouard Fournier ◽  
Jeremy Delerce ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Bacterial Species ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Genome Comparison ◽  
Antibiotics Use ◽  
High Level

Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.

scholarly journals Increased whiB7 expression and antibiotic resistance in Mycobacterium chelonae carrying two prophages

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jaycee Cushman ◽  
Emma Freeman ◽  
Sarah McCallister ◽  
Anna Schumann ◽  
Keith W. Hutchison ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Virulence Gene ◽  
Mycobacterium Chelonae ◽  
Mycobacterial Infections ◽  
Viral Genomes ◽  
First Time ◽  
Insight Into

Abstract Background The global rise in the incidence of non-tuberculosis mycobacterial infections is of increasing concern due their high levels of intrinsic antibiotic resistance. Although integrated viral genomes, called prophage, are linked to increased antibiotic resistance in some bacterial species, we know little of their role in mycobacterial drug resistance. Results We present here for the first time, evidence of increased antibiotic resistance and expression of intrinsic antibiotic resistance genes in a strain of Mycobacterium chelonae carrying prophage. Strains carrying the prophage McProf demonstrated increased resistance to amikacin. Resistance in these strains was further enhanced by exposure to sub-inhibitory concentrations of the antibiotic, acivicin, or by the presence of a second prophage, BPs. Increased expression of the virulence gene, whiB7, was observed in strains carrying both prophages, BPs and McProf, relative to strains carrying a single prophage or no prophages. Conclusions This study provides evidence that prophage alter expression of important mycobacterial intrinsic antibiotic resistance genes and additionally offers insight into the role prophage may play in mycobacterial adaptation to stress.

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