scholarly journals Staphylococcus arlettae Genomics: Novel Insights on Candidate Antibiotic Resistance and Virulence Genes in an Emerging Opportunistic Pathogen

2019 ◽  
Vol 7 (11) ◽  
pp. 580 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Rosa Monno ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Molecular Mechanisms ◽  
Genomic Sequence ◽  
Opportunistic Pathogen ◽  
Resistant Isolate ◽  
Virulence Determinants ◽  
Bacterial Strains ◽  
Coagulase Negative Staphylococci ◽  
Outgroup Species ◽  
Manual Selection

Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species Staphylococcus arlettae (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes. By comparing predicted antibiotic resistance and virulence-associated genes with those obtained from a manual selection of 148 bacterial strains belonging to 14 different species of staphylococci and to two “outgroup” species, Bacillus subtilis (BS) and Macrococcus caseoliticus (MC), we derived some interesting observations concerning the types and number of antibiotic resistance-related and virulence-like genes in SAR. Interestingly, almost 50% of the putative antibiotic resistance determinants identified in this work, which include the clinically relevant mec, van, and cls genes, were shared among all the SAR strains herein considered (Bari included). Moreover, comparison of predicted antibiotic resistance profiles suggest that SAR is closely related to well-known pathogenic Staphylococcus species, such as Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE). A similar analysis of predicted virulence factors, revealed that several genes associated with pathogenesis (including, for example, ica, nuc, and ssp), which are commonly found in the genomes of pathogenic staphylococci such as Staphylococcus haemolyticus (SH) and Staphylococcus saprophyticus (SS), are observed also in the SAR strains for which a genomic sequence is available. All in all, we believe that the analyses presented in the current study, by providing a consistent and comprehensive annotation of virulence and antibiotic resistance-related genes in SAR, can constitute a valuable resource for the study of molecular mechanisms of opportunistic pathogenicity in this species.

Development of antibiotic resistance in periprosthetic joint infection after total knee arthroplasty

2021 ◽  
Vol 103-B (6 Supple A) ◽  
pp. 171-176
Author(s):  
Antonio Klasan ◽  
Arne Schermuksnies ◽  
Florian Gerber ◽  
Matt Bowman ◽  
Susanne Fuchs-Winkelmann ◽  
...  
Keyword(s):  
Total Knee Arthroplasty ◽  
Antibiotic Resistance ◽  
Knee Arthroplasty ◽  
Periprosthetic Joint Infection ◽  
Joint Infection ◽  
Revision Arthroplasty ◽  
Bacterial Strains ◽  
Coagulase Negative Staphylococci ◽  
Primary Arthroplasty ◽  
Total Knee

Aims The management of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA) is challenging. The correct antibiotic management remains elusive due to differences in epidemiology and resistance between countries, and reports in the literature. Before the efficacy of surgical treatment is investigated, it is crucial to analyze the bacterial strains causing PJI, especially for patients in whom no organisms are grown. Methods A review of all revision TKAs which were undertaken between 2006 and 2018 in a tertiary referral centre was performed, including all those meeting the consensus criteria for PJI, in which organisms were identified. Using a cluster analysis, three chronological time periods were created. We then evaluated the antibiotic resistance of the identified bacteria between these three clusters and the effectiveness of our antibiotic regime. Results We identified 129 PJIs with 161 culture identified bacteria in 97 patients. Coagulase-negative staphylococci (CNS) were identified in 46.6% cultures, followed by Staphylococcus aureus in 19.8%. The overall resistance to antibiotics did not increase significantly during the study period (p = 0.454). However, CNS resistance to teicoplanin (p < 0.001), fosfomycin (p = 0.016), and tetracycline (p = 0.014) increased significantly. Vancomycin had an 84.4% overall sensitivity and 100% CNS sensitivity and was the most effective agent. Conclusion Although we were unable to show an overall increase in antibiotic resistance in organisms that cause PJI after TKA during the study period, this was not true for CNS. It is concerning that resistance of CNS to new antibiotics, but not vancomycin, has increased in a little more than a decade. Our findings suggest that referral centres should continuously monitor their bacteriological analyses, as these have significant implications for prophylactic treatment in both primary arthroplasty and revision arthroplasty for PJI. Cite this article: Bone Joint J 2021;103-B(6 Supple A):171–176.

Proteomic Analyses Uncover the Mechanisms Underlying Antibiotic Resistance Differences among Three Acinetobacter baumannii Isolates

2016 ◽  
Vol 26 (6) ◽  
pp. 401-409 ◽  
Author(s):  
Junrui Wang ◽  
Junli Zhang ◽  
Quan Fu ◽  
Sufang Guo ◽  
La Ta ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Molecular Mechanisms ◽  
Carbapenem Resistance ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Absolute Quantification ◽  
Functional Enrichment ◽  
Resistant Isolate ◽  
Gentamicin Resistance

This study aimed to investigate the molecular mechanisms underlying the antibiotic resistance difference among three <i>Acinetobacter baumannii</i> isolates. Fifty <i>A. baumannii</i> isolates were first subjected to an antimicrobial susceptibility test, then three isolates differing in antibiotic resistance were selected and subjected to iTRAQ (isobaric tags for relative and absolute quantification)-based proteomics analysis. Differential proteins among the three <i>A. baumannii</i> isolates were further identified and subjected to gene ontology functional enrichment analysis. A resistant isolate (A1), a less resistant one (A8) and a susceptible one (A9) were selected. In total, there were 424 differentially expressed proteins (DEPs) between the A1 and A8 isolates, 1,992 DEPs between the A9 and A1 isolates, and 1,956 DEPs between the A8 and A9 isolates. The upregulation of I6TUC8 and Q0GA83 in the A1 and A8 isolates may be responsible for their higher resistance to ceftriaxone. The higher gentamicin resistance of <i>A. baumannii</i> isolates A1 and A8 when compared to A9 may be related to the higher expression levels of O05286 and D0CCK1, while the higher Q2FCY1 expression level may contribute more to strong gentamicin resistance in A1. The higher levels of L9LWL7, L9MDB0, K9C9W3, E2IGU7, B6E129, G8HYR7, D2XTB0 and D2XTB0 may be responsible for the higher carbapenem resistance of isolate A1 as compared to A8.

scholarly journals Review on Multiple Facets of Drug Resistance: A Rising Challenge in the 21st Century

2021 ◽  
Vol 11 (4) ◽  
pp. 197-214
Author(s):  
Mousumi Saha ◽  
Agniswar Sarkar
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Molecular Mechanisms ◽  
In Silico Analysis ◽  
Relevant Information ◽  
High Rate ◽  
Resistant Bacteria ◽  
Bacterial Strains ◽  
Potential Threat

With the advancements of science, antibiotics have emerged as an amazing gift to the human and animal healthcare sectors for the treatment of bacterial infections and other diseases. However, the evolution of new bacterial strains, along with excessive use and reckless consumption of antibiotics have led to the unfolding of antibiotic resistances to an excessive level. Multidrug resistance is a potential threat worldwide, and is escalating at an extremely high rate. Information related to drug resistance, and its regulation and control are still very little. To interpret the onset of antibiotic resistances, investigation on molecular analysis of resistance genes, their distribution and mechanisms are urgently required. Fine-tuned research and resistance profile regarding ESKAPE pathogen is also necessary along with other multidrug resistant bacteria. In the present scenario, the interaction of bacterial infections with SARS-CoV-2 is also crucial. Tracking and in-silico analysis of various resistance mechanisms or gene/s are crucial for overcoming the problem, and thus, the maintenance of relevant databases and wise use of antibiotics should be promoted. Creating awareness of this critical situation among individuals at every level is important to strengthen the fight against this fast-growing calamity. The review aimed to provide detailed information on antibiotic resistance, its regulatory molecular mechanisms responsible for the resistance, and other relevant information. In this article, we tried to focus on the correlation between antimicrobial resistance and the COVID-19 pandemic. This study will help in developing new interventions, potential approaches, and strategies to handle the complexity of antibiotic resistance and prevent the incidences of life-threatening infections.

scholarly journals Bis-Thiourea Quaternary Ammonium Salts as Potential Agents against Bacterial Strains from Food and Environmental Matrices

Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1466
Author(s):  
Maria Grazia Bonomo ◽  
Teresa Giura ◽  
Giovanni Salzano ◽  
Pasquale Longo ◽  
Annaluisa Mariconda ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Molecular Mechanisms ◽  
Action Spectrum ◽  
Environmental Matrices ◽  
Bacterial Strains ◽  
Thiourea Derivatives ◽  
Small Series ◽  
Antibiotic Drugs ◽  
Agar Well Diffusion Assay

In recent years, the phenomenon of antibiotic resistance in hospitals, communities and the environment has increasingly grown, so antibiotic resistance has become an urgent problem that requires a decisive and global intervention. Incorrect/unnecessary use of antibiotics contributes to increase the ability of microorganisms to develop resistance faster and faster. Research efforts must, therefore, be made to ensure a future in which antibiotic drugs will still be useful in combating infectious diseases. The search for new antibacterial compounds is fundamental. In this study, the antimicrobial activity of the compounds was evaluated against selected bacterial strains from food and environmental matrices by using the Agar Well Diffusion Assay. A total of thirty-six Gram-positive and Gram-negative bacteria were employed to determine the action spectrum and the antimicrobial effectiveness of a small series of thiourea derivatives. Results showed that the highest activities were found for compounds 1 and 4. The important role of the alkyl chain length and/or guanidine moiety in the width of action spectrum was evidenced. Further studies will allow evaluating the efficacy of the inhibiting action and the molecular mechanisms underlying this activity in order to identify compounds capable of counteracting the phenomenon of antibiotic resistance and to identify possible future applications of these newly synthesized compounds that have shown a high bactericidal action potential.

scholarly journals Antibacterial properties of capsaicin and its derivatives and their potential to fight antibiotic resistance – A literature survey

2021 ◽  
Author(s):  
Samuel Füchtbauer ◽  
Soraya Mousavi ◽  
Stefan Bereswill ◽  
Markus M. Heimesaat
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Molecular Mechanisms ◽  
Antibacterial Properties ◽  
Treatment Strategies ◽  
Natural Compounds ◽  
Literature Survey ◽  
Bacterial Strains ◽  
Antibacterial Effects

AbstractAntibiotic resistance is endangering public health globally and gives reason for constant fear of virtually intractable bacterial infections. Given a limitation of novel antibiotic classes brought to market in perspective, it is indispensable to explore novel, antibiotics-independent ways to fight bacterial infections. In consequence, the antibacterial properties of natural compounds have gained increasing attention in pharmacological sciences. We here performed a literature survey regarding the antibacterial effects of capsaicin and its derivatives constituting natural compounds of chili peppers. The studies included revealed that the compounds under investigation exerted i.) both direct and indirect antibacterial properties in vitro depending on the applied concentrations and the bacterial strains under investigation; ii.) synergistic antibacterial effects in combination with defined antibiotics; iii.) resistance-modification via inhibition of bacterial efflux pumps; iv.) attenuation of bacterial virulence factor expression; and v.) dampening of pathogen-induced immunopathological responses. In conclusion, capsaicin and its derivatives comprise promising antimicrobial molecules which could complement or replace antibiotic treatment strategies to fight bacterial infections. However, a solid basis for subsequent clinical trials requires future investigations to explore the underlying molecular mechanisms and in particular pharmaceutical evaluations in animal infection models.

scholarly journals Exacerbations of Chronic Rhinosinusitis—Microbiology and Perspectives of Phage Therapy

Antibiotics ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 175 ◽  
Author(s):  
Szaleniec ◽  
Gibała ◽  
Pobiega ◽  
Parasion ◽  
Składzień ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Chronic Rhinosinusitis ◽  
Phage Therapy ◽  
Specific Treatment ◽  
Bacterial Strains ◽  
Coagulase Negative Staphylococci ◽  
Antibiotic Resistant ◽  
First Choice ◽  
Acute Bacterial Rhinosinusitis ◽  
Resistant Strains

The chronically inflamed mucosa in patients with chronic rhinosinusitis (CRS) can additionally be infected by bacteria, which results in an acute exacerbation of the disease (AECRS). Currently, AECRS is universally treated with antibiotics following the guidelines for acute bacterial rhinosinusitis (ABRS), as our understanding of its microbiology is insufficient to establish specific treatment recommendations. Unfortunately, antibiotics frequently fail to control the symptoms of AECRS due to biofilm formation, disruption of the natural microbiota, and arising antibiotic resistance. These issues can potentially be addressed by phage therapy. In this study, the endoscopically-guided cultures were postoperatively obtained from 50 patients in order to explore the microbiology of AECRS, evaluate options for antibiotic treatment, and, most importantly, assess a possibility of efficient phage therapy. Staphylococcus aureus and coagulase-negative staphylococci were the most frequently isolated bacteria, followed by Haemophilus influenzae, Pseudomonas aeruginosa, and Enterobacteriaceae. Alarmingly, mechanisms of antibiotic resistance were detected in the isolates from 46% of the patients. Bacteria not sensitive to amoxicillin were carried by 28% of the patients. The lowest rates of resistance were noted for fluoroquinolones and aminoglycosides. Fortunately, 60% of the patients carried bacterial strains that were sensitive to bacteriophages from the Biophage Pharma collection and 81% of the antibiotic-resistant strains turned out to be sensitive to bacteriophages. The results showed that microbiology of AECRS is distinct from ABRS and amoxicillin should not be the antibiotic of first choice. Currently available bacteriophages could be used instead of antibiotics or as an adjunct to antibiotics in the majority of patients with AECRS.

scholarly journals 2187

2017 ◽  
Vol 1 (S1) ◽  
pp. 25-25
Author(s):  
Marissa Valentine-King ◽  
Mary B. Brown
Keyword(s):  
Antibiotic Resistance ◽  
Molecular Mechanisms ◽  
Pcr Amplification ◽  
Tetracycline Resistance ◽  
Mycoplasma Hominis ◽  
Quinolone Resistance ◽  
Resistant Isolate ◽  
Tract Infections ◽  
First Time ◽  
Ureaplasma Spp

OBJECTIVES/SPECIFIC AIMS: Urinary tract infections (UTIs) serve as one of the most common infections affecting women. With rising reports of antibiotic resistance (ABR), which can prolong illness and limit treatment options, the Infectious Disease Society of America recommends using local resistance patterns to shape empirical treatment selection. Although no studies have evaluated ABR in Ureaplasma spp. urinary isolates in college-aged women, regional studies in the Southeast United States have found levels of tetracycline resistance in over 30% of Ureaplasma spp. clinical isolates. Thus, this study aims to determine the antibiogram for 73 Ureaplasma spp. and 10 Mycoplasma hominis isolates collected from women with first-time UTI against a panel of 9 antibiotics, and assess resistant isolates for genetic mechanisms associated with resistance. METHODS/STUDY POPULATION: This study used archival samples and data collected from college-aged women with first-time UTI recruited to participate in a prospective cohort study conducted at a student healthcare facility from 2001 to 2006 in Florida. Ureaplasma spp. and M. hominis isolates cultured from urine samples collected at the initial clinical presentation and for any recurrent UTI were evaluated for susceptibility to a panel of 9 antibiotics (8 for M. hominis) using validated microbroth and agar dilution methods, respectively. Ureaplasma spp. isolates were tested against azithromycin, chloramphenicol, ciprofloxacin, clindamycin, erythromycin, doxycycline, gentamicin, levofloxacin, and tetracycline. M. hominis isolates underwent the same testing, with the addition of linezolid and exclusion of azithromycin and erythromycin, as M. hominis is intrinsically resistance to 14 and 15-membered macrolides and azilides. PCR and Sanger sequencing were employed to identify molecular mechanisms associated with resistance. RESULTS/ANTICIPATED RESULTS: Of the 73 Ureaplasma spp. isolates, 1 isolate was resistant to levofloxacin (MIC: 4 µg/mL) and 1 to tetracycline (MIC: 8 µg/mL). All M. hominis isolates were sensitive. For the Ureaplasma spp. isolates, MIC90s were highest against gentamicin (32 µg/mL) and lowest against doxycycline (0.25 µg/mL). PCR amplification identified tetM present in the tetracycline resistant isolate, an established gene associated with tetracycline resistance in Ureaplasma spp. A S83W mutation within the quinolone-resistance-determining region (QRDR) of parC was detected in the levofloxacin resistant isolate. DISCUSSION/SIGNIFICANCE OF IMPACT: Overall, antibiotic resistance in this population of college-aged women with first-time UTI was low. A previous study detected a novel S83W substitution in a perinatal Ureaplasma spp. isolate from Japan, and provided in silico evidence that a S83W change would prevent levofloxacin from binding to its target. However, that study was unable to cultivate the isolate. Our study has provided the corresponding phenotypic evidence that a S83W substitution results in quinolone resistance in Ureaplasma spp.

Artificial Intelligence for epigenetics: towards personalized medicine

2020 ◽  
Vol 27 ◽  
Author(s):  
Giulia De Riso ◽  
Sergio Cocozza
Keyword(s):  
Biological Sciences ◽  
Artificial Intelligence ◽  
Personalized Medicine ◽  
Molecular Mechanisms ◽  
Genomic Sequence ◽  
Health Care Interventions ◽  
Genome Wide ◽  
Genetic And Environmental Factors ◽  
Opening Up ◽  
Omic Data

: Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mechanisms, that is in turn orchestrated by genetic and environmental factors. The epigenetic profile captures the unique regulatory landscape and the exposure to environmental stimuli of an individual. It thus constitutes a valuable reservoir of information for personalized medicine, which is aimed at customizing health-care interventions based on the unique characteristics of each individual. Nowadays, the complex milieu of epigenomic marks can be studied at the genome-wide level thanks to massive, highthroughput technologies. This new experimental approach is opening up new and interesting knowledge perspectives. However, the analysis of these complex omic data requires to face important analytic issues. Artificial Intelligence, and in particular Machine Learning, are emerging as powerful resources to decipher epigenomic data. In this review, we will first describe the most used ML approaches in epigenomics. We then will recapitulate some of the recent applications of ML to epigenomic analysis. Finally, we will provide some examples of how the ML approach to epigenetic data can be useful for personalized medicine.

scholarly journals Transfer of Plasmid DNA to Clinical Coagulase-Negative Staphylococcal Pathogens by Using a Unique Bacteriophage

2015 ◽  
Vol 81 (7) ◽  
pp. 2481-2488 ◽  
Author(s):  
Volker Winstel ◽  
Petra Kühner ◽  
Bernhard Krismer ◽  
Andreas Peschel ◽  
Holger Rohde
Keyword(s):  
Plasmid Dna ◽  
Genetic Manipulation ◽  
Current Knowledge ◽  
Virulence Determinants ◽  
Coagulase Negative Staphylococci ◽  
Reliable Technique ◽  
Content Type ◽  
Research Activities ◽  
Wide Range ◽  
Genetic Barriers

ABSTRACTGenetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a uniqueStaphylococcus aureusstrain via a specificS. aureusbacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinicalStaphylococcus epidermidisisolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.

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