NastyBugs: A simple method for extracting antimicrobial resistance information from metagenomes

Multidrug resistant bacteria are becoming a major threat to global public health. While there are many possible causes for this, there have so far been few adequate solutions to this problem. One of the major causes is a lack of clinical tools for efficient selection of an antibiotic in a reliable way. NastyBugs is a new program that can identify what type of antimicrobial resistance is most likely present in a metagenomic sample, which will allow for both smarter drug selection by clinicians and faster research in an academic environment.

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Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application

Microorganisms ◽

10.3390/microorganisms9050885 ◽

2021 ◽

Vol 9 (5) ◽

pp. 885

Author(s):

Dorcas Oladayo Fatoba ◽

Akebe Luther King Abia ◽

Daniel G. Amoako ◽

Sabiha Y. Essack

Keyword(s):

Antimicrobial Resistance ◽

Agricultural Soil ◽

Multidrug Resistant ◽

Diffusion Method ◽

Resistant Bacteria ◽

Manure Application ◽

Unamended Soil ◽

Enterococcus Spp ◽

Chicken Litter ◽

Amended Soil

The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert®/Quanti-Tray 2000® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 107 MPN/g) than unamended soil (2.89 × 107 MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.

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Liposomes as Antibiotic Delivery Systems: A Promising Nanotechnological Strategy against Antimicrobial Resistance

Molecules ◽

10.3390/molecules26072047 ◽

2021 ◽

Vol 26 (7) ◽

pp. 2047

Author(s):

Magda Ferreira ◽

Maria Ogren ◽

Joana N. R. Dias ◽

Marta Silva ◽

Solange Gil ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Bacterial Infections ◽

Private Investment ◽

Therapeutic Index ◽

Multidrug Resistant ◽

Current Treatment ◽

Delivery Systems ◽

Resistant Bacteria ◽

Bacterial Cells ◽

Antimicrobial Drugs

Antimicrobial drugs are key tools to prevent and treat bacterial infections. Despite the early success of antibiotics, the current treatment of bacterial infections faces serious challenges due to the emergence and spread of resistant bacteria. Moreover, the decline of research and private investment in new antibiotics further aggravates this antibiotic crisis era. Overcoming the complexity of antimicrobial resistance must go beyond the search of new classes of antibiotics and include the development of alternative solutions. The evolution of nanomedicine has allowed the design of new drug delivery systems with improved therapeutic index for the incorporated compounds. One of the most promising strategies is their association to lipid-based delivery (nano)systems. A drug’s encapsulation in liposomes has been demonstrated to increase its accumulation at the infection site, minimizing drug toxicity and protecting the antibiotic from peripheral degradation. In addition, liposomes may be designed to fuse with bacterial cells, holding the potential to overcome antimicrobial resistance and biofilm formation and constituting a promising solution for the treatment of potential fatal multidrug-resistant bacterial infections, such as methicillin resistant Staphylococcus aureus. In this review, we aim to address the applicability of antibiotic encapsulated liposomes as an effective therapeutic strategy for bacterial infections.

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Technologies to address antimicrobial resistance

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1717160115 ◽

2018 ◽

Vol 115 (51) ◽

pp. 12887-12895 ◽

Cited By ~ 47

Author(s):

Stephen J. Baker ◽

David J. Payne ◽

Rino Rappuoli ◽

Ennio De Gregorio

Keyword(s):

Antimicrobial Resistance ◽

Bacterial Infections ◽

Membrane Vesicles ◽

Multidrug Resistant ◽

Outer Membrane Vesicles ◽

Resistant Bacteria ◽

Multiple Stakeholders ◽

Global Challenge ◽

Life Threatening ◽

Bacterial Outer Membrane

Bacterial infections have been traditionally controlled by antibiotics and vaccines, and these approaches have greatly improved health and longevity. However, multiple stakeholders are declaring that the lack of new interventions is putting our ability to prevent and treat bacterial infections at risk. Vaccine and antibiotic approaches still have the potential to address this threat. Innovative vaccine technologies, such as reverse vaccinology, novel adjuvants, and rationally designed bacterial outer membrane vesicles, together with progress in polysaccharide conjugation and antigen design, have the potential to boost the development of vaccines targeting several classes of multidrug-resistant bacteria. Furthermore, new approaches to deliver small-molecule antibacterials into bacteria, such as hijacking active uptake pathways and potentiator approaches, along with a focus on alternative modalities, such as targeting host factors, blocking bacterial virulence factors, monoclonal antibodies, and microbiome interventions, all have potential. Both vaccines and antibacterial approaches are needed to tackle the global challenge of antimicrobial resistance (AMR), and both areas have the underpinning science to address this need. However, a concerted research agenda and rethinking of the value society puts on interventions that save lives, by preventing or treating life-threatening bacterial infections, are needed to bring these ideas to fruition.

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Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens

BioMed Research International ◽

10.1155/2016/2475067 ◽

2016 ◽

Vol 2016 ◽

pp. 1-8 ◽

Cited By ~ 324

Author(s):

Sirijan Santajit ◽

Nitaya Indrawattana

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Resistance Mechanisms ◽

Global Public Health ◽

Drug Usage ◽

Inappropriate Use ◽

Public Health Challenges ◽

Eskape Pathogens

The ESKAPE pathogens (Enterococcus faecium,Staphylococcus aureus,Klebsiella pneumoniae,Acinetobacter baumannii,Pseudomonas aeruginosa, andEnterobacterspecies) are the leading cause of nosocomial infections throughout the world. Most of them are multidrug resistant isolates, which is one of the greatest challenges in clinical practice. Multidrug resistance is amongst the top three threats to global public health and is usually caused by excessive drug usage or prescription, inappropriate use of antimicrobials, and substandard pharmaceuticals. Understanding the resistance mechanisms of these bacteria is crucial for the development of novel antimicrobial agents or other alternative tools to combat these public health challenges. Greater mechanistic understanding would also aid in the prediction of underlying or even unknown mechanisms of resistance, which could be applied to other emerging multidrug resistant pathogens. In this review, we summarize the known antimicrobial resistance mechanisms of ESKAPE pathogens.

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Retail Chicken Carcasses as a Reservoir of Antimicrobial- Resistant Escherichia coli

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0115 ◽

2020 ◽

Author(s):

Nahla Omer Eltai ◽

Hadi M. Yassine ◽

Sara H. Al-Hadidi ◽

Tahra ElObied ◽

Asmaa A. Al Thani ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Growth Promotion ◽

Multidrug Resistant ◽

Chicken Meat ◽

Resistant Bacteria ◽

Antibiotic Resistant ◽

E Coli ◽

Inappropriate Use ◽

Esbl Producers

The dissemination of antimicrobial resistance (AMR) bacteria has been associated with the inappropriate use of antibiotics in both humans and animals and with the consumption of food contaminated with resistant bacteria. In particular, the use of antibiotics as prophylactic and growth promotion purposes in food-producing animals has rendered many of the antibiotics ineffective. The increased global prevalence of AMR poses a significant threat to the safety of the world’s food supply. Objectives: This study aims at determining the prevalence of antibiotic-resistant Escherichia coli (E. coli) isolated from local and imported retail chicken meat in Qatar. Methodology: A total of 270 whole chicken carcasses were obtained from three different hypermarket stores in Qatar. A total of 216 E. coli were isolated and subjected to antibiotic susceptibility testing against 18 relevant antibiotics using disc diffusion and micro- dilution methods. Furthermore, extended-spectrum β-lactamase (ESBL) production was determined via a double-disc synergetic test. Isolates harboring colistin resistance were confirmed using multiplex-PCR and DNA sequencing. Results: Nearly 89% (192/216) of the isolates were resistant to at least one antibiotics. In general, isolates showed relatively higher resistance to sulfamethoxazole (62%), tetracycline (59.7%), ampicillin and trimethoprim (52.3%), ciprofloxacin (47.7%), cephalothin, and colistin (31.9%). On the other hand, less resistance was recorded against amoxicillin/clavulanic acid (6%), ceftriaxone (5.1%), nitrofurantoin (4.2%) and piperacillin/tazobactam (4.2%), cefepime (2.3%), meropenem (1.4%), ertapenem (0.9%), and amikacin (0.9%). Nine isolates (4.2%) were ESBL producers. Furthermore, 63.4% were multidrug-resistant (MDR). The percentage of MDR, ESBL producers, and colistin-resistant isolates was significantly higher among local isolates compared to imported chicken samples. Conclusion: We reported a remarkably high percentage of the antibiotic-resistant E. coli in chicken meat sold at retail in Qatar. The high percentage of MDR and colistin isolates is troublesome to the food safety of raw chicken meat and the potential of antibiotic resistance spread to public health. Our findings support the need for the implementation of one health approach to address the spread of antimicrobial resistance and the need for a collaborative solution.

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Synthesis, Structure Elucidation, Antibacterial Activities, and Synergistic Effects of Novel Juglone and Naphthazarin Derivatives Against Clinical Methicillin-Resistant Staphylococcus aureus Strains

Frontiers in Chemistry ◽

10.3389/fchem.2021.773981 ◽

2021 ◽

Vol 9 ◽

Author(s):

Valentin Duvauchelle ◽

Chaimae Majdi ◽

David Bénimélis ◽

Catherine Dunyach-Remy ◽

Patrick Meffre ◽

...

Keyword(s):

Synergistic Effects ◽

Antibacterial Properties ◽

Clinical Importance ◽

Antibacterial Activities ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Global Public Health ◽

Gram Positive ◽

Drug Resistant Bacteria ◽

Mrsa Strains

Infections caused by drug-resistant bacteria are a serious threat to human and global public health. Moreover, in recent years, very few antibiotics have been discovered and developed by pharmaceutical companies. Therefore, there is an urgent need to discover and develop new antibacterial agents to combat multidrug-resistant bacteria. In this study, two novel series of juglone/naphthazarin derivatives (43 compounds) were synthesized and evaluated for their antibacterial properties against various clinical and reference Gram-positive MSSA, clinical Gram-positive MRSA, and clinical and reference Gram-negative bacteria E. coli and P. aeruginosa. These strains are of clinical importance because they belong to ESKAPE pathogens. Compounds 3al, 5ag, and 3bg showed promising activity against clinical and reference MSSA (MIC: 1–8 µg/ml) and good efficacy against clinical MRSA (MIC: 2–8 µg/ml) strains. 5am and 3bm demonstrated better activity on both MSSA (MIC: 0.5 µg/ml) and MRSA (MIC: 2 µg/ml) strains. Their MICs were similar to those of cloxacillin against clinical MRSA strains. The synergistic effects of active compounds 3al, 5ag, 5am, 3bg, and 3bm were evaluated with reference antibiotics, and it was found that the antibiotic combination with 3bm efficiently enhanced the antimicrobial activity. Compound 3bm was found to restore the sensitivity of clinical MRSA to cloxacillin and enhanced the antibacterial activity of vancomycin when they were added together. In the presence of 3bm, the MIC values of vancomycin and cloxacillin were lowered up to 1/16th of the original MIC with an FIC index of 0.313. Moreover, compounds 3al, 5ag, 5am, 3bg, and 3bm did not present hemolytic activity on sheep red blood cells. In silico prediction of ADME profile parameter results for 3bm is promising and encouraging for further development.

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Multidrug Resistant and Extensively Drug Resistant Bacteria: A Study

Journal of Pathogens ◽

10.1155/2016/4065603 ◽

2016 ◽

Vol 2016 ◽

pp. 1-5 ◽

Cited By ~ 46

Author(s):

Silpi Basak ◽

Priyanka Singh ◽

Monali Rajurkar

Keyword(s):

Antimicrobial Resistance ◽

Antibiotic Susceptibility ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Close Monitoring ◽

Care Hospital ◽

Drug Resistant ◽

Bacterial Isolates ◽

Bacterial Strains ◽

Extensively Drug Resistant

Background and Objective. Antimicrobial resistance is now a major challenge to clinicians for treating patients. Hence, this short term study was undertaken to detect the incidence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR) bacterial isolates in a tertiary care hospital.Material and Methods. The clinical samples were cultured and bacterial strains were identified in the department of microbiology. The antibiotic susceptibility profile of different bacterial isolates was studied to detect MDR, XDR, and PDR bacteria.Results. The antibiotic susceptibility profile of 1060 bacterial strains was studied. 393 (37.1%) bacterial strains were MDR, 146 (13.8%) strains were XDR, and no PDR was isolated. All (100%) Gram negative bacterial strains were sensitive to colistin whereas all (100%) Gram positive bacterial strains were sensitive to vancomycin.Conclusion. Close monitoring of MDR, XDR, or even PDR must be done by all clinical microbiology laboratories to implement effective measures to reduce the menace of antimicrobial resistance.

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Combination Therapy as a Strategy to control Infections caused by Multiresistant Bacteria. Current Review

Current Drug Targets ◽

10.2174/1389450122666210614122352 ◽

2021 ◽

Vol 22 ◽

Author(s):

Patricia Hernandez-Rodriguez ◽

Ludy Pabon Baquero

Keyword(s):

Antimicrobial Resistance ◽

Selective Pressure ◽

Combined Therapy ◽

Multidrug Resistant ◽

Multiple Infections ◽

Resistant Bacteria ◽

Infectious Disease Control ◽

Current Review ◽

Multiresistant Bacteria ◽

Bibliographic Search

: Antimicrobial resistance (AMR) is one of the main challenges of today's medicine because it has become a global problem that affects the treatment of multiple infections and impacts public health. This resistance is caused because the bacteria have generated selective pressure promoting mechanisms to evade the action of conventional drugs, which are also associated with adverse effects. Infections caused by these multi-resistant bacteria potentially reduce the possibility of effective therapy; this situation increases morbidity and mortality and treatment costs. To establish combined therapy as a strategy for the control of infections caused by multi-resistant bacteria. A bibliographic search was carried out between 2015 and 2020 in databases such as PubMed, Scopus and Science Direct. The exhaustive review of the articles allowed a critical analysis of the information. They have identified the mechanisms for obtaining drugs with antimicrobial potential, their biological activity and the possible effect of their combination against multidrug-resistant bacteria as an alternative for infectious disease control and as a response to reduce the use of antibiotics. Combined therapy is presented as an innovative therapeutic alternative, which uses non-antibiotic substances that can be obtained by three routes: the repositioning of drugs, synthetic substances and natural products. In this way, important elements are provided to guide researches who seek to reduce antimicrobial resistance.

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Genome Sequence of Resistant Serratia sp. Strain HRI, Isolated from a Bottle of Didecyldimethylammonium Chloride-Based Disinfectant

Microbiology Resource Announcements ◽

10.1128/mra.00095-20 ◽

2020 ◽

Vol 9 (18) ◽

Author(s):

Samantha J. Mc Carlie ◽

Julius E. Hellmuth ◽

Jeffrey Newman ◽

Charlotte E. Boucher ◽

Robert R. Bragg

Keyword(s):

Antimicrobial Resistance ◽

Genome Sequence ◽

Bacterial Infections ◽

Multidrug Resistant ◽

Whole Genome Sequence ◽

Resistant Isolate ◽

Resistant Bacteria ◽

Hybrid Assembly ◽

Pacbio Sequencing ◽

Didecyldimethylammonium Chloride

Antimicrobial resistance is a significant issue, and it threatens the prevention and effective treatment of a range of bacterial infections. Here, we report the whole-genome sequence of the multidrug-resistant isolate Serratia sp. strain HRI. A hybrid assembly was created using sequences from a first (MiSeq) and second (PacBio) sequencing run. This work is imperative for understanding antimicrobial resistance and adds to the knowledge base for combating multidrug-resistant bacteria.

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Bacteriocins of Gram-positive bacteria having activity spectra extending beyond closely-related species

Beneficial Microbes ◽

10.3920/bm2018.0126 ◽

2019 ◽

Vol 10 (3) ◽

pp. 315-328 ◽

Cited By ~ 17

Author(s):

S.D. Todorov ◽

B.D.G. de Melo Franco ◽

J.R. Tagg

Keyword(s):

Critical Points ◽

Anticancer Agents ◽

Multidrug Resistant ◽

Food Preservation ◽

Resistant Bacteria ◽

Closely Related Species ◽

Gram Positive Bacteria ◽

Activity Spectrum ◽

Novel Applications ◽

Selection Of

Bacteriocins are bacterially-produced antimicrobial peptides that have killing activity principally against other relatively closely-related bacteria. Some bacteriocins of the lactic acid bacteria (LAB) have for many years been extensively applied in food biopreservation. However, especially during the last decade, a number of reports have appeared about unanticipated extensions to the generally rather narrow anti-bacterial activity spectrum of some of the LAB bacteriocins and novel applications have been proposed for bacteriocins ranging from controlling the growth of an increasingly-heterogeneous variety of pathogens, including Gram-negative multidrug resistant bacteria, viruses, yeasts, and in particular, difficult to control Mycobacterium spp., to their potential application as anticancer agents. How best can we assess this now rapidly-accumulating stream of reports on potential future applications of bacteriocins? Where is the line between realistic, science-based proposals and highly-speculative fiction and what are the ‘critical points’ that might help us to draw this line? In this review, we have attempted to analyse a selection of the presently-available data concerning relatively ‘unorthodox’ (i.e. beyond food preservation) applications of bacteriocins, and, by utilising our set of ‘critical points’, we endeavour to identify essential or/and missing information that appear crucial for success of the proposed applications.

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