Are we living in an antibiotic resistance nightmare?

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families

CRISPR-Cas is a widespread anti-viral adaptive immune system in the microorganisms. Viruses living in bacteria or some phages carry anti-CRISPR proteins to evade immunity by CRISPR-Cas. The anti-CRISPR proteins are prevalent in phages capable of lying dormant in a CRISPR-carrying host, while their orthologs frequently found in virulent phages. Here, we propose a probabilistic strategy of ancestral sequence reconstruction (ASR) and Hidden Markov Model (HMM) profile search to fish out sequences of anti-CRISPR proteins from environmental metagenomic, human microbiome metagenomic, human microbiome reference genome, and NCBI's non-redundant databases. Our results revealed that the metagenome database dark matter might contain anti-CRISPR encoding genes.

3D bioprinting of nanoparticle-laden hydrogel scaffolds with enhanced antibacterial and imaging properties

Biomaterial-associated microbial contaminations in biologically conducive three-dimensional (3D) tissue-engineered constructs have significantly limited the clinical applications of scaffold systems. To prevent such infections, antimicrobial biomaterials are rapidly evolving. Yet, the use of such materials in bioprinting-based approaches of scaffold fabrication has not been examined. This study introduces a new generation of bacteriostatic gelatin methacryloyl (GelMA)-based bioinks, incorporated with varying doses of antibacterial superparamagnetic iron oxide nanoparticles (SPIONs). The SPION-laden GelMA scaffolds showed significant resistance against the Staphylococcus aureus growth, while providing a contrast in magnetic resonance imaging. We simulated the bacterial contamination of cellular 3D GelMA scaffolds in vitro and demonstrated the significant effect of functionalized scaffolds in inhibiting bacterial growth, while maintaining cell viability and growth. Together, these results present a new promising class of functionalized bioinks to 3D bioprint tissue-engineered scaffold with markedly enhanced properties for the use in a variety of in vitro and clinical applications.

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Functionalized bioinks with bacteriostatic properties are developed and thoroughly characterized

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The 200 μg/mL group yielded an optimal balance of printed scaffold properties

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Incorporating nanoparticle also enabled noninvasive imaging of the bioprinted scaffold

MXene-based hybrid composites as photocatalyst for the mitigation of pharmaceuticals

Environmental contamination is a burning issue and has gained global attention in the present era. Pharmaceuticals are emerging contaminants affecting the natural environment worldwide owing to their extensive consumption particularly in developing countries where self-medication is a common practice. These pharmaceuticals or their degraded active metabolites enter water bodies via different channels and are continuous threat to the whole ecological system. There is a dire need to find efficient approaches for their removal from all environmental matrices. Photocatalysis is one of the most effective and simple approach, however, finding a suitable photocatalyst is a challenging task. Recently, MXenes (two-dimensional transition metal carbides/nitrides), a relatively new material has attracted increasing interest as photocatalysts due to their exceptional properties, such as large surface area, appreciable safety, huge interlayer spacing, thermal conductivity, and environmental flexibility. This review describes the recent advancements of MXene-based composites and their photocatalytic potential for the elimination of pharmaceuticals. Furthermore, present limitations and future research requirements are recommended to attain more benefits of MXene-based composites for the purification of wastewater.

Epidemiology of mobile colistin resistance (mcr) genes in aquatic environments

Colistin is one of the last-line therapies against multidrug-resistant Gram-negative pathogens, especially carbapenemase-producing isolates, making resistance to this compound a major global public-health crisis. Until recently, colistin resistance in Gram-negative bacteria was known to arise only by chromosomal mutations. However, a plasmid-mediated colistin resistance mechanism was described in late 2015. This mechanism is encoded by different mobile colistin resistance (mcr) genes that encode phosphoethanolamine (pEtN) transferases. These enzymes catalyse the addition of a pEtN moiety to lipid A in the bacterial outer membrane leading to colistin resistance. MCR-producing Gram-negative bacteria have been largely disseminated worldwide. However, their environmental dissemination has been underestimated. Indeed, water environments act as a connecting medium between different environments, allowing them to play a crucial role in the spread of antibiotic resistance between the natural environment and humans and other animals. For a better understanding of the role of such environments as reservoirs and/or dissemination routes of mcr genes, this review discusses primarily the various water habitats contributing to the spread of antibiotic resistance. Thereafter, we provide an overview of existing knowledge regarding the global epidemiology of mcr genes in water environments. This review confirms the global distribution of mcr genes in several water environments, including wastewater from different origins, surface water and tap water, making these environments reservoirs and dissemination routes of concern for this resistance mechanism.

Antibiotic resistance surveillance systems: A review

OBJECTIVES

Epidemiological surveillance is one critical approach to estimate and fight the burden of antibiotic resistance (AR). Here we summarise the characteristics of surveillance systems devoted to the surveillance of AR worldwide and published in the literature.

METHODS

We performed a systematic review of the literature available on PubMed from January 2007 to July 2019 (12.5 years). The keywords ('surveillance system' OR 'laboratory-based surveillance' OR 'syndromic surveillance' OR 'sentinel surveillance' OR 'integrated surveillance' OR 'population-based surveillance') AND ('antibiotic resistance' OR 'antimicrobial resistance') were used. This research was completed with AR monitoring systems available on websites.

RESULTS

We identified 71 AR surveillance systems described by 90 publications from 35 countries, including 64 (90.1%) national and 7 (9.9%) multinational surveillance systems. Two regions accounted for ∼72% of systems: European region (37; 52.1%) and Region of the Americas (14; 19.7%). Fifty-three focused on AR surveillance in humans, 12 studied both humans and animals, and 6 focused only on animals. The two most common bacterial species reported were Staphylococcus aureus (42; 59.2%) and Escherichia coli (39; 54.9%). Of the 71 AR surveillance systems, 20 (28.2%) used prevalence as an indicator, 3 (4.2%) used incidence and 7 (9.9%) used both. Methicillin-resistant S. aureus (MRSA), vancomycin-resistant Enterococcus spp., S. aureus and Streptococcus pneumoniae, penicillin-resistant S. pneumoniae, and extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant E. coli and Klebsiella pneumoniae were monitored.

CONCLUSIONS

Our results showed heterogeneous surveillance systems. A 'One Health' approach is needed to monitor AR, with reference to the WHO Global Action Plan.

Inactivation of thymidine kinase as a cause of resistance to zidovudine in clinical isolates of Escherichia coli: a phenotypic and genomic study

Objectives

The antiviral zidovudine has been recently identified as an active drug against resistant Enterobacteriaceae, but prevalence of resistance to this compound remains unknown. The aim was to estimate the prevalence of clinical Escherichia coli isolates resistant to zidovudine and to decipher the mechanism of zidovudine resistance.

Methods

We screened 537 isolates on zidovudine-containing agar plates and studied their thymidine kinase (tdk) gene sequences, the putative target involved in zidovudine resistance. Moreover, sequence analysis of 633 complete genomes of E. coli was performed to investigate mutation in the tdk gene. A comparative genomic analysis was done on an in vitro zidovudine-resistant mutant.

Results

After screening on our medium containing 2.7 mg/L (10 μM) zidovudine, nine strains had a zidovudine MIC >26.7 mg/L. The gene was absent in three isolates, inactivated by an IS (IS1X2 and ISApl1) in two isolates and mutated in four isolates. A genomic analysis of 633 E. coli genomes showed heterogeneity of the tdk gene sequence, with 27 different sequences. Among them, three genomes showed an inactivation of the gene (IS, stop codon and no tdk gene sequence). The in vitro mutant E. coli had 27 SNPs in eight genes of the core genome compared with the initial strain.

Conclusions

Our study reports zidovudine-resistant clinical isolates of E. coli, presumably related to tdk inactivation. Diversity of Tdk in bacterial genomes can be large. Other mechanisms need to be considered in zidovudine resistance. The use of zidovudine in antibiotic-resistant infections needs to be in combination and should be tested before clinical administration.

Hechtia glomerata Zucc: Phytochemistry and Activity of Its Extracts and Major Constituents Against Resistant Bacteria

Hechtia glomerata Zucc. is used both as a source of food and in ethnomedicine to treat various diseases derived from bacterial infections such as bronchitis, laryngitis, nephritis, whooping cough, urethritis, and sepsis. There are no previous reports about its chemistry and biological activities. Therefore, the aims of this study were to identify components from organic and aqueous extracts of H. glomerata and test the extracts and major isolate compounds against resistant bacteria. Hexane, CHCl₃/MeOH, and aqueous extracts were prepared and analyzed by different chromatographic techniques. Structural elucidation was carried out by NMR spectroscopy and X-ray diffraction. The antibacterial activities of extracts, phytochemicals, and semisynthetic derivatives against resistant bacteria were determined by the broth micro-dilution method. From the hexane extract nonacosane (1), hexatriacontanyl stearate (2), hexacosanol (3), oleic acid (4), and β-sitosterol (5) were isolated and characterized. From the CHCl₃/MeOH extract, p-coumaric acid (6), margaric acid (7), caffeic acid (8), daucosterol (9), and potassium chloride (10) were isolated and characterized. A total of 58 volatile compounds were identified by GC-MS from the hexane extract and two solids were isolated from the CHCl₃/MeOH extract. The UPLC-QTOF-MS analysis of the aqueous extract allowed the identification of 55 polar compounds. Hexane and aqueous extracts showed antibacterial activity against ESBL Escherichia coli, and three strains of Klebsiella pneumoniae ESBL, NDM-1 +, and OXA-48 with MIC values of 500 µg/mL. The CHCl₃/MeOH extract was devoid of activity. The activity of phytocompounds and their semisynthetic derivatives toward resistant bacteria was weak. The most active compound was β-sitosterol acetate, with a MIC value of 100 µg/mL against carbapenem-resistant A. baumannii. This is the first report of the secondary metabolites of H. glomerata Zucc. and the activity of its extracts and major pure compounds against resistant bacterial strains.

Does Enterococcus faecalis from Traditional Raw Milk Cheeses Serve as a Reservoir of Antibiotic Resistance and Pathogenic Traits?

Enterococcus faecalis is not only a prevalent species among dairy microbial community but also a well-documented opportunistic pathogen. Food safety should exclude the possibility of consumer exposure to its virulence traits through consumption of dairy products. In this study, an integrated approach based on both phenotypic and genotypic methods was applied to investigate the incidence of antibiotic resistance and pathogenicity potential in 40 E. faecalis isolated from 10 Italian raw milk cheeses over a 13-year period (1997-2009). Among the 14 tested antibiotics, resistance to tetracycline, rifampicin, chloramphenicol, and erythromycin was observed, whereas vancomycin-resistant enterococci were not found. A high incidence (90% of strains) of the tet(M) gene emerged, whereas tet(K), tet(S), tet(L), int, and ermB genes were occasionally amplified (12.5%, 10%, 7.5%, 2.5% and 30%, respectively). No strain was positive for vancomycin-resistant determinants. Among the seven virulence determinants considered, the asa1, gelE, esp, and efaA genes were harbored. No other gene encoding for either different virulence factors (cylA, hyl, and ace) or amino acid decarboxylase activity (hdc, tdc, and odc) was detected. Consequently, E. faecalis isolated from raw milk cheeses does not represent a substantial reservoir of antimicrobial resistance and virulence factors if compared with clinical strains. However, this species occasionally harbors detrimental traits; thus, the possibility that it could be a route for transmission of pathogenic genes through dairy products should never be disregarded.

Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries

Surveillance of antibiotic resistance has become a public global concern after the rapid worldwide dissemination of several antibiotic resistance genes. Here we report the role of the Institut Hospitalo-Universitaire Méditerranée Infection created in 2011 in the identification and description of multidrug-resistant bacteria thanks to collaborations and training of students from the Mediterranean basin and from African countries. Since the creation of the institute, 95 students and researchers have come from 19 different countries from these areas to characterize 6359 bacterial isolates from 7280 samples from humans (64%), animals (28%) and the environment (8%). Most bacterial isolates studied were Gram-negative bacteria (n = 5588; 87.9%), mostly from Algeria (n = 4190), Lebanon (n = 946), Greece (n = 610), Saudi Arabia (n = 299) and Senegal (n = 278). Antibiotic resistance was diversified with the detection and characterization of extended-spectrum β-lactamases, carbapenemases and resistance to colistin, vancomycin and methicillin. All those studies led to 97 indexed international scientific papers. Over the last 6 years, our institute has created a huge network of collaborations by training students that plays a major role in the surveillance of resistance to antibiotics in these countries.

Extremely and pandrug-resistant bacteria extra-deaths: myth or reality?

In 2009, the European Centre for Disease Prevention and Control (ECDC) estimated that multidrug-resistant (MDR) bacterial infections were responsible for 25,000 extra-deaths per year. In 2015, another report estimated that 12,500 extra-deaths were attributable to MDR bacteria every year in France. Recently, the United Nations claimed that resistance to antimicrobials was a global scourge, forecasting 10 million deaths in 2050. Surprisingly, our antibiotic resistance surveillance system in Marseille, France, did not allowed us to observe similar trends. We herein compared our data on extremely drug-resistant (XDR)/pandrug-resistant (PDR) patient extra-deaths to evaluations and predictions from these reports. First, we retrospectively collect and analyze antibiotic resistance data produced by our settings between November 2009 and March 2015 to look for 30-day deaths attributable to XDR/PDR strains belonging to 11 bacterial species/genus. In parallel, we performed a PubMed literature search to look for articles published prior to July 2016 and describing human deaths due to PDR strains. Overall, 35,723 patients were infected by at least one bacterial species/genus of interest and 85 by XDR/PDR strains. Of these patients, only one death was attributable to a XDR bacterial infection in a patient with strong comorbidities and two consecutive septic shocks. Our literature review shows that only four articles described human deaths due to PDR bacteria. All together, these data allowed us to conclude that there is a large discrepancy between the real count of deaths attributable to XDR/PDR bacteria and alarmist predictions.