Antimicrobial resistance: a global multifaceted phenomenon

Granzyme B Attenuates Bacterial Virulence by Targeting Secreted Factors

Pathogenic bacteria secrete virulence factors that interact with the human host to establish infections. The human immune system evolved multiple mechanisms to fight bacterial invaders, including immune proteases that were demonstrated to contribute crucially to antibacterial defense. Here we show that granzyme B degrades multiple secreted virulence mediators from Listeria monocytogenes, Salmonella typhimurium, and Mycobacteria tuberculosis. Pathogenic bacteria, when infected in the presence of granzyme B or granzyme-secreting killer cells, fail to grow in human macrophages and epithelial cells owing to their crippled virulence. A granzyme B-uncleavable mutant form of the major Listeria virulence factor, listeriolysin O, rescued the virulence defect in response to granzyme treatment. Hence, we link the degradation of a single factor with the observed decrease in virulent bacteria growth. Overall, we reveal here an innate immune barrier function of granzyme B by disrupting bacterial virulence to facilitate bacteria clearance by bystander immune and non-immune cells.

Naked Selenium Nanoparticles for Antibacterial and Anticancer Treatments

Currently, antibiotic resistance and cancer are two of the most important public health problems killing more than ∼1.5 million people annually, showing that antibiotics and current chemotherapeutics are not as effective as they were in the past. Nanotechnology is presented here as a potential solution. However, current protocols for the traditional physicochemical synthesis of nanomaterials are not free of environmental and social drawbacks, often involving the use of toxic catalysts. This article shows the production of pure naked selenium nanoparticles (SeNPs) by a novel green process called pulsed laser ablation in liquids (PLAL). After the first set of irradiations, another set was performed to reduce the size below 100 nm, which resulted in a colloidal solution of spherical SeNPs with two main populations having sizes around ∼80 and ∼10 nm. The particles after the second set of irradiations also showed higher colloidal stability. SeNPs showed a dose-dependent antibacterial effect toward both standard and antibiotic-resistant phenotypes of Gram-negative and Gram-positive bacteria at a range of concentrations between 0.05 and 25 ppm. Besides, the SeNPs showed a low cytotoxic effect when cultured with human dermal fibroblasts cells at a range of concentrations up to 1 ppm while showing an anticancer effect toward human melanoma and glioblastoma cells at the same concentration range. This article therefore introduces the possibility of using totally naked SeNPs synthesized by a new PLAL protocol as a novel and efficient nanoparticle fabrication process for biomedical applications.

Prevalence of Vancomycin resistant enterococci (VRE) in Ethiopia: a systematic review and meta-analysis

Background

The emergence of Vancomycin resistant enterococci (VRE) poses a major public health problem since it was first reported. Although the rising rates of VRE infections are being reported elsewhere in the worldwide; there is limited national pooled data in Ethiopia. Therefore, this study was aimed to estimate the pooled prevalence of VRE and antimicrobial resistance profiles of enterococci in Ethiopia.

Methods

Literature search was done at PubMed, EMBASE, Google scholar, African Journals online (AJOL) and Addis Ababa University repository following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. Both published and unpublished studies reporting the prevalence of VRE until June 30, 2019 were included. Data were extracted using Microsoft Excel and copied to Comprehensive Meta-analysis (CMA 2.0) for analysis. Pooled estimate of VRE was computed using the random effects model and the 95% CIs. The level of heterogeneity was assessed using Cochran’s Q and I² tests. Publication bias was checked by visual inspection of funnel plots and Begg’s and/or Egger’s test.

Results

Twenty studies fulfilled the eligibility criteria and found with relevant data. A total of 831 enterococci and 71 VRE isolates were included in the analysis. The pooled prevalence of VRE was 14.8% (95% CI; 8.7–24.3; I² = 74.05%; P <  0.001). Compared to vancomycin resistance, enterococci had higher rate of resistance to Penicillin (60.7%), Amoxicillin (56.5%), Doxycycline (55.1%) and Tetracycline (53.7%). Relatively low rate of resistance was found for Daptomycin and Linezolid with a pooled estimate of 3.2% (95% CI, 0.5–19.7%) and 9.9% (95% CI, 2.8–29.0%); respectively. The overall pooled multidrug resistance (MDR) rate of enterococci was 60.0% (95% CI, 42.9–75.0%).

Conclusion

The prevalence of VRE and drug resistant enterococci are on the rise in Ethiopia. Enterococcal isolates showed resistance to one or more of the commonly prescribed drugs in different or the same drug lines. Multidrug resistant (MDR) enterococci were also found. Although the rates were low, the emergence of resistance to Daptomycin and Linezolid is an alarm for searching new ways for the treatment and control of VRE infections. Adherence to antimicrobial stewardship, comprehensive testing and ongoing monitoring of VRE infections in the health care settings are required.

Prevalence of Genes Encoding Aminoglycoside-Modifying Enzymes in Clinical Isolates of Gram-Positive Cocci in Iran: A Systematic Review and Meta-Analysis

Introduction: Several studies have investigated the genes encoding aminoglycoside-modifying enzymes (AMEs) among gram-positive cocci (GPC) such as Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), coagulase-negative staphylococci (CoNS), and Enterococcus spp. in Iran; however, a comprehensive analysis has not yet been performed. Thus, the present systematic review and meta-analysis was conducted to determine the prevalence of genes encoding AMEs among GPC in Iran. Methods: A systematic review of the data published in the English and Persian languages from January 2000 to October 2018 was performed by searching different electronic databases (Medline, Embase, Web of Science, and the Iranian Database). Meta-analysis was performed by using the Comprehensive Meta-Analysis (Biostat V2.2) software. Cochran's Q and I² statistics were used to test heterogeneity, and publication bias was assessed by using funnel plot and Begg's and Egger's tests. Results: Out of 117 studies, 28 were considered eligible for inclusion in the current meta-analysis. The most prevalent AMEs gene among GPC was aac(6')-Ie-aph(2'')-Ia, with a prevalence of 97.7% (95% CI; 94.4-99) in high-level gentamicin-resistant enterococci and 67.7% (95% CI; 59.2-75.2) in MRSA. The second most common gene was ant(4')Ia, with a prevalence of 45.3% (95% CI; 23.9-68.6) in MRSA. Conclusions: It was ultimately determined that the prevalence of AMEs genes among GPC had reached alarming levels in Iran; therefore, aminoglycosides should be prescribed with caution by clinicians. The implementation of a regional and nationwide surveillance system to monitor antimicrobial resistance, especially aminoglycosides, and increasing the awareness of AMEs genes among clinicians are essential to guiding empirical and pathogen-specific therapy.

Increased multidrug resistant isolates: new clinical burdens for 66 hospitals in Shanghai, 2015 to 2017

Background

To investigate the etiology of urinary tract and respiratory infections and the rate of drug resistant bacteria in Shanghai from 2015 to 2017, provide the support to the promotion of the correct clinical etiological specimens detection.

Methods

The retrospective questionnaire survey was conducted to obtain the antibiotic prescription rate, pathogen detection rate, and isolation rate of drug-resistant bacteria of the inpatients in 66 hospitals of Shanghai in 2015 and 2017.

Results

Although the detection rate of multidrug-resistant bacteria in sputum specimens has decreased, the clinical pathogen detection still relied mainly on sputum specimens in 2017. Among the sputum specis, the detection rates of extended-spectrum β-lactamase-producing Escherichia (ESBL-ESC), extended-spectrum β-lactamase Klebsiella pneumoniae (ESBL-KP), carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Pseudomonas aeruginosa (CRPA) and methicillin-resistant Staphylococcus aureus (MRSA) in 2017 were 66.67%, 32.46%, 61.74%, 32.01% and 58.55% respectively. The detection rates of ESBL-ESC, ESBL-KP, CRAB, CRPA in 2017 were increased while the MRSA was decreased than 2015 (P<0.001). Among the blood samples, the detection rates of ESBL-ESC, ESBL-KP, CRAB, CRPA, MRSA and vancomycin-resistant Enterococcus sp (VRE) in 2017 were 53.71%, 31.43%, 50.80%, 19.43%, 43.87% and 0.55% respectively. The detection rates of ESBL-KP, CRAB, CRPA and MRSA increased while the rates of ESBL-ESC and VRE decreased compared with 2015 (P<0.005). The pathogens of multi-drug resistant bacteria were mainly detected from sputum specimens in 2017, which were all higher than detected from the blood specimens (P<0.001).

Conclusions

Most of the multi-drug resistant bacteria in Shanghai, especially in Acinetobacter baumannii or Pseudomonas aeruginosa are mainly detected from sputum specimens, indicating that the actual drug resistance may be overestimated.

ZTW-41, a Potent Indolizinoquinoline-5,12-Dione Derivative Against Drug-Resistant Staphylococci and Enterococci Bacteria

ZTW-41, an indolizinoquinoline-5,12-dione derivative, was investigated for antibacterial activity against Gram-positive bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA). In our study, the MIC₉₀s (minimum inhibitory concentrations) of ZTW-41 against MRSA (MRSA, n = 200), methicillin-sensitive S. aureus (MSSA, n = 100), Enterococcus faecalis (E. faecalis, n = 32), and Enterococcus faecium (E. faecium n = 32) were 0.25, 0.25, 0.125, and 8 μg/mL, respectively, whereas the MBC₉₀s (minimum bactericidal concentrations) were 2, 1, 1, and >32 μg/mL, respectively. ZTW-41 maintained its potency at different pH levels (range 5-9) and in starting inoculum size up to 10⁷ CFU/mL. The presence of human serum (25-75%) increased ZTW-41 MICs by two- to eightfold. Time-kill curves showed that ZTW-41 had bactericidal activity against MRSA, MSSA, and E. faecalis strains within 8 hours, and rebound growth occurred after 8 hours except at higher multiples of the MIC (4 × and 8 × ). In the acute toxicity study, no mortality or signs of toxicity was noted in mice after 14 days of observation at doses <50 mg/kg. ZTW-41 exhibited good selectivity indices (SIs) (SI = IC₅₀/MIC₉₀) ranging from 1.12 to 71.76 against clinical isolates, demonstrating excellent therapeutic selectivity in MRSA, MSSA, and E. faecalis strains. Moreover, the in vivo efficacy (effective dose [ED]₅₀ = 6.59 mg/kg) of ZTW-41 was found comparable with vancomycin. Collectively, our favorable results supported ZTW-41 as a promising investigational candidate for treating drug-resistant bacteria infection.

Ongoing strategies to improve the management of upper respiratory tract infections and reduce inappropriate antibiotic use particularly among lower and middle-income countries: findings and implications for the future

Introduction: Antibiotics are indispensable to maintaining human health; however, their overuse has resulted in resistant organisms, increasing morbidity, mortality and costs. Increasing antimicrobial resistance (AMR) is a major public health threat, resulting in multiple campaigns across countries to improve appropriate antimicrobial use. This includes addressing the overuse of antimicrobials for self-limiting infections, such as upper respiratory tract infections (URTIs), particularly in lower- and middle-income countries (LMICs) where there is the greatest inappropriate use and where antibiotic utilization has increased the most in recent years. Consequently, there is a need to document current practices and successful initiatives in LMICs to improve future antimicrobial use.Methodology: Documentation of current epidemiology and management of URTIs, particularly in LMICs, as well as campaigns to improve future antimicrobial use and their influence where known.Results: Much concern remains regarding the prescribing and dispensing of antibiotics for URTIs among LMICs. This includes considerable self-purchasing, up to 100% of pharmacies in some LMICs. However, multiple activities are now ongoing to improve future use. These incorporate educational initiatives among all key stakeholder groups, as well as legislation and other activities to reduce self-purchasing as part of National Action Plans (NAPs). Further activities are still needed however. These include increased physician and pharmacist education, starting in medical and pharmacy schools; greater monitoring of prescribing and dispensing practices, including the development of pertinent quality indicators; and targeted patient information and health education campaigns. It is recognized that such activities are more challenging in LMICs given more limited resources and a lack of healthcare professionals.Conclusion: Initiatives will grow across LMICs to reduce inappropriate prescribing and dispensing of antimicrobials for URTIs as part of NAPs and other activities, and these will be monitored.

Risk factors for carbapenem-resistant Klebsiella pneumoniae infection relative to two types of control patients: a systematic review and meta-analysis

Background

Studies on risk factors for carbapenem-resistant Klebsiella pneumoniae (CRKP) infection have provided inconsistent results, partly due to the choice of the control group. We conducted a systematic review and meta-analysis to assess the risk factors for CRKP infection by comparing CRKP-infected patients with two types of controls: patients infected with carbapenem-susceptible Klebsiella pneumoniae (comparison 1) or patients not infected with CRKP (comparison 2).

Methods

Data on potentially relevant risk factors for CRKP infection were extracted from studies indexed in PubMed, EMBASE, Web of Science or EBSCO databases from January 1996 to April 2019, and meta-analyzed based on the outcomes for each type of comparison.

Results

The meta-analysis included 18 studies for comparison 1 and 14 studies for comparison 2. The following eight risk factors were common to both comparisons: admission to intensive care unit (ICU; odds ratio, OR_{comparison 1} = 3.20, OR_{comparison 2} = 4.44), central venous catheter use (2.62, 3.85), mechanical ventilation (2.70, 4.78), tracheostomy (2.11, 8.48), urinary catheter use (1.99, 0.27), prior use of antibiotic (6.07, 1.61), exposure to carbapenems (4.16, 3.84) and exposure to aminoglycosides (1.85, 1.80). Another 10 risk factors were unique to comparison 1: longer length of hospital stay (OR = 15.28); prior hospitalization (within the previous 6 months) (OR = 1.91); renal dysfunction (OR = 2.17); neurological disorders (OR = 1.52); nasogastric tube use (OR = 2.62); dialysis (OR = 3.56); and exposure to quinolones (OR = 2.11), fluoroquinolones (OR = 2.03), glycopeptides (OR = 3.70) and vancomycin (OR = 2.82).

Conclusions

Eighteen factors may increase the risk of carbapenem resistance in K. pneumoniae infection; eight factors may be associated with both K. pneumoniae infections in general and CRKP in particular. The eight shared factors are likely to be ‘true’ risk factors for CRKP infection. Evaluation of risk factors in different situations may be helpful for empirical treatment and prevention of CRKP infections.

Microgels and hydrogels as delivery systems for antimicrobial peptides

Due to rapid development of bacterial resistance against antibiotics, an emerging health crisis is underway, where 'simple' infections may no longer be treatable. Antimicrobial peptides (AMPs) constitute a class of substances attracting interest in this context. So far, research on AMPs has primarily focused on the identification of potent and selective peptides, as well as on the action mode of such peptides. More recently, there has been an increasing awareness that the delivery of AMPs is challenging due to their size, net positive charge, amphiphilicity, and proteolytic susceptibility. Hence, successful development of AMP therapeutics will likely require also careful design of efficient AMP delivery systems. In the present brief review, we discuss microgels, as well as related polyelectrolyte complexes and macroscopic hydrogels, as delivery systems for AMPs. In doing so, key factors for peptide loading and release are outlined and exemplified, together with consequences of this for functional performance relating to antimicrobial effects and cell toxicity.

European perspectives on efforts to reduce antimicrobial usage in food animal production

New regulations on veterinary medicines and medicated feed will substantially influence antimicrobial prescribing and usage throughout Europe into the future. These regulations have been informed by a very large body of work, including the substantial progress towards reduced antimicrobial usage in food animal production in a number of member states of the European Union (EU). This paper seeks to summarise European perspectives on efforts to reduce antimicrobial usage in food animal production. Work within the EU is informed by the global action plan of the World Health Organization, which includes a strategic objective to optimise the use of antimicrobial medicines in human and animal health. There is ongoing measurement of trends in antimicrobial usage and resistance throughout the EU, and detailed information on strategies to reduce the need to use antimicrobials in food animal production. Substantial scientific progress has been made on the measurement of antimicrobial usage, including at herd-level, and on the objective assessment of farm biosecurity. In a number of EU member states, monitoring systems for usage are well-established, allowing benchmarking for veterinarians and farms, and monitoring of national and industry-level trends. Several countries have introduced restrictions on antimicrobial prescribing and usage, including strategies to limit conflicts of interest around antimicrobial prescribing and usage. Further, a broad range of measures are being used across member states to reduce the need for antimicrobial usage in food animal production, focusing both at farm level and nationally. Veterinarians play a central role in the reduction of antimicrobial usage in farm animals. Ireland's National Action Plan on Antimicrobial Resistance 2017-20 (iNAP) provides an overview of Ireland's commitment to the development and implementation of a holistic, cross-sectoral 'One Health' approach to the problem of antimicrobial resistance. The new regulations offer an important springboard for further progress, in order to preserve the efficacy of existing antimicrobials, which are a critical international resource.

Genomic Analysis of Carbapenemase-Producing Extensively Drug-Resistant Klebsiella pneumoniae Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding blaNDM-1 in South Africa

Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant Klebsiella pneumoniae strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from patients admitted to the intensive care unit (ICU) in a public hospital in South Africa. Five isolates were from rectal swabs of colonized patients and five from blood cultures of patients with invasive carbapenem-resistant infections. Following microbial identification and antibiotic susceptibility tests, the isolates were subjected to WGS on the Illumina MiSeq platform. All the isolates showed genotypic resistance to tested β-lactams (NDM-1, OXA-1, CTX-M-15, TEM-1B, SHV-1) and other antibiotics. All but one isolate belonged to the ST152 with a novel sequence type, ST3136, differing by a single-locus variant. The isolates had the same plasmid multilocus sequence type (IncF[K12:A-:B36]) and capsular serotype (KL149), supporting the epidemiological linkage between the clones. Resistance to carbapenems in the 10 isolates was conferred by the bla_NDM-1 mediated by the acquisition of multi-replicon [ColRNAI, IncFIB(pB171), Col440I, IncFII, IncFIB(K) and IncFII(Yp)] p18-43_01 plasmid. These findings suggest that the acquisition of bla_NDM-1-bearing plasmid structure (p18-43_01), horizontal transfer and clonal dissemination facilitate the spread of carbapenemases in South Africa. This emphasizes the importance of targeted infection control measures to prevent dissemination.

Warding Off Recurrent Yeast and Bacterial Vaginal Infections: Lactoferrin and Lactobacilli

Vaginal infections are the most prevalent women's health problem. Incompetent diagnosis, inappropriate treatments, and antibiotic resistance are the main causes of the unsatisfactory results of conventional, antimicrobic treatment for these infections. Research has thus been conducted to identify new treatments for these genital diseases. The significant enhancement in our knowledge of vaginal microbiota has permitted the development of new, nonpharmacological strategies for the treatment of vaginal infections that seek to restore the balance of vaginal microflora, as opposed to modifying its components. Among these approaches, bioactive compounds, such as probiotics and nutraceutical proteins (such as lactoferrin), deserve particular attention. The aim of this review is to examine the role of probiotics (mainly Lactobacillus spp.) and lactoferrin as new strategies for counteracting bacterial and fungal vaginal infections.

Novel high-throughput screening method using quantitative PCR to determine the antimicrobial susceptibility of Orientia tsutsugamushi clinical isolates

Objectives

To develop a method to enable the large-scale antimicrobial susceptibility screening of Orientia tsutsugamushi clinical isolates, using one timepoint and one concentration of antibiotics to considerably speed up the time to result.

Methods

Growth, harvesting, multiplicity of infection (moi) and the day to determine the MICs were optimized using five O. tsutsugamushi reference strains [susceptible (Karp, Kato and Gilliam) and putatively resistant (AFC-3 and AFSC-4)], one clinical isolate (UT76) and one rodent isolate (TA763). Subsequently, the MICs of azithromycin, chloramphenicol and doxycycline for these strains and 51 clinical isolates including AFSC-7 were determined. An optimal concentration was calculated using the epidemiological cut-off value.

Results

The conditions for O. tsutsugamushi infection, growth and harvesting were determined to be an moi of 100:1 and trypsinization with the peak growth on day 10. The resulting MICs were in line with previously published susceptibility data for all reference strains, except for Karp and AFSC-4, which showed azithromycin MICs of 0.0156 and 0.0313 mg/L, compared with 0.0078 and 0.0156 mg/L, respectively, in previous reports. The MIC of doxycycline for AFC-3 was 0.125 mg/L compared with >4 mg/L in earlier reports. The final single screening concentrations were identified as: azithromycin, 0.125 mg/L; chloramphenicol, 8 mg/L; and doxycycline, 1 mg/L.

Conclusions

This simplified procedure facilitates the simultaneous screening of 48 isolates for actively monitoring potential resistance of this important fever pathogen, with an 8-fold throughput improvement over early methods. The data do not support the existence of doxycycline- and chloramphenicol-resistant scrub typhus.

Direct medical burden of antimicrobial-resistant healthcare-associated infections: empirical evidence from China

BACKGROUND

Antimicrobial resistance (AMR) and healthcare-associated infections (HAIs) are among the biggest global public health challenges, and overlap widely. These infections cause significant morbidity and mortality, put pressure on health systems, and incur rising direct and indirect costs.

AIM

This study analysed the direct medical burden attributable to AMR-HAIs in Chinese public tertiary hospitals, and aimed to inform both the medical regulators and hospital managers for better control of HAIs and containment of AMR.

METHODS

The propensity score matching method (γ= 0.25σ, nearest neighbor 1:1 matching) was applied to conduct a retrospective cohort study in five public tertiary hospitals in the Hubei province of China during 2013-2015. Descriptive analysis, Pearson's chi-squared test, Mann-Whitney U-test, Wilcoxon signed-rank test and paired/independent Z/T test were conducted. The statistically significant level was set at P<0.05.

FINDINGS

From 2013 to 2015 overall, the additional total medical expenditure per HAI-AMR inpatient was US$15,557.25 compared with that of the non-HAIs, and the additional length of per hospital stay of the HAI-AMR inpatient was 41 days compared with that of the non-HAIs (P<0.001).

CONCLUSIONS

In combination with AMR, HAIs caused significant additional medical expenses and affected the turnover rate of hospital beds. Most of the increased medical costs fell to patients and their families. These findings call for more effective control of HAIs and containment of AMR. A national study is needed to estimate the medical, social and economic burden of HAIs in combination with AMR.

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

Antimicrobial resistance (AMR) is a threat to global public health and the identification of genetic determinants of AMR is a critical component to epidemiological investigations. High-throughput sequencing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysis of AMR within metagenomic samples (i.e. the resistome). Along with MEGARes, we released AmrPlusPlus, a bioinformatics pipeline that interfaces with MEGARes to identify and quantify AMR gene accessions contained within a metagenomic sequence dataset. Here, we present MEGARes 2.0 (https://megares.meglab.org), which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 2.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 57 classes, 220 mechanisms of resistance, and 1,345 gene groups that classify the 7,868 accessions. In addition, we present an updated version of AmrPlusPlus (AMR ++ version 2.0), which improves accuracy of classifications, as well as expanding scalability and usability.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

Exploring Antimicrobials from the Flora and Fauna of Marine: Opportunities and Limitations

About 95% of earth living space lies deep below the ocean's surface and it harbors extraordinary diversity of marine organisms. Marine biodiversity is an exceptional reservoir of natural products, bioactive compounds, nutraceuticals and other potential compounds of commercial value. Timeline for the development of the drug from a plant, synthetic and other alternative sources is too lengthy. Exploration of the marine environment for potential bioactive compounds has gained focus and huge opportunity lies ahead for the exploration of such vast resources in the ocean. Further, the evolution of superbugs with increasing resistance to the currently available drugs is alarming and it needs coordinated efforts to resolve them. World Health Organization recommends the need and necessity to develop effective bioactive compounds to combat problems associated with antimicrobial resistance. Based on these factors, it is imperative to shift the focus towards the marine environment for potential bioactive compounds that could be utilized to tackle antimicrobial resistance. Current research trends also indicate the huge strides in research involving marine environment for drug discovery. The objective of this review article is to provide an overview of marine resources, recently reported research from marine resources, challenges, future research prospects in the marine environment.

Lipidated α/Sulfono-α-AA heterogeneous peptides as antimicrobial agents for MRSA

Though antibiotics have been used for decades to treat bacterial infections, there is a great need for new treatment methods. Bacteria are becoming resistant to conventional antibiotics, as is the case with Methicillin resistant Staphylococcus aureus (MRSA). Herein we report the design of a series of lipidated α/Sulfono-α-AA heterogeneous peptides as mimics for Host Defense Peptides (HDPs). Utilizing fluorescence microscopy and depolarization techniques, our compounds demonstrate the ability to kill Gram-positive bacteria through cell membrane disruption. This mechanism of action makes it difficult for bacteria to develop resistance. Further time kill studies and hemolytic assays have also proven these compounds to be efficient in their ability to eradicate bacteria cells while remaining non-toxic to human red blood cells. This new class of peptidomimetics shows promise for the future antibiotic treatment of MRSA.

Evidence of mutations conferring resistance to clarithromycin in wastewater and activated sludge

The occurrence of clarithromycin in wastewater samples and of the activated sludge bacteria possibly resistant to this pharmaceutical was the object of the study. Samples of wastewater or activated sludge were taken from a municipal wastewater treatment plant in summer and winter and characterised regarding their clarithromycin concentrations and the presence of nucleic acid fragments (Cla-sequences) known to be responsible for clarithromycin resistance in Helicobacter pylori. The concentrations of clarithromycin in raw wastewater were about 1086-2271 ng/L. Around 50-60% less of the pharmaceutical was found in treated wastewater. The concentrations were much higher in winter samples, as compared to summer samples. The clarithromycin resistance markers in H. pylori were detected by fluorescence in situ hybridisation in activated sludge bacterial cells. Cla-sequences were found in all the detected Proteobacteria, independently of the sampling season. Among nitrifying or phosphate or glycogen accumulating bacteria only Nitrosomonas spp. revealed presence of the clarithromycin sequences.

Considerations and Caveats in Combating ESKAPE Pathogens against Nosocomial Infections

ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are among the most common opportunistic pathogens in nosocomial infections. ESKAPE pathogens distinguish themselves from normal ones by developing a high level of antibiotic resistance that involves multiple mechanisms. Contemporary therapeutic strategies which are potential options in combating ESKAPE bacteria need further investigation. Herein, a broad overview of the antimicrobial research on ESKAPE pathogens over the past five years is provided with prospective clinical applications.

Therapeutic lipid-coated hybrid nanoparticles against bacterial infections

One of the most important health concerns in society is the development of pathogen-causing nosocomial infections. Since the first discovery of antibiotics, bacterial infections have been highly treatable. However, with evolution and the nondiscretionary usage of antibiotics, pathogens have also found new ways to survive the onslaught of antibiotics by surviving intracellularly or through the formation of obstinate biofilms, and through these, the outcomes of regular antibiotic treatments may now be unsatisfactory. Lipid-coated hybrid nanoparticles (LCHNPs) are the next-generation core–shell structured nanodelivery system, where an inorganic or organic core, loaded with antimicrobials, is enveloped by lipid layers. This core–shell structure, with multifarious decorations, not only improves the loading capabilities of therapeutics but also has the potential to improve therapeutic delivery, especially for targeting biofilm-based and intracellular bacterial infections. Although there has been significant interest in the development of LCHNPs, they have yet to be widely exploited for bacterial infections. In this review, we will provide an overview on the latest development of LCHNPs and the various approaches in synthesizing this nano-delivery system. In addition, a discussion on future perspectives of LCHNPs, in combination with other novel anti-bacterial technologies, will be provided towards the end of this review.

Lipid-coated hybrid nanoparticles are next-generation core–shell structured nanodelivery systems, which improve the loading capabilities of therapeutics and can improve therapeutic delivery, especially for targeting biofilm-based and intracellular bacterial infections.

New and promising anti-bacterials: Can this promise be sustained?

The World Health Organization (WHO) announced antimicrobial resistance (AMR) as a major threat to public health which requires that new antimicrobials need to be developed faster than ever before. The rapid development of resistance has rendered many promising antibacterials useless in treating critically ill patients. This article discusses new antibacterials, which got Food and Drug Administration (FDA) approval in the last few years, along with their key pharmacokinetic and pharmacodynamic (PK/PD) advantages, added antimicrobial spectrum, indications, strengths and weaknesses of these drugs from an intensivist point of view. A brief mention has been made on antimicrobial peptides (AMPs), bacteriophages and nanoparticles, which are likely to dominate the future of antibacterials. Finally, it must be understood that the battle against AMR can only be won by a combination of innovative therapies, good infection control practices, strong antibiotic stewardship in the hands of informed healthcare workers.

Pathogens Causing Respiratory Tract Infections in Children Less Than 5 Years of Age in Senegal

Introduction:

While acute respiratory tract infections are the main cause of paediatric mortality and morbidity worldwide, pathogen patterns shift due to factors such as hygiene, vaccinations, and antibiotic resistance. Knowledge about current cause of respiratory infections is lacking, particularly in low- and middle-income countries. The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal.

Methods:

A case-control study was performed in September and October 2018. Oropharyngeal swabs were collected from cases; infants with fever and respiratory symptoms, and controls; children involved in the vaccination programme. Viral identification was conducted by polymerase chain reaction for 21 different viruses; bacteria were identified by culture studies. Associations between microorganisms, acute respiratory infection and severity of disease were calculated by multivariate regression adjusting for confounders such as age, sex, and living area.

Results:

Overall, 102 cases and 96 controls were included. Microorganisms were detected in 90.1% of cases and 53.7% of controls (P < .001). Influenza virus A (including H1N1), influenza virus B, respiratory syncytial virus (RSV), and Streptococcus pneumoniae were independently associated with acute respiratory tract infections. Co-detection of two or more pathogens was present in 49.5% of cases; 31.7% of cases had a pneumonia and 90.2% was treated with antibiotics.

Conclusions:

This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. We recommend evaluation of antibiotics prescription behaviour in this setting.

New Napyradiomycin Analogues from Streptomyces sp. Strain CA-271078

As part of our continuing efforts to discover new bioactive compounds from microbial sources, a reinvestigation of extracts of scaled-up cultures of the marine-derived Streptomyces sp. strain CA-271078 resulted in the isolation and structural elucidation of four new napyradiomycins (1-3, 5). The known napyradiomycin SC (4), whose structural details had not been previously described in detail, and another ten related known compounds (6-15). The structures of the new napyradiomycins were characterized by HRMS and 1D- and 2D-NMR spectroscopies and their relative configurations were established through a combination of molecular modelling with nOe and coupling constants NMR analysis. The absolute configuration of each compound is also proposed based on biosynthetic arguments and the comparison of specific rotation data with those of related compounds. Among the new compounds, 1 was determined to be the first non-halogenated member of napyradiomycin A series containing a functionalized prenyl side chain, while 2-4 harbor in their structures the characteristic chloro-cyclohexane ring of the napyradiomycin B series. Remarkably, compound 5 displays an unprecedented 14-membered cyclic ether ring between the prenyl side chain and the chromophore, thus representing the first member of a new class of napyradiomycins that we have designated as napyradiomycin D1. Anti-infective and cytotoxic properties for all isolated compounds were evaluated against a set of pathogenic microorganisms and the HepG2 cell line, respectively. Among the new compounds, napyradiomycin D1 exhibited significant growth-inhibitory activity against methicillin-resistant Staphylococcus aureus, Mycobacterium tuberculosis, and HepG2.

Antimicrobial Resistance: Implications and Costs

Antimicrobial resistance (AMR) has developed as one of the major urgent threats to public health causing serious issues to successful prevention and treatment of persistent diseases. In spite of different actions taken in recent decades to tackle this issue, the trends of global AMR demonstrate no signs of slowing down. Misusing and overusing different antibacterial agents in the health care setting as well as in the agricultural industry are considered the major reasons behind the emergence of antimicrobial resistance. In addition, the spontaneous evolution, mutation of bacteria, and passing the resistant genes through horizontal gene transfer are significant contributors to antimicrobial resistance. Many studies have demonstrated the disastrous financial consequences of AMR including extremely high healthcare costs due to an increase in hospital admissions and drug usage. The literature review, which included articles published after the year 2012, was performed using Scopus, PubMed and Google Scholar with the utilization of keyword searches. Results indicated that the multifactorial threat of antimicrobial resistance has resulted in different complex issues affecting countries across the globe. These impacts found in the sources are categorized into three different levels: patient, healthcare, and economic. Although gaps in knowledge about AMR and areas for improvement are obvious, there is not any clearly understood progress to put an end to the persistent trends of antimicrobial resistance.

Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments

The mankind relies on the use of antibiotics for a healthy life. The epidemic-like emergence of drug-resistant bacterial strains is increasingly becoming one of the leading causes of morbidity and mortality, which gives rise to design a potential antimicrobial peptide (AMP). Here, we have designed the potential AMP using the extensive dynamics simulation since protein-peptide interactions are linked to large conformational changes. Therefore, we have employed the advanced computational avenue CABS molecular docking method that enabled the flexible peptide-protein molecular docking with a large-scale rearrangement of the protein. Lead AMP was investigated against the wild-type (WT) and mutant-PBP5 (MT-PBP5) proteins (antiresistance property). AMP20 showed strong interactions with wtPBP5 and mtPBP5 and involvement of a large number of elements in interactions determined through an atomic model study. Full flexibility analysis showed the stable interaction of AMP20 with both the wild-type and mutant form of PBP5 with root-mean-square deviation (RMSD) values of ∼4.51 and 4.85 Å, respectively. Moreover, peptide dynamics showed involvement of all residues of AMP20 through contact map analysis, and extensive simulation confirmed the stable interaction of AMP20, with lower values of RMSD, radius of gyration, and root-mean-square fluctuation. This study paves the way for a potential approach to design the AMP with amino acid walking and large-scale conformational rearrangements of amino acids.

Biofilm formation and antibiotic resistance of Klebsiella pneumoniae isolated from clinical samples in a tertiary care hospital, Klaten, Indonesia

Background

Klebsiella pneumoniae (K. pneumoniae) is a common cause of health-care associated infections (HAIs) and has high levels of antibiotic resistance. These bacteria are well-known for their ability to produce biofilm. The purpose of this study was to identify the antibiotic resistance pattern and biofilm-producing capacity of K. pneumoniae isolated from clinical samples in a tertiary care hospital in Klaten, Indonesia.

Methods

K. pneumoniae was isolated from inpatients in Soeradji Tirtonegoro Hospital Klaten from June 2017 to May 2018. Identification of K. pneumoniae isolate was done by analyzing colony morphology, microscopic examination, and by performing biochemical testing. Testing of antibiotics susceptibility and biofilm-producing capacity used the Kirby-Bauer disk diffusion method and adherence quantitative assays, respectively.

Results

A total of 167 (17.36%) K. pneumoniae isolates were isolated from 962 total clinical bacterial isolates during the study. Most of them were collected from patients aged more than 60 years old and were mainly obtained from respiratory specimens (51.50%). Most of K. pneumoniae isolates were extensively resistant to antibiotics. A more favorable profile was found only towards meropenem, amikacin, and piperacillin-tazobactam, showing 1.20%; 4.79% and 10.53% of resistance, respectively. The overall proportion of multidrug-resistant K. pneumoniae isolates was 54.49%. In addition, 148 (85.63%) isolates were biofilm producers, with 45 (26.95%) isolates as strong, 48 (28.74%) isolates as moderate, and 50 (29.94%) isolates as weak biofilm producers.

Conclusion

Most of the K. pneumoniae isolates demonstrated resistance to a wide range of antibiotics and are biofilm producers.

Antimicrobial resistance in a war-torn country: Lessons learned in the Eastern Democratic Republic of the Congo

There is no doubt that antibiotics have reduced the burden of bacterial infectious diseases. Antimicrobial resistance threatens the effectiveness of successful treatment of infections and constitutes a public health concern with national and global dimensions. This problem is worrisome in war-torn areas like the Eastern Democratic Republic of the Congo. The difficulties experienced by war-torn nations in addressing antimicrobial resistance are significant for the rest of the globe as microbes do not acknowledge boundaries and do not distinguish between peace and wartime. In this paper, we describe the impact of warfare on the social determinants of health, the environment and biodiversity, and its consequences on the antibiotic use and the host-pathogen interplay. Furthermore, we describe different pillars to be taken into account, learned in a war-torn area, in combating antimicrobial resistance. These lessons are summarized in terms of tools to be used for combating antimicrobial resistance, challenges to overcome in war-torn setting and core actions to be undertaken. Surveillance is a valuable tool to combat antimicrobial resistance as it helps to detect resistant bacteria, enables correct decisions to be taken, guides policy recommendations and tracks the antibiotic use and misuse. The challenges encountered in this region include the shortage of competent laboratories, poor infrastructure and data management, lack of standard protocols, low coverage of surveillance, lack of intersectoral cooperation, and inadequate national, regional and international collaboration. Regarding this situation, the core actions to be undertaken include the establishment of ABR surveillance and monitoring systems, building laboratory capacity for rapid and reliable diagnostic testing, and engagement in national, regional and global surveillance networks. Therefore, this study showed an urgent need for establishing and implementing sentinel site surveillance laboratories and elaborating and implementing national action plans for combating antimicrobial resistance.

Effect of drug combinations on the kinetics of antibiotic resistance emergence in Escherichia coli CFT073 using an in vitro hollow-fibre infection model

Antibiotic resistance is one of the major threats to public health today. To address this problem requires an urgent comprehensive approach. Strategic and multitargeted combination therapy has been increasingly used clinically to treat bacterial infections. The hollow-fibre infection model (HFIM) is a well-controlled in vitro bioreactor system that is increasingly being used in the assessment of resistance emergence with monotherapies and combination antibiotic therapies. In this study, the HFIM was evaluated as a reliable in vitro method to quantitatively and reproducibly analyse the emergence of antibiotic resistance using ampicillin, fosfomycin and ciprofloxacin and their simultaneous combinations against Escherichia coli CFT073, a clinical uropathogenic strain. Bacteria were exposed to clinically relevant pharmacokinetic (PK) concentrations of the drugs for 10 days. Drug and bacterial samples were collected at different time points for PK analysis and to enumerate total and resistant bacterial populations, respectively. The results demonstrated that double or triple combinations significantly delayed the emergence of resistant E. coli CFT073 subpopulations. These findings suggest that strategic combinations of antimicrobials may play a role in controlling the emergence of resistance during treatment. Further animal and human trials will be needed to confirm this and to ensure that there is no adverse impact on the host microbiome or unexpected toxicity. The HFIM system could potentially be used to identify clinically relevant combination dosing regimens for use in a clinical trial evaluating the appearance of resistance to antibacterial drugs.

Production of bacteriophage-encoded endolysin, LysP11, in Nicotiana benthamiana and its activity as a potent antimicrobial agent against Erysipelothrix rhusiopathiae

KEY MESSAGE

We produced a biologically active phage-encoded endolysin, LysP11, in N. benthamiana. Plant-produced LysP11 exhibited robust antimicrobial activity against E. rhusiopathiae, and C-terminal domain of LysP11 bound specifically to E. rhusiopathiae. Bacterial resistance to antibiotics, a serious issue in terms of global public health, is one of the leading causes of death today. Thus, new antimicrobial agents are needed to combat pathogens. Recent research suggests that bacteriophages and endolysins derived from bacteriophages are potential alternatives to traditional antibiotics. Here, we examined the antimicrobial activity of LysP11, which is encoded by Propionibacterium phage P1.1 and comprises an N-terminal amidase-2 domain and a C-terminal domain with no homology to other bacteriophage endolysins. LysP11 was produced in Nicotiana benthamiana (N. benthamiana) using an Agrobacterium-mediated transient expression strategy. LysP11 was purified on microcrystalline cellulose-binding resin after attachment of the Clostridium thermocellum-derived family 3 cellulose-binding domain as an affinity tag. The affinity tag was removed using the small ubiquitin-related modifier (SUMO) domain and SUMO-specific protease. Plant-produced LysP11 showed strong antimicrobial activity toward Erysipelothrix rhusiopathiae (E. rhusiopathiae), mediated via lysis of the cell wall. Lytic activity was optimal at pH 8.0-9.0 (37 °C) and increased at higher concentrations of NaCl up to 400 mM. Furthermore, the C-terminal domain of LysP11 bound specifically to the E. rhusiopathiae cell wall. Based on these results, we propose that LysP11 is a potential candidate antimicrobial agent against E. rhusiopathiae.

Knowledge of Antimicrobial Resistance among Veterinary Students and Their Personal Antibiotic Use Practices: A National Cross-Sectional Survey

The challenge of antimicrobial resistance (AMR) is grave in developing countries. Antimicrobials are misused yet stakeholders' contribution to antimicrobial stewardship is low. Veterinary students are future prescribers and their knowledge could influence progress in combating AMR; hence, there is a need to assess their knowledge, attitude, and awareness of AMR. A multi-institutional questionnaire was administered to undergraduates in Nigerian veterinary schools. It comprised demographics, own personal antibiotic usage, and knowledge, attitude, and awareness of AMR in humans and animals. Descriptive statistics and logistic regression were used for analyses. Of the 426 respondents, 39.2% reported personal antimicrobial use in the previous six months. Over 60% received knowledge scores lower than average and >87% requested more education on clinical use and prescriptions pre-graduation, monitored dispensing of antimicrobials, conducting AMR research, and confirmed link among human, animal, and environmental health. Less than 25% of respondents were aware of antimicrobial stewardship and global efforts/organizations for AMR. Final year students have 9-fold and 14-fold more satisfactory knowledge on antimicrobials in humans and animals compared with other students, respectively (p = 0.001). Final year students also have more knowledge (13×) and awareness of contributory factors (3×) on AMR (p = 0.001) than other students. Unsatisfactory knowledge on AMR issues exists among veterinary students yet willingness to improve was observed. Identified knowledge, attitude, and gaps in AMR awareness should be targeted by veterinary schools in Nigeria.

Knowledge, attitudes and practices relating to antibiotic use among community members of the Rupandehi District in Nepal

Background

The development of antibiotic resistance is one of the biggest threats to global public health. Inappropriate use of antibiotics is recognised as a leading cause of antibiotic resistance. The aim of this study was to explore the knowledge, attitudes and practices (KAP) towards antibiotic use among adults in Nepal.

Methods

A quantitative survey was conducted with 220 community members of the Rupandehi district of Nepal, with cluster sampling techniques applied to select households. Interviews were carried out face-to-face using a structured questionnaire. Responses were presented using descriptive analysis, with chi-squared tests and regression analysis applied to identify factors associated with KAP about antibiotic use and the Spearman’s rank order correlation coefficient calculated to examine the relationship between responses to the KAP questions.

Results

The sample comprised more females (54%) than males, the average age of respondents was 38.5 years and almost 60% of respondents lived in rural areas. Respondents had relatively good knowledge about aspects of antibiotic use other than identifying antibiotics. The concept of antibiotic resistance was well known but imperfectly understood. Half of respondents (50.9%) were unsure whether skipping doses would contribute to the development of antibiotic resistance, 88.2% indicated they would go to another doctor if not prescribed an antibiotic when they thought one was needed and nearly half (47.7%) believed antibiotics helped them get better more quickly if they had a fever. Most respondents reported correct practices accessing and using antibiotics, however, 84.6% at least sometimes preferred an antibiotic when they have a cough and sore throat.

Logistic regression showed respondents with higher levels of education tended to have better knowledge, more appropriate attitudes and better practices about antibiotic use. Rural respondents were less likely to have better knowledge about antibiotic use, while females were more likely to report better practices.

Conclusion

The study provides baseline evidence about the knowledge, attitudes and practices regarding antibiotic use among the population of the Rupandehl district. Its findings will be useful in designing effective and targeted interventions to decrease misconceptions about antibiotic use and to increase awareness about the risks of inappropriate use of antibiotics in the community.

Anti-biofilm investigation of graphene/chitosan nanocomposites against biofilm producing P. aeruginosa and K. pneumoniae

In this study graphene/chitosan nanoparticles (GR/CS NCs) were developed. The homogenous combination of GR and CS was confirmed by FTIR spectroscopy. The combination of CS with GR sheets reduced the XRD intensity of the GR peak in GR/CS NCs, while TEM images revealed the immobile CS coating of GR sheets. Further, the anti-biofilm activity of GR/CS NCs was tested. The tests showed that the formation of biofilm by Pseudomonas aeruginosa and Klebsiella pneumoniae was inhibited at 40□g/mL GR/CS NCs up to 94 and 92 %, respectively. The intracellular and cell surface damage of the bacteria was observed by CLSM and SEM. Also, GR/CS NCs produced a toxic effect of 90 % on Artemia franciscana at 70□g/mL upon 24 h incubation. The recorded properties of the synthesized GR/CS NCs qualify them as potential agents against multi-drug resistant bacteria.

Prevalence and risk factors for multi-drug resistant Escherichia coli among poultry workers in the Federal Capital Territory, Abuja, Nigeria

Background

Antimicrobial resistance has emerged as a global health threat. Antimicrobial resistant Escherichia coli infections are associated with high morbidity and expenditure when compared with infections caused by susceptible strains. In Nigeria, antimicrobial drugs are readily available over-the-counter with potential for indiscriminate use by poultry farmers and eventual development of drug resistance. The objective of this study was to investigate prevalence and risk factors for multi-drug resistant E. coli among poultry workers (PW) in Abuja, Nigeria.

Materials and methods

A cross-sectional study was conducted among 122 randomly selected apparently healthy poultry workers (poultry-farmers/ sellers) in Municipal and Kuje Area Councils from December 2018 to April 2019. Data was collected on socio-demographics and exposure factors using a structured interviewer-administered questionnaire. E. coli was isolated and identified from stool samples of poultry workers. Antibiotic susceptibility testing was done using Kirby-Bauer disk diffusion method. Multidrug resistance (MDR) was defined as resistance to three or more classes of antimicrobials. Data was analyzed by computing proportions, prevalence odds-ratios (POR) and logistic regression at 5% significance level.

Results

Among PW, there were 121 males (99.2%). Mean age of the male workers was 30.6 ± 9.7years, 54.6% (n = 66) married, 57.9% (n = 70) had secondary education and 62.0% (n = 75) were farm-workers. Prevalence of E. coli was 39.7% (n = 48), highest among farm-workers (POR = 2.7, 95% Confidence Interval [CI] = 1.3–5.7; p = 0.01) compared to poultry-sellers. Of the 48 E. coli isolates, 16.7% (n = 8) were extended spectrum beta lactamase (ESBL) producers and 79.2% (n = 38) were MDR. We detected resistance against Tetracycline: (83.3%, n = 40), Sulfamethoxazole-Trimethoprim: (79.2%, n = 38), Ampicillin: (77.1%, n = 37), Streptomycin: (72.9%, n = 35), Nalidixic acid: (50%, n = 24), Gentamicin: (41.7%, n = 20), Chloramphenicol: (31.3%, n = 15), Cephalothin: (27.1%, n = 13), Nitrofurantoin: (10.4%, n = 5) and Imipenem: (6.3%, n = 3). Absence of lavatory (POR = 2.7, 95% CI = 1.1–6.7); existence of farm/market for >10years (POR = 2.5, 95% CI = 1.1–5.4) and PW’s history of diarrhea in last three months (POR = 2.8, CI = 1.2–6.3) were associated with MDR. Controlling for age, absence of lavatory (adjusted OR [aOR] = 4.31, 95% CI = 1.6–11.9); PW’s history of diarrhea in last three months (aOR = 3.3,95%CI = 1.3–8.5) and work exposure >10years (aOR = 0.3, 95%CI = 0.1–0.9) remained independent risk factors for MDR.

Conclusion

Prevalence of resistant E. coli was highest among farm-workers and associated with older farms/markets, occupational exposure of over 10 years and poor hygienic measures. The management of Municipal and Kuje Area Councils were recommended to provide lavatories for public use in farm-settlements/markets. The importance of hand-hygiene and responsible use of antimicrobials in poultry production was emphasized.

Exploitation of plant extracts and phytochemicals against resistant Salmonella spp. in biofilms

Salmonella is one of the most frequent causes of foodborne outbreaks throughout the world. In the last years, the resistance of this and other pathogenic bacteria to antimicrobials has become a prime concern towards their successful control. In addition, the tolerance and virulence of pathogenic bacteria, such as Salmonella, are commonly related to their ability to form biofilms, which are sessile structures encountered on various surfaces and whose development is considered as a universal stress response mechanism. Indeed, the ability of Salmonella to form a biofilm seems to significantly contribute to its persistence in food production areas and clinical settings. Plant extracts and phytochemicals appear as promising sources of novel antimicrobials due to their cost-effectiveness, eco-friendliness, great structural diversity, and lower possibility of antimicrobial resistance development in comparison to synthetic chemicals. Research on these agents mainly attributes their antimicrobial activity to a diverse array of secondary metabolites. Bacterial cells are usually killed by the rupture of their cell envelope and in parallel the disruption of their energy metabolism when treated with such molecules, while their use at sub-inhibitory concentrations may also disrupt intracellular communication. The purpose of this article is to review the current available knowledge related to antimicrobial resistance of Salmonella in biofilms, together with the antibiofilm properties of plant extracts and phytochemicals against these detrimental bacteria towards their future application to control these in food production and clinical environments.

Combined Action of Piperitenone Epoxide and Antibiotics Against Clinical Isolates of Staphylococcus aureus and Escherichia coli

The aim of this study was to determine the antimicrobial efficiency of piperitenone epoxide (PEO) - a principal component of various aromatic plants' essential oil - in combination with various antibiotics against 28 strains of Staphylococcus aureus and 10 strains of Escherichia coli isolated from clinical samples. Mentha spicata's essential oil, initially collected by hydrodistillation, was then subjected to flush column chromatography affording PEO of high purity. Minimum inhibitory concentrations of PEO alone and in combination with various concentrations of antibiotics were assessed using the microdilution method. The combined action was estimated calculating the fractional inhibitory concentration (FIC) index from checkerboard assays. Our results showed that the average minimum inhibitory concentration (mg/l) of PEO alone against E. coli was 512 ± 364.7 μg/ml, which was significantly higher than 172.8 ± 180.7 μg/ml observed for S. aureus. From checkerboard assays, FIC values below the 0.5 index, indicating synergy, were observed for 59% of the drugs tested. Twelve percent of FIC index values were between 0.5 and 1, indicating additive effects, while 21% were indifferent. According to our results, PEO could be a promising antimicrobial compound when combined with specific antibiotics and deserves further study.

A dose response model for quantifying the infection risk of antibiotic-resistant bacteria

Quantifying the human health risk of microbial infection helps inform regulatory policies concerning pathogens, and the associated public health measures. Estimating the infection risk requires knowledge of the probability of a person being infected by a given quantity of pathogens, and this relationship is modeled using pathogen specific dose response models (DRMs). However, risk quantification for antibiotic-resistant bacteria (ARB) has been hindered by the absence of suitable DRMs for ARB. A new approach to DRMs is introduced to capture ARB and antibiotic-susceptible bacteria (ASB) dynamics as a stochastic simple death (SD) process. By bridging SD with data from bench experiments, we demonstrate methods to (1) account for the effect of antibiotic concentrations and horizontal gene transfer on risk; (2) compute total risk for samples containing multiple bacterial types (e.g., ASB, ARB); and (3) predict if illness is treatable with antibiotics. We present a case study of exposure to a mixed population of Gentamicin-susceptible and resistant Escherichia coli and predict the health outcomes for varying Gentamicin concentrations. Thus, this research establishes a new framework to quantify the risk posed by ARB and antibiotics.

Antimicrobial Peptides as Anti-Infective Agents in Pre-Post-Antibiotic Era?

Resistance to antibiotics is one of the main current threats to human health and every year multi-drug resistant bacteria are infecting millions of people worldwide, with many dying as a result. Ever since their discovery, some 40 years ago, the antimicrobial peptides (AMPs) of innate defense have been hailed as a potential alternative to conventional antibiotics due to their relatively low potential to elicit resistance. Despite continued effort by both academia and start-ups, currently there are still no antibiotics based on AMPs in use. In this study, we discuss what we know and what we do not know about these agents, and what we need to know to successfully translate discovery to application. Understanding the complex mechanics of action of these peptides is the main prerequisite for identifying and/or designing or redesigning novel molecules with potent biological activity. However, other aspects also need to be well elucidated, i.e., the (bio)synthetic processes, physiological and pathological contexts of their activity, and a quantitative understanding of how physico-chemical properties affect activity. Research groups worldwide are using biological, biophysical, and algorithmic techniques to develop models aimed at designing molecules with the necessary blend of antimicrobial potency and low toxicity. Shedding light on some open questions may contribute toward improving this process.

A Toxicity Screening Approach to Identify Bacteriophage-Encoded Anti-Microbial Proteins

The rapid emergence of antibiotic resistance among many pathogenic bacteria has created a profound need to discover new alternatives to antibiotics. Bacteriophages, the viruses of microbes, express special proteins to overtake the metabolism of the bacterial host they infect, the best known of which are involved in bacterial lysis. However, the functions of majority of bacteriophage encoded gene products are not known, i.e., they represent the hypothetical proteins of unknown function (HPUFs). In the current study we present a phage genomics-based screening approach to identify phage HPUFs with antibacterial activity with a long-term goal to use them as leads to find unknown targets to develop novel antibacterial compounds. The screening assay is based on the inhibition of bacterial growth when a toxic gene is expression-cloned into a plasmid vector. It utilizes an optimized plating assay producing a significant difference in the number of transformants after ligation of the toxic and non-toxic genes into a cloning vector. The screening assay was first tested and optimized using several known toxic and non-toxic genes. Then, it was applied to screen 94 HPUFs of bacteriophage φR1-RT, and identified four HPUFs that were toxic to Escherichia coli. This optimized assay is in principle useful in the search for bactericidal proteins of any phage, and also opens new possibilities to understanding the strategies bacteriophages use to overtake bacterial hosts.

Genetic characterisation of staphylococci of food-producing animals in Senegal. PVL detection among MSSA

Background

Food-producing animals can be a vehicle for staphylococcal species as well as their virulence and antimicrobial resistance genes. This work aimed to analyse the diversity of staphylococcal species in food-producing animals in Dakar/Senegal, and to determine the antimicrobial resistance phenotype/genotype and virulence factors of recovered isolates. Nasal samples of 149 cows and 199 chickens (348 animals) were collected from one slaughterhouse and a local market respectively, and were inoculated on selective media for staphylococci recovery. For S. aureus isolates, molecular typing (spa-type, MLST) was performed by PCR/sequencing, and the presence of 27 virulence genes (exfoliative and toxic shock toxins, PVL, haemolysins and enterotoxins) as well as the gene scn were analysed by PCR. Susceptibility to twelve antibiotics was studied by disc-diffusion method for all staphylococci; the resistance genes involved were screened by PCR.

Results

Staphylococcus spp. was present in 3 and 26.8% of chicken and cow nasal samples, respectively. Seven S. aureus isolates and forty isolates of other staphylococcal species were identified. S. aureus isolates were recovered from cow (n = 6) and chicken (n = 1) samples, belonging to four genetic lineages: t084/ST15 (n = 1); t10579/ST291 (n = 3); t355, t4690/ST152 (n = 2); and t6618/ST6 (n = 1). All S. aureus were methicillin-susceptible, penicillin-resistant (blaZ), and two of them were also tetracycline-resistant [tet(K)]. All the isolates carried at least one of the virulence genes tested. The PVL genes were detected in three ST15 and ST152 isolates. They all harboured haemolysins encoding genes and lacked the scn gene. The other staphylococci recovered were S. sciuri (n = 16), S. simulans (n = 11), S. hyicus (n = 5), S. haemolyticus (n = 4), S. chromogenes (n = 3), and S. hominis (n = 1); they were all methicillin-susceptible and 27.5% tetracycline-resistant [tet(K) and tet(L)].

Conclusions

A low prevalence of S. aureus was detected among food-producing animals, all susceptible to methicillin. However, the presence of virulence genes (lukF/lukS-PV, eta, tst, sea and see) is worrisome to the extent that they could be transferred to derived food and therefore, to humans.

Antimicrobial Resistance, Virulence, and Genetic Lineages of Staphylococci from Horses Destined for Human Consumption: High Detection of S. aureus Isolates of Lineage ST1640 and Those Carrying the lukPQ Gene

Simple Summary

Staphylococci are opportunistic pathogens which colonize humans and animals. Zoonotic transfer of staphylococcal species between domestic animals and humans is common and can occur through direct contact, the environment, and animal-derived food processing, implying a risk of the spread of antimicrobial resistance mechanisms and virulence factors into different ecosystems. Our work aimed at studying the diversity of staphylococcal species in nasal and faecal samples of healthy horses intended for human consumption and their resistance and virulence determinants. Staphylococci were detected in 90% and 66% of nasal and faecal samples tested, respectively. Eight staphylococcal species were detected, with the most prevalent ones being Staphylococcus aureus (all isolates were methicillin-susceptible), Staphylococcus delphini, and Staphylococcus sciuri. The predominant S. aureus lineage, ST1640, is associated with horses for the first time in this study. S. aureus isolates, except those of lineage ST1640, produced equid-adapted leukocidin (LukPQ) and blocker of equine complement system activation (eqSCIN). The toxic shock syndrome toxin-encoding gene was also detected in some S. aureus isolates. Multidrug resistance was observed among S. sciuri isolates, but not among S. aureus. Measures of hygiene and control should be implemented during horse slaughter and meat processing.

Abstract

This work aimed to determine the frequency and diversity of Staphylococcus species carriage in horses intended for human consumption, as well as their resistance and virulence determinants. Eighty samples (30 nasal; 50 faecal) were recovered from 73 healthy horses in a Spanish slaughterhouse. The samples were cultured for staphylococci and methicillin-resistant staphylococci (MRS) recovery. The phenotype/genotype of antimicrobial resistance was analysed for all isolates. The spa-type and sequence-type (ST) were determined in Staphylococcus aureus strains; moreover, the presence of virulence and host-adaptation genes (tst, eta, etb, pvl, lukPQ, scn-eq, and scn) was studied by PCR. Staphylococcus species were detected in 27/30 (90%) and 33/50 (66%) of nasal and faecal samples, respectively. Ninety isolates belonging to eight species were recovered, with predominance of S. aureus (n = 34), Staphylococcus delphini (n = 19), and Staphylococcus sciuri (n = 19). S. aureus strains were all methicillin-susceptible (MSSA), 28/34 were susceptible to all the antibiotics tested, and the remaining six showed resistance to (gene-detected) streptomycin (ant (6)-Ia), penicillin (blaZ), and trimetroprim/sulphametoxazole (SXT) (dfrA, dfrG). The lineage ST1640/t2559 was predominant (n = 21). The genes lukPQ and scn-eq were present in all but the ST1640 isolates. Three S. sciuri isolates were multidrug-resistant. Healthy horses in Spain seem to be a reservoir for virulent MSSA and the lineage ST1640, although the presence of the latter in horses is described for the first time in this study. Moreover, the equine-adapted leukocidin gene lukPQ is frequent among S. aureus strains. A large variety of staphylococcal species with low antibiotic resistance rate were also observed.