Antimicrobial Resistance Genes Analysis of Publicly Available Staphylococcus aureus Genomes

[EN]Staphylococcus aureus is a pathogen that can cause severe illness and express resistance to multiple antimicrobial agents. It is part of the ESKAPE organisms and it has been included by the Centers for Disease Control and Prevention (CDC) of USA in the list of serious threats to humans. Many antimicrobial mechanisms have been identified, and, in particular, antimicrobial resistance genes (ARGs) can be determined by whole genome sequencing. Mobile genetic elements (MGEs) can determine the spread of these ARGs between strains and species and can be identified with bioinformatic analyses. The scope of this work was to analyse publicly available genomes of S. aureus to characterise the occurrence of ARGs present in chromosomes and plasmids in relation to their geographical distribution, isolation sources, clonal complexes, and changes over time. The results showed that from a total of 29,679 S. aureus genomes, 24,765 chromosomes containing 73 different ARGs, and 21,006 plasmidic contigs containing 47 different ARGs were identified. The most abundant ARG in chromosomes was mecA (84%), while blaZ was the most abundant in plasmidic contigs (30%), although it was also abundant in chromosomes (42%). A total of 13 clonal complexes were assigned and differences in ARGs and CC distribution were highlighted among continents. Temporal changes during the past 20 years (from 2001 to 2020) showed that, in plasmids, MRSA and macrolide resistance occurrence decreased, while the occurrence of ARGs associated with aminoglycosides resistance increased. Despite the lack of metadata information in around half of the genomes analysed, the results obtained enable an in-depth analysis of the distribution of ARGs and MGEs throughout different categories to be undertaken through the design and implementation of a relatively simple pipeline, which can be also applied in future works with other pathogens, for surveillance and screening purposes.S

Prevalence and persistence of Listeria monocytogenes in premises and products of small food business operators in Northern Ireland

peer-reviewedListeriosis is a foodborne disease, with a high mortality rate, that predominantly affects the elderly. Under European Union legislation, EC 2073/2005, food business operators are encouraged to undertake sampling to ensure that the food processing environment, and required to ensure that food products, are free of Listeria monocytogenes. To determine the prevalence of L. monocytogenes in smaller food processing facilities in Northern Ireland, 24 companies submitted six processing environment swabs and two food samples every two months for eighteen months (July 2015 to November 2016) for L. monocytogenes examination. The prevalence of L. monocytogenes was 4.6% in food samples, and 6.3% in processing environment swabs. Over the duration of the study, 96 isolates of L. monocytogenes were obtained, one from each positive sample, except for two meat samples that had >100 cfu/g, where two isolates were obtained from each sample. No seasonality in occurrence of L. monocytogenes was seen for food isolates but significantly higher numbers of positive processing environment swabs were found in the warmer months of May, July and September (p = .007). Pulsed Field Gel Electrophoresis (PFGE) analysis revealed the presence of 27 pulsotypes; 9 pulsotypes were shared between different facilities and 9 were persistent. Based on a Combase predictive growth model, 77.5% (n = 130) of the foods tested were predicted to support the growth of L. monocytogenes. All of the isolates carried the pathogenicity genes inlA and actA and 71.4% carried qacH, which confers resistance to quaternary ammonium compounds which are frequently used in sanitizers. Whole genome sequencing of the isolates allowed multi-locus sequence typing to be undertaken. The data indicated that the sequence types identified included those with disease-causing ability, highlighting the disease-causing potential of the isolates

Revolutionizing orthopedic healthcare: a systematic review unveiling recombinant antimicrobial peptides

The increasing demand for orthopedic surgeries, including joint replacements, is driven by an aging population and improved diagnosis of joint conditions. Orthopedic surgeries carry a risk of infection, especially in patients with comorbidities. The rise of antibiotic resistance exacerbates this issue, necessitating alternatives like in vitro bioengineered antimicrobial peptides (AMPs), offering broad-spectrum activity and multiple action mechanisms. This review aimed to assess the prevalence of antimicrobial potential and the yield after purification among recombinant AMP families. The antimicrobial potential was evaluated using the Minimum Inhibitory Concentration (MIC) values against the most common bacteria involved in clinical infections. This systematic review adhered to PRISMA guidelines, focusing on in vitro studies of recombinant AMPs. The search strategy was run on PubMed, Scopus and Embase up to 30th March 2023. The Population, Exposure and Outcome model was used to extract the data from studies and ToxRTool for the risk of bias analysis. This review included studies providing peptide production yield data and MIC values against pathogenic bacteria. Non-English texts, reviews, conference abstracts, books, studies focusing solely on chemical synthesis, those reporting incomplete data sets, using non-standard MIC assessment methods, or presenting MIC values as ranges rather than precise concentrations, were excluded. From 370 publications, 34 studies on AMPs were analyzed. These covered 46 AMPs across 18 families, with Defensins and Hepcidins being most common. Yields varied from 0.5 to 2,700 mg/L. AMPs were tested against 23 bacterial genera, with MIC values ranging from 0.125 to >1,152 μg/mL. Arenicins showed the highest antimicrobial activity, particularly against common orthopedic infection pathogens. However, AMP production yields varied and some AMPs demonstrated limited effectiveness against certain bacterial strains. This systematic review emphasizes the critical role of bioengineered AMPs to cope infections and antibiotic resistance. It meticulously evaluates recombinant AMPs, focusing on their antimicrobial efficacy and production yields. The review highlights that, despite the variability in AMP yields and effectiveness, Arenicins and Defensins are promising candidates for future research and clinical applications in treating antibiotic-resistant orthopedic infections. This study contributes significantly to the understanding of AMPs in healthcare, underscoring their potential in addressing the growing challenge of antibiotic resistance. Systematic review registration:https://osf.io/2uq4c/

Evaluation of lactic acid bacteria strains isolated from fructose-rich environments for their mannitol-production and milk-gelation abilities

peer-reviewedMannitol is a sugar alcohol, or polyol, widely used in the food industry because of its low-calorie properties. Industrial production of mannitol is difficult and expensive. However, certain bacterial species are known to produce mannitol naturally, including certain lactic acid bacteria and fructophilic lactic acid bacteria (LAB). In this study, bacterial strains isolated from fructose-rich sources, including flowers, leaves, and honey, were identified by 16S rRNA sequence analysis as Leuconostoc, Fructobacillus, Lactococcus, and Lactobacillus species and 4 non-LAB species. DNA profiles generated by pulsed-field gel electrophoresis discriminated 32 strains of Leuconostoc mesenteroides and 6 Fructobacillus strains. Out of 41 LAB strains isolated, 32 were shown to harbor the mdh gene, which encodes the mannitol dehydrogenase enzyme, and several showed remarkable fructose tolerance even at 50% fructose concentrations, indicating their fructophilic nature. Several of the strains isolated, including Leuconostoc mesenteroides strains DPC 7232 and DPC 7261, Fructobacillus fructosus DPC 7237, and Fructobacillus fructosus DPC 7238, produced higher mannitol concentrations than did the positive control strain Limosilactobacillus reuteri DSM 20016 during an enzymatic screening assay. Mannitol concentrations were also examined via HPLC in 1% fructose de Man, Rogosa, and Sharpe medium (FMRS) or 1% fructose milk (FM). Among the strains, Fructobacillus fructosus DPC 7238 displayed high fructose utilization (9.27 g/L), high mannitol yield (0.99 g of mannitol/g of fructose), and greatest volumetric productivities (0.46 g/L per h) in FMRS. However, Leuconostoc mesenteroides DPC 7261 demonstrated the highest fructose utilization (8.99 g/L), mannitol yield (0.72 g of mannitol/g of fructose), and volumetric productivities (0.04 g/L per h) in FM. Storage modulus G′ (>0.1 Pa) indicated a shorter gelation time for Limosilactobacillus reuteri DSM 20016 (8.73 h), followed by F. fructosus DPC 7238 (11.57 h) and L. mesenteroides DPC 7261 (14.52 h). Our results show that fructose-rich niches can be considered important sources of fructophilic LAB strains, with the potential to be used as starter cultures or adjunct cultures for the manufacture of mannitol-enriched fermented dairy products and beverages

Inhibition of L. monocytogenes Biofilm Formation by the Amidase Domain of the Phage vB_LmoS_293 Endolysin

peer-reviewedListeria monocytogenes is a ubiquitous Gram-positive bacterium that is a major concern for food business operators because of its pathogenicity and ability to form biofilms in food production environments. Bacteriophages (phages) have been evaluated as biocontrol agents for L. monocytogenes in a number of studies and, indeed, certain phages have been approved for use as anti-listerial agents in food processing environments (ListShield and PhageGuard Listex). Endolysins are proteins produced by phages in the host cell. They cleave the peptidoglycan cell wall, thus allowing release of progeny phage into the environment. In this study, the amidase domain of the phage vB_LmoS_293 endolysin (293-amidase) was cloned and expressed in Escherichia. coli(E. coli). Muralytic activity at different concentrations, pH and temperature values, lytic spectrum and activity against biofilms was determined for the purified 293-amidase protein. The results showed activity on autoclaved cells at three different temperatures (20 °C, 37 °C and 50 °C), with a wider specificity (L. monocytogenes 473 and 3099, a serotype 4b and serogroup 1/2b-3b-7, respectively) compared to the phage itself, which targets only L. monocytogenes serotypes 4b and 4e. The protein also inhibits biofilm formation on abiotic surfaces. These results show the potential of using recombinant antimicrobial proteins against pathogens in the food production environment

Effectiveness of current hygiene practices on minimization of Listeria monocytogenes in different mushroom production‐related environments

peer-reviewedBackground: The commercial production of Agaricus bisporus is a three stage process: 1) production of compost, also called “substrate”; 2) production of casing soil; and 3) production of the mushrooms. Hygiene practices are undertaken at each stage: pasteurization of the substrate, hygiene practices applied during the production of casing soil, postharvest steam cookout, and disinfection at the mushroom production facilities. However, despite these measures, foodborne pathogens, including Listeria monocytogenes, are reported in the mushroom production environment. In this work, the presence of L. monocytogenes was evaluated before and after the application of hygiene practices at each stage of mushroom production with swabs, samples of substrate, casing, and spent mushroom growing substrates. Results: L. monocytogenes was not detected in any casing or substrate sample by enumeration according to BS EN ISO 11290-2:1998. Analysis of the substrate showed that L. monocytogenes was absent in 10 Phase II samples following pasteurization, but was then present in 40% of 10 Phase III samples. At the casing production facility, 31% of 59 samples were positive. Hygiene improvements were applied, and after four sampling occasions, 22% of 37 samples were positive, but no statistically significant difference was observed (p > .05). At mushroom production facilities, the steam cookout process inactivated L. monocytogenes in the spent growth substrate, but 13% of 15 floor swabs at Company 1 and 19% of 16 floor swabs at Company 2, taken after disinfection, were positive. Conclusion: These results showed the possibility of L. monocytogenes recontamination of Phase III substrate, cross-contamination at the casing production stage and possible survival after postharvest hygiene practices at the mushroom growing facilities. This information will support the development of targeted measures to minimize L. monocytogenes in the mushroom industry.Food Institutional Research Measur

Reduced Rate of Hospital Admissions for ACS during Covid-19 Outbreak in Northern Italy

To address the coronavirus (Covid-19) pandemic,1 strict social containment measures have been adopted worldwide, and health care systems have been reorganized to cope with the enormous increase in the numbers of acutely ill patients.2,3 During this same period, some changes in the pattern of hospital admissions for other conditions have been noted. The aim of the present analysis is to investigate the rate of hospital admissions for acute coronary syndrome (ACS) during the early days of the Covid-19 outbreak

Variability in Cold Tolerance of Food and Clinical <i>Listeria monocytogenes</i> Isolates

The aim of this study was to investigate the level of strain variability amongst food and clinical Listeria monocytogenes isolates growing at low temperatures (4 and 7 °C) in both laboratory media and real food matrices. Isolates (n = 150) grown in laboratory media demonstrated a large variation in growth profiles measured using optical density. Overall, it was noted that clinical isolates exhibited a significantly higher growth rate (p ≤ 0.05) at 7 °C than the other isolates. Analysis of variance (ANOVA) tests of isolates grouped using Multi Locus Sequence Typing (MLST) revealed that clonal complex 18 (CC18) isolates were significantly (p ≤ 0.05) faster growing at 4 °C than other CC-type isolates while CC101, CC18, CC8, CC37 and CC14 were faster growing than other CC types at 7 °C. Euclidean distance and Ward method-based hierarchical clustering of mean growth rates classified 33.33% of isolates as faster growing. Fast and slow growing representative isolates were selected from the cluster analysis and growth rates were determined using plate count data in laboratory media and model food matrices. In agreement with the optical density experiments, CC18 isolates were faster and CC121 isolates were slower than other CC types in laboratory media, UHT milk and fish pie. The same trend was observed in chocolate milk but the differences were not statistically significant. Moreover, pan-genome analysis (Scoary) of isolate genome sequences only identified six genes of unknown function associated with increased cold tolerance while failing to identify any known cold tolerance genes. Overall, an association that was consistent in laboratory media and real food matrices was demonstrated between isolate CC type and increased cold tolerance

Antimicrobial Resistance Genes Analysis of Publicly Available Staphylococcus aureus Genomes

Staphylococcus aureus is a pathogen that can cause severe illness and express resistance to multiple antimicrobial agents. It is part of the ESKAPE organisms and it has been included by the Centers for Disease Control and Prevention (CDC) of USA in the list of serious threats to humans. Many antimicrobial mechanisms have been identified, and, in particular, antimicrobial resistance genes (ARGs) can be determined by whole genome sequencing. Mobile genetic elements (MGEs) can determine the spread of these ARGs between strains and species and can be identified with bioinformatic analyses. The scope of this work was to analyse publicly available genomes of S. aureus to characterise the occurrence of ARGs present in chromosomes and plasmids in relation to their geographical distribution, isolation sources, clonal complexes, and changes over time. The results showed that from a total of 29,679 S. aureus genomes, 24,765 chromosomes containing 73 different ARGs, and 21,006 plasmidic contigs containing 47 different ARGs were identified. The most abundant ARG in chromosomes was mecA (84%), while blaZ was the most abundant in plasmidic contigs (30%), although it was also abundant in chromosomes (42%). A total of 13 clonal complexes were assigned and differences in ARGs and CC distribution were highlighted among continents. Temporal changes during the past 20 years (from 2001 to 2020) showed that, in plasmids, MRSA and macrolide resistance occurrence decreased, while the occurrence of ARGs associated with aminoglycosides resistance increased. Despite the lack of metadata information in around half of the genomes analysed, the results obtained enable an in-depth analysis of the distribution of ARGs and MGEs throughout different categories to be undertaken through the design and implementation of a relatively simple pipeline, which can be also applied in future works with other pathogens, for surveillance and screening purposes

Prevalence, virulence characterization, and genetic relatedness of Listeria monocytogenes isolated from chicken retail points and poultry slaughterhouses in Turkey

PubMed: 31478167Listeria monocytogenes is one of the most important foodborne pathogens and is a causal agent of listeriosis in humans and animals. The aim of this study was to determine the prevalence, serogroups, antibiotic susceptibility, virulence factor genes, and genetic relatedness of L. monocytogenes strains isolated from 500 poultry samples in Turkey. The isolation sources of 103 L. monocytogenes strains were retail markets (n = 100) and slaughterhouses (n = 3). L. monocytogenes strains were identified as serogroups 1/2a-3a (75.7%, lineage I), 1/2c-3c (14.56%, lineage I), 1/2b-3b-7 (5.82%, lineage II), 4a-4c (2.91%, lineage III), and 4b-4d-4e (0.97%, lineage III). Most of the L. monocytogenes strains (93.2%) were susceptible to the antibiotics tested. PCR analysis indicated that the majority of the strains (95% to 100%) contained most of the virulence genes (hylA, plcA, plcB, prfA, mpl, actA, dltA, fri, flaA inlA, inlC, and inlJ). Pulsed-field gel electrophoresis (PFGE) demonstrated that there were 18 pulsotypes grouped at a similarity of >90% among the strains. These results indicate that it is necessary to prevent the presence of L. monocytogenes in the poultry-processing environments to help prevent outbreaks of listeriosis and protect public health