Functional and comparative genomics of Enterococcus faecium isolated from animals

Enterococci are Gram-positive bacteria that inhabit the gastrointestinal tract of humans and animals as commensal flora. In recent years two species, Enterococcus faecalis and Enterococcus faecium, have become an increasing medical concern by virtue of their ability to gain and spread antibiotic resistance. In this study, genomes of vancomycin-resistant isolates of E. faecium from pig, chicken and calf were sequenced using 454 and PacBio platforms. The assembled genomes were annotated and compared with human E. faecium isolates to identify their repertoire of genes potentially associated with colonising each host. Phylogenomics of E. faecium was used to investigate the relationship between animal and human strains. The genomes of the chicken, pig and calf isolates differed in size (2.5 Mb to 3.3 Mb) with the size difference due to horizontally-acquired elements (mostly phage, transposons and insertion sequences); the chicken isolate genome contained five prophages. A mega-plasmid present in each of the sequenced E. faecium was revealed to be integrated into the genome of the chicken isolate. Comparison of the three genomes identified putative niche adaptation genes with a variety of proposed functions, particularly carbohydrate utilisation. Possible factors that explain E. faecium sub-populations, including clinical, commensal and animal isolate clades were examined. Use of the PhenoLink relationship tool to examine the E. faecium sub-populations identified that putative niche specific genes include carbohydrate utilisation genes and mobile genetic elements. Temperate bacteriophages are known to be important drivers of genome plasticity in E. faecium species. The diversity of prophages and their relationship between was investigated after locating 56 prophage elements containing integrase and lysin genes encoded in the 139 publicly available E. faecium genomes. Comparative analysis of these prophages identified eight sequence types, which differed in size and gene content. The prophage genomes comprised between 17 to 72 ORFs and their size ranged from 13.9 to 55.1 kb with 35% to 37.9% average G+C content. Based on alignment analyses of the major functional proteins encoded in the prophage genomes (integrase, terminase large subunit, tail protein and holin) each was assigned a sequence type. All of the prophage integrases were identified to be tyrosine (XerC) recombinases and many of their respective attP/attR sequences were identified. The mosaic nature of E. faecium prophage genome sequence types supports previous hypotheses that extensive genetic recombination drives chimeric phage types

Comparative Genomics of Enterococcus Faecium Bacteriophages

Temperate bacteriophages are known to be important drivers of genome plasticity in E.  faecium species. The diversity of prophages and their relationship between was investigated after locating 56 prophage elements containing integrase and lysin genes encoded in the 139 publicly available E.  faecium genomes by the end of 2014. Comparative analysis of the seprophages identified eight sequence types, which differed in size and gene content. The prophage genomes comprised between 17 to 72 ORFs and their size ranged from 13.9  to  55.1  kb with 35%  to  37.9% average  G+C  content. Based on alignment analyses of the major functional proteins encoded in the prophage genomes (integrase, terminaselarge subunit, tail protein and holin) each was assigned a sequence type. All of the prophage integrases were identified to be tyrosine  (XerC) recombinases  and  many  of  their  respective attP/attR sequences  were  identified. The mosaic nature of E.  faecium prophage genome sequence types supports previous hypotheses that extensive genetic recombination drives chimeric phage types

Incidence and Susceptibility Patterns of Urine Bacterial Flora in Young Saudi Females

It has been established that the urinary tract is not sterile; however, research related to the study of urinary bacteria is limited. This study aimed to investigate the frequency and patterns of resistance of normal urinary aerobic bacterial flora and clean catch midstream urine specimens collected from 120 young healthy females and cultured. Bacterial identification and antimicrobial susceptibility were performed using the Biomérieux VITEK® 2 automated system. Participants who had undergone antimicrobial treatment within one month were not included. The incidence of positive bacterial cultures was 54.2%, of which 21.5% were polymicrobial. Approximately 107 bacterial isolates that encompass 12 genera and 27 species that were predominated by gram-positive bacteria (72%) were cultivated. Staphylococcaceae (46.1%) and Enterobacteriaceae (17.8%) were the most frequent isolates among gram-positive and gram-negative bacteria, respectively, of which 36 species have been identified as β-lactamase producers. The top four frequently isolated bacteria were Micrococcus spp. (16%), Staphylococcus haemolyticus (13.2%), Staphylococcus aureus (10%), and Klebsiella pneumoniae (10%). Twenty-two bacterial species were subjected to antimicrobial susceptibility testing using broad- and narrow-spectrum antibiotics and antimicrobials, which showed the lowest susceptibility rate against gram-positive bacteria, followed by erythromycin and azithromycin. A lower antimicrobial susceptibility potential among gram-negative bacteria was observed against ampicillin, followed by piperacillin and cefotaxime. Our findings emphasize the importance of highlighting urine bacterial flora in studies, especially those related to susceptibility patterns, by employing more advanced culture methods as multiple drug-resistant bacteria were isolated

Assessing the probiotic potential, antioxidant, and antibacterial activities of oat and soy milk fermented with Lactiplantibacillus plantarum strains isolated from Tibetan Kefir

Sufficient intake of probiotics has been shown to help in the digestion, protect the body against pathogenic microorganisms and boost the immune system. Recently, due to high prevalence of milk allergies and lactose intolerance in population, the non-dairy based probiotic alternative are becoming increasing popular. In this context, the oat milk and soya milk-based fermented products can be an ideal alternative for the development of Lactic acid bacteria bacteria based probiotics. These bacteria can not only improve the product’s flavor and bioavailability but also increases its antibacterial and antioxidant capabilities due to fermentation process. The purpose of the resent work was to assess the antioxidant and probiotic properties of oat and soy milk that had been fermented with three different strains of Lactiplantibacillus plantarum (L. plantarum) including L. plantarum 12–3, L. plantarum K25, and L. plantarum YW11 isolated from Tibetan Kefir. Different validated assays were used to evaluate the probiotic properties, adhesion and survival in the digestive system (stomach, acid and bile salts resistance), antioxidant and antimicrobial activities and safety (ABTS and DPPH scavenging assays) of these strains. Results of the study showed that soya milk and oat milk fermented with L. plantarum strains possess promising probiotic, antibacterial and antioxidant properties. These results can be helpful to produce dairy-free probiotic replacements, which are beneficial for those who are unable to consume dairy products due to dietary or allergic restrictions

Antimicrobial Resistance Strategies: Are We Approaching the End?

This review provides an overview regarding the main aspects of fatal bacterial infections and antibiotics; in recent years, it has been observed that gram-negative bacteria are prevalent in infections owing to a failure to treat the infection and antibiotic resistance. This has led to the phrase “the end of the antibiotic era,” which was revealed in late 2017. This topic has gained momentum among the journalists, specialists, and broadcasters, who have developed immense interest in exploring new approaches and substitutes for antibiotics to treat infections. Several factors contribute to the increasing antibiotic resistance; these can be divided into two main categories, that is, those caused by human behaviors with respect to antibiotic use and those enacted by pathogens as they attempt to protect themselves against antibiotics. Therefore, the main purpose of this review is to discuss and summarize the most important factors and emphasize the measures to tackle drug resistance worldwide. A comprehensive studies were conducted to evaluate the reasons of antimicrobial resistance, studying different factors including bacterial strains (either positive or negative) gram bacteria, antimicrobial agent, in case of negative gram bacteria that’s mean the isolates are not inhibited by the selected antimicrobial agent or by achievable concentrations, the normal dose schedules and / or the diameters of the area in the range, that’s lead to a specific mechanisms of microbial resistance (e.g., beta-lactamase)

The Prevalence of Staphylococcus aureus and Methicillin Resistant Staphylococcus aureus in Processed Food Samples in Riyadh, Saudi Arabia

Staphylococcus aureus mainly Methicillin Resistant Staphylococcus aureus(MRSA) is a life-threatening infection that occurring in food and caused a public health concern. This study designed to examine the prevalence of S. aureus and MRSA in different types of processed food. Food samples were screened for the recovered strains of S. aureus and MRSA, and they were examined for antimicrobial susceptibility and by molecular characterization of mecA and staphylococcal cassette chromosome mec(SCCmec). Detection of virulence factors like Panton-Valentine Leukocidin (PVL), Staphylococcus aureus protein A(spa) and Staphylococcal enterotoxins(SEs) by PCR using specific primers. Among the 150 collected processed food samples, 62.7% were contaminated by S. aureus bacteria, 56.4% of which were proved as MRSA. 17% of MRSA isolates were positive for mecA genes with the SCCmec type IVb and V (11.1% each) as the solely existing types of SCCmec. None of the MRSA isolates carried mecC or mecB genes. Most of MRSA isolates were multidrug resistance and 33.3% of MRSA-mecA positive isolates also carried vancomycin resistance genes (i.e., vanB). In addition, spa gene was found among 7.5% of MRSA isolates; none of which were positive for PVL gene. Further, there were variant presence of SEs among MRSA isolates and the highest presence was from type SEH (49.1%). Generally, our results confirmed that processed foods in Saudi Arabia (Riyadh) are potential vehicles for multidrug resistant S. aureus and MRSA transmission; which are serious public health risks, and underlined the need for good hygiene practices