Sulaiman M. Alnaimat

Objectives: To investigate the genetic diversity and molecular characteristics of methicillin-resistant staphylococcus aureus (MRSA) isolates from healthcare workers in a Jordanian hospital, focusing on the role of the mecA gene in antibiotic resistance. Methods: A total of 25 staphylococcus aureus isolates were collected from healthcare workers’ skin, nasal passages, and environmental sources. Biochemical tests identified MRSA isolates, and DNA extraction was followed by polymerase chain reaction amplification of the 16SrRNA gene for genetic analysis. The sequences were analyzed using phylogenetic methods, sequence demarcation tool (SDT) analysis, and median-joining network analysis to determine genetic diversity and evolutionary relationships. Results: Out of the 25 staphylococcus aureus isolates, 10 were identified as methicillin-resistant. Phylogenetic analysis revealed distinct clustering patterns, indicating genetic heterogeneity. SDT analysis highlighted the genetic complexity of the MRSA strains. The median-joining network identified haplotype 1 as the predominant haplotype, underscoring significant genetic diversity. The mecA gene was detected in all MRSA isolates, emphasizing its critical role in methicillin resistance. Conclusion: The study demonstrates significant genetic diversity among MRSA isolates from healthcare workers in a Jordanian hospital, with the mecA gene playing a vital role in antibiotic resistance. These findings underscore the importance of molecular diagnostics in MRSA detection and the need for targeted infection control strategies to manage antibiotic resistance effectively in healthcare settings.

Extreme environments like arid and semi-arid deserts harbor unique microbial diversity, offering rich sources of specialized microbial metabolites. This study explores Bacillus velezensis RVMD2, a strain isolated from rock varnish in the Ma’an Desert, Jordan. The genome was sequenced using the Illumina NextSeq 2000 platform, resulting in a 4,212,579 bp assembly with a GC content of 45.94%. The assembled genome comprises 112 contigs and encodes 4,250 proteins, 77 tRNA genes, and 4 rRNA genes. Phylogenetic analysis of the 16S rRNA gene indicated a 99.84% similarity to previously identified B. velezensis strains. Whole-genome phylogeny using EzBiome, MiGA, and TYGS confirmed its classification as B. velezensis. Functional annotation identified genes involved in carbohydrate metabolism, including 324 carbohydrate-active enzyme (CAZyme) genes, stress response, and secondary metabolite biosynthesis. The genome also contains 50 genes associated with heavy metal resistance and plant growth promotion. Analysis using AntiSMASH identified 12 biosynthetic gene clusters involved in the production of secondary metabolites, including fengycin, surfactin, polyketides, terpenes, and bacteriocins. Notably, several clusters did not match any known sequences, suggesting the presence of potentially novel antimicrobial compounds. The genomic features of RVMD2 highlight its adaptability to extreme environments and its potential for biotechnological applications, including bioremediation and the discovery of novel bioactive metabolites.

Here, we report the draft genome sequence of Salinicoccus roseus H15, isolated from desert rock varnish in Ma'an, Jordan. The genome size is 2,457,773 bp with a GC content of 49.31 mol%. The genome includes 3,064 genes and 135 carbohydrate-active enzymes, demonstrating adaptations for survival in extreme environments.

Desert environments harbor unique microbial communities. This study focuses on Cellulosimicrobium funkei isolate RVMD1, isolated from rock varnish in the Ma’an Desert. Initial identification was achieved using 16S rRNA gene sequencing, followed by whole-genome sequencing (WGS) for comprehensive characterization. The genome comprises 4,264,015 base pairs (857 contigs) with a high G + C content of 74.59%. A total of 4,449 proteins were predicted. Comparative analysis utilizing OrthoANI, ANI, AAI, and dDDH metrics suggests that RVMD1 belongs to the C. cellulans group, with the highest similarity to C. funkei (97.71% ANI). Phylogenomic analysis of 43 Cellulosimicrobium genomes revealed significant heterogeneity within the genus. Our results challenge current systematics, with C. cellulans potentially representing up to 9 distinct genomospecies. Isolate RVMD1 shows genetic adaptations to its desert environment, including genes for denitrification, oxygen and sulfur cycling, and diverse hydrogen metabolism. Pangenomic analysis uncovered a considerable number of unique genes within RVMD1, highlighting its genetic distinctiveness. Gene family expansions suggest evolution in response to stressors like UV radiation and nutrient limitation. This study represents the first whole-genome analysis of a bacterium isolated from Jordanian rock varnish, emphasizing the value of WGS in understanding microbial diversity and adaptation in extreme environments.

Artemisia herba-alba (AHA), known as sheeh in Jordan, is recommended by regional traditional healers for the treatment of a variety of diseases. AHA has been used in folk medicine to treat colds, coughing, bronchitis, intestinal disturbances, diarrhea, neuralgias, arterial hypertension, and diabetes. The objectives of the current study were to identify the chemical compositions of the essential oil extracted from dried leaf powder of AHA cultivated in Jordan and investigate its antibacterial and antioxidant activities. The essential oil was isolated using hydro distillation, and the identification of artemisia herba-alba essential oil (AHEO) composition was performed using validated gas chromatography-mass spectrometry (GC-MS). The antibacterial activity of AHEO was assessed against escherichia coli, pseudomonas aeruginosa, klebsiella pneumonia, and staphylococcus aureus and two clinical isolates (methicillin-resistant staphylococcus aureus and methicillin-resistant staphylococcus epidermidis [MRSE]) using a disc diffusion method, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) values, using the micro-dilution broth method. Additionally, antioxidant activities were determined using DPPH and ABTS radical scavenging assays. The results revealed that the yield of AHEO was 4.41% v/w, with nearly 22 identified compounds, constituting approximately 96.80% of the total mass of essential oils. Monoterpenoids was the major compounds (71.90%), with alpha pinene being the major component, accounting for 17.20% of the composition. The total phenolic and flavonoid contents were 43.97 mg GAE/g and 30.11 mg CE/g, respectively. The antibacterial activity of AHEO against MRSE exhibited the highest inhibitory effect, while E.coli showed the highest MBC value. Furthermore, AHEO demonstrated significant antioxidant activity (IC50= 64.57 and 34.01 for DPPH and ABTS, respectively). The results indicate that AHEO possess good antioxidant and antibacterial properties, suggesting that they may be used as a supplementary food and antimicrobial agent.

Indole synthase (INS), a homologous cytosolic enzyme of the plastidal tryptophan synthase A (TSA), has been reported as the first enzyme in the tryptophan-independent pathway of auxin synthesis. This suggestion was challenged as INS or its free indole product may interact with tryptophan synthase B (TSB) and, therefore, with the tryptophan-dependent pathway. Thus, the main aim of this research was to find out whether INS is involved in the tryptophan-dependent or independent pathway. The gene coexpression approach is widely recognized as an efficient tool to uncover functionally related genes. Coexpression data presented here were supported by both RNAseq and microarray platforms and, hence, considered reliable. Coexpression meta-analyses of Arabidopsis genome was implemented to compare between the coexpression of TSA and INS with all genes involved in the production of tryptophan via the chorismate pathway. Tryptophan synthase A was found to be coexpressed strongly with TSB1/2, anthranilate synthase A1/B1, phosphoribosyl anthranilate transferase1, as well as indole-3-glycerol phosphate synthase1. However, INS was not found to be coexpressed with any target genes suggesting that it may exclusively and independently be involved in the tryptophan-independent pathway. Additionally, annotation of examined genes as ubiquitous or differentially expressed were described and subunits-encoded genes available for the assembly of tryptophan and anthranilate synthase complex were suggested. The most probable TSB subunits expected to interact with TSA is TSB1 then TSB2. Whereas TSB3 is only used under limited hormone conditions to assemble tryptophan synthase complex, putative TSB4 is not expected to be involved in the plastidial synthesis of tryptophan in Arabidopsis.

Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria including Geodermatphilaceae. A culture-dependent approach was performed as a companion study with this culture-independent metagenomic analysis of these stone samples and resulted in the isolation of eleven Geodermatphilaceae strains (2 Geodermatophilus and 9 Blastococcus strains). The genomes of the 11 Geodermatphilaceae strains were sequenced and analyzed. The genomes for the two Geodermatophilus isolates, DF1-2 and TF2-6, were 4.45 and 4.75 Mb, respectively, while the Blastococcus genomes ranged in size from 3.98 to 5.48 Mb. Phylogenetic analysis, digital DNA:DNA hybridization (dDDH), and comparisons of the average nucleotide identities (ANI) suggest the isolates represent novel Geodermatophilus and Blastococcus species. Functional analysis of the Geodermatphilaceae genomes provides insight on the stone microbiome niche.

The purpose of this study was to assess the health of stony coral Porites sp. based on the presence of bacterial pathogens, specifically Vibrio coralliilyticus, in the Gulf of Aqaba, and to assess the impact of anthropogenic activities on Porites sp. Porites sp. specimens were collected from the Marine Science Station (MSS) and a public beach (Yamanyeh) in Jordan. Mucus, water and sediment samples were collected throughout the year. The Vibrio-like population was higher in diseased samples than in healthy samples and was slightly higher in Yamanyeh than in MSS in all the samples. In samples from both sites, there was a seasonal variation in the Vibrio-like population, with a decline in population as the temperature reduced. All samples contained virulent isolates clustered with V. coralliilyticus strains. Inoculation of healthy Porites sp. fragments with virulent isolates and V. coralliilyticus strain caused bleaching of the coral after 48 h. Therefore, V. coralliilyticus represents a pathogenic agent which may contribute to bleaching in Porites sp. in the Gulf of Aqaba and may not be affected considerably by anthropogenic activities. This is the first report of a bacterial pathogen of corals in Jordan; future studies should identify other coral pathogens in this region.

The reverse genetic approach has uncovered indole synthase (INS) as the first enzyme in the tryptophan (trp)-independent pathway of IAA synthesis. The importance of INS was reevaluated suggesting it may interact with tryptophan synthase B (TSB) and therefore involved in the trp-dependent pathway. Thus, the main aim of this study was to clarify the route of INS through the analysis of Arabidopsis genome. Analysis of the top 2000 co-expression gene lists in general and specific conditions shows that TSA is strongly positively co-expressed with TSB in general, hormone, and abiotic conditions with mutual ranks of 89, 38, and 180 respectively. Moreover, TSA is positively correlated with TSB (0.291). However, INS was not found in any of these coexpressed gene lists and negatively correlated with TSB (− 0.046) suggesting unambiguously that these two routes are separately and independently operated. So far, the remaining steps in the INS pathway have remained elusive. Among all enzymes reported to have a role in IAA synthesis, amidase was found to strongly positively co-expressed with INS in general and light conditions with mutual ranks of 116 and 141 respectively. Additionally, amidase1 was found to positively correlate with INS (0.297) and negatively coexpressed with TSB concluding that amidase may exclusively involve in the trp-independent pathway.