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Background. Salmonellosis most commonly presents clinically as typhoid fever or gastroenteritis. Pleuropulmonary infections due to Salmonella are still rare, even though they have often been described in immunocompromised patients. Case presentation. We report a rare case of purulent pleurisy caused by Salmonella enterica subsp. arizonae, occurring in a 50-year-old female with breast cancer who is currently treated with chemotherapy and radiotherapy along with chronic renal failure requiring haemodialysis, who presented with acute chest pain, dyspnoea and haemodynamic instability. After bacteriological identification of Salmonella enterica subsp. arizonae in pleural fluid, antibiotic susceptibility testing was performed. The patient was then started on a broad-spectrum antibiotic, which successfully improved her condition. Conclusion. Our case highlights the implication of Salmonella enterica subsp. arizonae in purulent pleurisy in an immunocompromised patient. An early diagnosis and a proper antibiotic therapy enabled us to reduce the morbidity and mortality risk in our patient.

Here, we report the draft 5.8 Mb genome sequence of a Flavobacterium aquidurense isolate from untreated wastewater in Liverpool, United Kingdom. The reported isolate has the potential to produce both flexirubin and β-carotene pigments, and contains an additional biosynthetic gene cluster for a putative novel β-lactone. The genome also contains a gene for a putative β-lactamase bla_JOHN-1 analogue, and there are multiple copies of a putative novel insertion sequence of the IS3 family. This genome adds to a growing resource of Flavobacterium spp. sequencing data which can be utilized to investigate microbial pigment production, antimicrobial resistance genes and mobile genetic elements within this genus.

The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed Pseudomonadota (67-69%), Bacteroidota (6-8%), Bacillota (5-8%), Campylobacterota (4-5%), Acidobacteriota (3-4%), Planctomycetota (2-4%) and Actinomycetota (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of Burkholderiaceae, Bacillaceae and Enterobacteriaceae suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.

Experiential learning is the pedagogic foundation of practical laboratory education. This process of learning through experience enables students to develop a deeper understanding of the theoretical material as well as valuable real-world skills. However, there is often a disconnect between the authentic, real-world context of performing laboratory skills and the method of instruction within higher education. This study developed two student laboratory manuals; one which followed a traditionally linear 'week by week' format, and another which took inspiration from a publication format and listed the protocols in a distinct 'methods' section. The effect the change of layout had on student learning was assessed through analysis of student summative assessment and interaction with the online learning environment. Additionally, the effect on student confidence and perceived technical skills development was assessed through a student survey. The differences in layout resulted in no significant differences in student assessment performance but did result in higher levels of engagement with the online learning environment. The student survey reported an increase in technical confidence (21%) and skill (31%) with the authentic 'methods' section layout changes compared to the traditional format. The increase in student engagement, confidence and perceived skill shows that experiential learning benefits from placing the information in an authentic context.

Methicillin-resistant Staphylococcus aureus (MRSA) causes considerable morbidity and mortality in both community-acquired and healthcare-associated infections, but detecting colonization with MRSA has been shown to improve patient outcomes in certain clinical settings. MRSA colonization detection has been carried out in a variety of ways, with molecular assays having superior sensitivity in most studies relative to culture, but culture is disadvantaged in some comparisons by utilization of low specimen volumes. We compared a commercial molecular assay to both low-volume (10 µl) and high-volume (650 µl) cultures and found that increasing the volume utilized for culture led to the detection of 25% more cases than low-volume culture.

Introduction. Coccidioidomycosis, or Valley fever, is a fungal disease caused by Coccidioides species, prevalent in parts of the southwestern United States. It usually results from inhaling spores from soil and is a common cause of pneumonia in these regions. Case Presentation. We present a unique case of coccidioidomycosis in an immunodeficient male patient secondary to human immunodeficiency virus infection with poor adherence to anti-retroviral treatment. After presenting with non-specific symptoms and pre-syncope, he was initially diagnosed with pneumonia based on chest X-ray findings, but his symptoms failed to improve with antibiotics. He was treated for presumed pulmonary histoplasmosis following a positive histoplasma urine antigen test. However, the patient worsened clinically. Following a computed tomography scan demonstrating a large necrotic lung consolidation, fungal stain and culture of tissue biopsied through endobronchial ultrasound confirmed coccidioidomycosis. The patient received 2 weeks of liposomal amphotericin with clinical improvement before discharge with itraconazole. Conclusion. The histoplasma antigen test can be falsely positive due to cross-reaction with other fungal infections like blastomycosis, paracoccidioidomycosis or talaromycosis, and less frequently, coccidioidomycosis or aspergillosis. Diagnosis of coccidioidomycosis requires a high index of suspicion outside the expected geographic distribution in the appropriate clinical setting. Our case highlights the risk of false-positive antigen test results and the importance of invasive diagnostics, including bronchoscopy to obtain fungal cultures, if the diagnosis remains uncertain.

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related Staphylococcus aureus isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling (such as reduced computational requirements and simpler data management) can be realized.

Introduction. To describe two cases of crystalline lens dislocation as a presenting feature of invasive group A Streptococcus (GAS) infection and its management. Case presentation. We report on a 58-year-old woman and a 36-year-old man who presented in 2024 with acute vision loss and severe ocular and systemic symptoms. Both patients were found to have lens dislocation and were diagnosed with invasive GAS infection. The 58-year-old woman had a complicated clinical course leading to enucleation, while the 36-year-old man responded favourably to early and aggressive treatment with systemic and intravitreal antibiotics. The responsible GAS strains were sequence type (ST) 28 and ST433, respectively. Conclusion. These cases highlight the importance of recognizing crystalline lens dislocation as a potential sign of ocular GAS infection. Two specific strain types of GAS associated with these findings, ST28 and ST433, are reported. In patients with GAS sepsis presenting with corneal oedema and zonular loss, clinicians should immediately initiate treatment, including intravitreal antibiotic injections and systemic therapy. Prompt and aggressive management can be crucial in preserving ocular structures.

This study explores the genomic basis of heavy metal resistance in Staphylococcus warneri strain TWSL_1, isolated from industrial textile effluent. The strain exhibited strong resistance to Cd²⁺, Pb²⁺ and Cu²⁺, with MICs of 50, 1,200 and 75 mg l^-1, respectively. Whole-genome sequencing revealed a 2.66 Mb genome with 2,567 CDSs and a 99.81% average nucleotide identity to S. warneri WS479. Comparative genomic analysis at the genus level revealed that S. warneri strain TWSL_1 possesses a unique and expanded repertoire of heavy metal resistance genes, including the cadmium efflux system accessory protein and cadmium resistance protein, which are absent in pathogenic Staphylococcus sp. used for the comparison. Phylogenetic analysis confirmed its classification within S. warneri, with strong bootstrap support (100). Functional annotation highlighted metabolic versatility and stress response capabilities, supporting its adaptation to metal-rich environments. S. warneri TWSL_1 demonstrated high Pb²⁺ removal efficiency, reducing concentrations by over 70%. These findings highlight S. warneri TWSL_1 as a promising candidate for heavy metal bioremediation with potential applications in environmental detoxification and monitoring strategies.

Aim. Antimicrobial resistance poses a critical global health threat, driven by the dissemination of resistance genes via mobile genetic elements (MGEs). This study aims to enhance the detection of MGE insertions in multidrug-resistant Escherichia coli by derivatizing the pBACpAK entrapment vector. Methods and results. Three derivatives were constructed with additional nucleotides upstream of the cI repressor gene, based on conserved regions identified from GenBank sequences containing known IS26 and IS1 insertions. Using colony PCR, intracellular transposition screening was performed on 194 tetracycline-resistant colonies from four E. coli ESI123 strains carrying different pBACpAK constructs. The derivatives showed increased MGE capture rates (10.7-73.1 %) compared to the WT vector (3.75%), identifying multiple MGEs, including the novel composite transposon Tn7824. Tn7824 harbours the bla _OXA-181 carbapenem resistance gene and the qnrS1 quinolone resistance gene, highlighting the clinical relevance of these findings. Long-read sequencing of transposants confirmed the accuracy of MGE identification and structural characterization, which also revealed chromosomal integration events of the pBACpAK derivatives mediated by flanking insertion sequences. Conclusions. The modifications introduced in the pBACpAK derivatives could increase the detection of transposition events by alleviating spatial constraints, allowing for more robust MGE detection.