- Volume 7, Issue 6, 2025

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.

Non-typeable Haemophilus influenzae (NTHi) is an early pathogen isolated from the lungs of children with cystic fibrosis (CF). However, its role in the progression of CF lung infection is poorly understood. Additionally, whether it forms biofilms in the lungs of people with CF is an open question. The development of synthetic CF sputum media (SCFM) has given key insights into the microbiology of later CF pathogens, Pseudomonas aeruginosa and Staphylococcus aureus, through replicating the chemical composition of CF sputum. However, the growth of NTHi in these media has not previously been reported. We show that NTHi grows poorly in three variants of SCFM commonly used to induce in vivo-like growth of P. aeruginosa and S. aureus (SCFM1, SCFM2 and SCFM3). The addition of NAD and haemin to SCFM1 and SCFM2 promoted the planktonic growth and biofilm formation of both laboratory and clinical NTHi isolates, and we were able to develop a modified variant of SCFM2 that allows culture of NTHis. We show that NTHi cannot be identified in an established ex vivo model of CF infection, which uses SCFM and porcine bronchiolar tissue. This may in part be due to the presence of endogenous bacteria on the pig lung tissue, which outcompete NTHi, but the lack of selective agar to isolate NTHi from endogenous bacteria, and the fact that NTHi is an exclusively human pathogen, makes it hard to conclude that this is the case. Through spiking modified SCFM2 with filter-sterilized lung homogenate, biofilm growth of clinical NTHi isolates was enhanced. Our results highlight that there are crucial components present in the lung tissue, which NTHi require for growth, which are not present in any published variant of SCFM from the Palmer et al. Endres and Konstan in JAMA (2022;137:191-1) lineage. Our results may inform future modifications to SCFM recipes to truly mimic the environment of CF lung sputum and thus, to facilitate the study of a wide range of CF pathogens.

Background. Blastocystis, the most prevalent microbial eukaryote in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the interplay of antibiotic administration, Blastocystis and the surrounding gut microbiome remains understudied. This case study aimed to explore antibiotic consumption and the presence of Blastocystis with subsequent changes in the gut microbiome and metabolome of an individual diagnosed with irritable bowel syndrome (IBS).

Methods. Stool samples from an IBS patient, collected at 12 time points, were tested for the presence of Blastocystis using real-time PCR targeting the SSUrRNA gene, followed by sequencing of positive samples. Illumina sequencing determined the gut microbiome composition, while one-dimensional proton NMR spectroscopy was used to analyse the metabolome composition. Statistical analyses were conducted to identify relationships between antibiotic consumption, bacterial diversity, metabolome composition and Blastocystis presence.

Results. Antibiotics significantly impacted the gut microbiome, with diversity declining early in the antibiotic course, then recovering later and post-course. Blastocystis was detected early, late and post-course but was not detectable mid-course, coinciding with the decline in bacterial diversity. Significant differences were observed between Blastocystis-positive and Blastocystis-negative samples, with bacterial composition significantly changing between samples collected before, early and after the antibiotic course compared to those collected mid-course. Metabolite groups, including short-chain fatty acids, amino acids and succinate, exhibited changes throughout the antibiotic course, indicating that gut metabolite composition is affected by antibiotic consumption.

Discussion/Conclusion. While antibiotics did not significantly impact Blastocystis colonization, they did cause a mid-course decline in microbial diversity and Blastocystis presence. The study also revealed significant alterations in important metabolites such as short-chain fatty acids and amino acids throughout the antibiotic course, with an altered metabolome observed post-course. This case study underscores the complex interactions between antibiotics, gut microbiota and metabolites, highlighting the resilience of Blastocystis in the gut ecosystem.

Antibiotic-resistant infections cause an estimated 2.8 million illnesses and 35,900 deaths annually in the USA. Carbapenems are a class of antibiotics that are generally reserved to treat life-threatening invasive infections including sepsis. Accurate diagnosis of carbapenem-resistant infections is critical for early and appropriate treatment. bla IMP encodes bacterial production of the IMP metallo-beta-lactamase (MBL), which can confer resistance to all the beta-lactams including carbapenems. Zinc is an essential co-factor in the IMP MBL enzymatic hydrolysis of carbapenems. Tests for the presence of IMP carbapenemase, such as the Carba NP, include zinc sulphate (ZnSO4) although broth dilution methods for determining MIC for carbapenems may vary. We hypothesized that ZnSO4 availability would improve the accuracy of carbapenem MIC determination for bacteria expressing bla IMP. Thus, the objective of this study was to determine if supplemental ZnSO4 affects the carbapenem MICs of Enterobacterales, Alteromonadales and Moraxellales expressing bla IMP. Isolates utilized for this study were originally recovered from environmental samples collected at farms, wastewater treatment plants and surface water. They were selected based on phenotypic non-susceptibility to carbapenems and genetic confirmation of bacterial carriage of bla IMP. Cation-adjusted Mueller–Hinton broth suspensions of each isolate standardized to a 0.5 MacFarland standard were tested with and without ZnSO4 added at 0.1 mmol l−1 concentration to determine MICs using standard extended-spectrum beta-lactamase microbroth dilution MIC panels. Although we observed that Morganellaceae imipenem MICs were higher (P<0.001) than those from other bacteria harbouring bla IMP, the inclusion of supplemental ZnSO4 did not influence carbapenem MIC. This suggests that supplemental ZnSO4 will not improve the accuracy of carbapenem MICs in environmental bacteria expressing IMP carbapenemase. Additional research will be required to identify important factors that may influence the expression of carbapenemase including IMP and the accurate determination of clinical MICs, which is critical to appropriate therapeutic decision-making.

Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease, primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide valuable insights into the genetic virulence factors and genomic variations of Xoo strains isolated in Thailand. Furthermore, we present the first complete genomic database of Thai Xoo, offering a comprehensive resource for studying pathogen diversity, tracking virulence evolution and supporting disease management strategies in rice production. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and US strains. Remarkably, the average nt identity values, in comparison with Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types. Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit a clustered regularly interspaced short palindromic repeats-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D and E) and the X. oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management and comparative studies of this critical pathogen in the future.

Tuberculosis (TB) is a preventable and usually curable disease but remains a major health problem worldwide, particularly in developing countries. TB of the lumbosacral junction is rare and occurs in only 1–2% of all cases of spinal TB. Moreover, isolated sacrococcygeal TB is extremely rare. We present a case of a 64-year-old patient with a history of diabetes who presented with chronic back pain and cough. Physical examinations revealed a perianal fistula and left elbow joint arthritis. The patient is diagnosed with disseminated TB with coccygeal involvement. Diagnosis was achieved non-invasively using Xpert MTB/RIF, confirming Mycobacterium tuberculosis infection. The patient experienced complete resolution of symptoms following the commencement of anti-TB therapy. We highlight the importance of this case due to the rare coccygeal localization of TB in an immunocompetent patient, diagnosed through non-invasive means.