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Fulltext Isolation and identification of gastrointestinal microbiota from the short-nosed fruit bat Cynopterus brachyotis brachyotis

Daniel DS, Ng YK, Chua EL, Arumugam Y, Wong WL, Kumaran JV

Microbiol Res, 2013 Oct 1;168(8):485-96.
PMID: 23706760 DOI: 10.1016/j.micres.2013.04.001

Studies on the microbial ecology of gut microbiota in bats are limited and such information is necessary in determining the ecological significance of these hosts. Short-nosed fruit bats (Cynopterus brachyotis brachyotis) are good candidates for microbiota studies given their close association with humans in urban areas. Thus, this study explores the gut microbiota of this species from Peninsular Malaysia by means of biochemical tests and 16S rRNA gene sequences analysis. The estimation of viable bacteria present in the stomach and intestine of C. b. brachyotis ranged from 3.06×10(10) to 1.36×10(15)CFU/ml for stomach fluid and 1.92×10(10) to 6.10×10(15)CFU/ml for intestinal fluid. A total of 34 isolates from the stomach and intestine of seven C. b. brachyotis were retrieved. A total of 16 species of bacteria from eight genera (Bacillus, Enterobacter, Enterococcus, Escherichia, Klebsiella, Pantoea, Pseudomonas and Serratia) were identified, Enterobacteriaceae being the most prevalent, contributing 12 out of 16 species isolated. Most isolates from the Family Enterobacteriaceae have been reported as pathogens to humans and wildlife. With the possibility of human wildlife transmission, the findings of this study focus on the importance of bats as reservoirs of potential bacterial pathogens.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Pathogenicity of Aeromonas hydrophila isolated from the Malaysian Sea against coral (Turbinaria sp.) and sea bass (Lates calcarifer)

Hamid R, Ahmad A, Usup G

Environ Sci Pollut Res Int, 2016 Sep;23(17):17269-76.
PMID: 27221587 DOI: 10.1007/s11356-016-6655-8

A study was carried out to determine the pathogenicity (hemolytic activity) on corals (Turbinaria sp.) and sea bass (Lates calcarifer) of Aeromonas hydrophila from water, sediment, and coral. Samples were collected from coastal water and coral reef areas. One hundred and sixty-two isolates were successfully isolated. Out of 162, 95 were from seawater, 49 from sediment, and 18 from coral. Sixteen isolates were picked and identified. Isolates were identified using a conventional biochemical test, the API 20NE kit, and 16S rRNA nucleotide sequences. Hemolytic activity was determined. Out of 16 isolates, 14 isolates were β-hemolytic and two isolates were non-hemolytic. Corals infected with A. hydrophila suffered bleaching. Similar effect was observed for both hemolytic and non-hemolytic isolates. Intramuscular injection of A. hydrophila into sea bass resulted in muscular bleeding and death. Higher infection rates were obtained from hemolytic compared to non-hemolytic strains of A. hydrophila isolates.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
The impact of tropical forest logging and oil palm agriculture on the soil microbiome

Tripathi BM, Edwards DP, Mendes LW, Kim M, Dong K, Kim H, et al.

Mol Ecol, 2016 May;25(10):2244-57.
PMID: 26994316 DOI: 10.1111/mec.13620

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Loop-Mediated Isothermal Amplification Assay for Identification of Five Human Plasmodium Species in Malaysia

Lau YL, Lai MY, Fong MY, Jelip J, Mahmud R

Am J Trop Med Hyg, 2016 Feb;94(2):336-339.
PMID: 26598573 DOI: 10.4269/ajtmh.15-0569

The lack of rapid, affordable, and accurate diagnostic tests represents the primary hurdle affecting malaria surveillance in resource- and expertise-limited areas. Loop-mediated isothermal amplification (LAMP) is a sensitive, rapid, and cheap diagnostic method. Five species-specific LAMP assays were developed based on 18S rRNA gene. Sensitivity and specificity of LAMP results were calculated as compared with microscopic examination and nested polymerase chain reaction. LAMP reactions were highly sensitive with the detection limit of one copy for Plasmodium vivax, Plasmodium falciparum, and Plasmodium malariae and 10 copies for Plasmodium knowlesi and Plasmodium ovale. LAMP positively detected all human malaria species in all positive samples (N = 134; sensitivity = 100%) within 35 minutes. All negative samples were not amplified by LAMP (N = 67; specificity = 100%). LAMP successfully detected two samples with very low parasitemia. LAMP may offer a rapid, simple, and reliable test for the diagnosis of malaria in areas where malaria is prevalent.

Matched MeSH terms: RNA, Ribosomal, 18S/genetics
Fulltext Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests

Miyashita NT

Genes Genet Syst, 2015;90(2):61-77.
PMID: 26399766 DOI: 10.1266/ggs.90.61

Soil bacterial community structures of six dominant phyla (Acidobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes and Actinobacteria) and unclassified bacteria detected in tropical Sarawakian and temperate Japanese forests were compared based on 16S rRNA gene sequence variation. The class composition in each phylum was similar among the studied forests; however, significant heterogeneities of class frequencies were detected. Acidobacteria and Proteobacteria were the most dominant phyla in all six forests, but differed in the level of bacterial species diversity, pattern of species occurrence and association pattern of species composition with physicochemical properties in soil. Species diversity among Acidobacteria was approximately half that among Proteobacteria, based on the number of clusters and the Chao1 index, even though a similar number of sequence reads were obtained for these two phyla. In contrast, species diversity within Planctomycetes and Bacteroidetes was nearly as high as within Acidobacteria, despite many fewer sequence reads. The density of species (the number of sequence reads per cluster) correlated negatively with species diversity, and species density within Acidobacteria was approximately twice that within Proteobacteria. Although the percentage of forest-specific species was high for all bacterial groups, sampling site-specific species varied among bacterial groups, indicating limited inter-forest migration and differential movement of bacteria in forest soil. For five of the seven bacterial groups, including Acidobacteria, soil pH appeared to strongly influence species composition, but this association was not observed for Proteobacterial species. Topology of UPGMA trees and pattern of NMDS plots among the forests differed among the bacterial groups, suggesting that each bacterial group has adapted and evolved independently in each forest.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Complete mitochondrial genome reveals genetic diversity of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae)

Yong HS, Song SL, Eamsobhana P, Goh SY, Lim PE

Acta Trop, 2015 Dec;152:157-164.
PMID: 26348256 DOI: 10.1016/j.actatropica.2015.09.001

Angiostrongylus cantonensis is a zoonotic parasite that causes eosinophilic meningitis in humans. Earlier work on its mitochondrial genome was based on long polymerase chain reaction method. To date, only the mitogenome of the isolates from China has been studied. We report here the complete mitogenome of the Thailand isolate based on next generation sequencing and compare the genetic diversity with other isolates. The mitogenome of the Thailand isolate (13,519bp) is longer than those of the China isolates (13,497-13,502bp). Five protein-coding genes (atp6, cox1, cox2, cob, nad2) show variations in length among the isolates. The stop codon of the Thailand isolate differs from the China and Taiwan isolates in 4 genes (atp6, cob, nad2, nad6). Additionally, the Thailand isolate has 4 incomplete T stop codon compared to 3 in the China and Taiwan isolates. The control region is longer in the Thailand isolate (258bp) than the China (230-236bp) and Taiwan (237bp) isolates. The intergenic sequence between nad4 and cox1 genes in the Thailand isolate lacks 2bp (indels) at the 5'-end of the sequence as well as differs at 7 other sites compared to the China and Taiwan isolates. In the Thailand isolate, 18 tRNAs lack the entire TΨC-arm, compared to 17 in the China isolate and 16 in the Taiwan isolate. Phylogenetic analyses based on 36 mt-genes, 12 PCGs, 2 rRNA genes, 22 tRNA genes and control region all indicate closer genetic affinity between the China and Taiwan isolates compared to the Thailand isolate. Based on 36 mt-genes, the inter-isolate genetic distance varies from p=3.2% between China and Taiwan isolates to p=11.6% between Thailand and China isolates. The mitogenome will be useful for population, phylogenetics and phylogeography studies.

Matched MeSH terms: RNA, Ribosomal/genetics
Fulltext Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, et al.

Syst Appl Microbiol, 2015 Jul;38(5):330-9.
PMID: 26138047 DOI: 10.1016/j.syapm.2015.05.006

Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Support from Phylogenomic Networks and Subspecies Signatures for Separation of Mycobacterium massiliense from Mycobacterium bolletii

Tan JL, Ngeow YF, Choo SW

J Clin Microbiol, 2015 Sep;53(9):3042-6.
PMID: 26157149 DOI: 10.1128/JCM.00541-15

Mycobacterium abscessus subspecies classification has important clinical implications. We used phylogenomic network and amino acid analyses to provide evidence for the separation of Mycobacterium bolletii and Mycobacterium massiliense into two distinct subspecies which can potentially be differentiated rapidly by their protein signatures.

Matched MeSH terms: RNA, Ribosomal/genetics
Fulltext Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams

Siew SW, Musa SM, Sabri N', Farida Asras MF, Ahmad HF

Environ Res, 2023 Feb 15;219:115139.
PMID: 36565841 DOI: 10.1016/j.envres.2022.115139

The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study aimed to profile the complete microbial community and correlate it with the antibiotic compounds identified in microwave pre-treated healthcare wastes collected from three different waste operators in Peninsular Malaysia. The bacterial and fungal compositions were determined via amplicon sequencing by targeting the full-length 16S rRNA gene and partial 18S with full-length ITS1-ITS2 regions, respectively. The antibiotic compounds were characterized using high-throughput spectrometry. There was significant variation in bacterial and fungal composition in three groups of samples, with alpha- (p-value = 0.04) and beta-diversity (p-values <0.006 and

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Adalimumab therapy is associated with increased faecal short chain fatty acids in hidradenitis suppurativa

Tatian A, Bordbar S, Sarkissian S, Woods JA, Cains GD, Chong CW, et al.

Exp Dermatol, 2022 Dec;31(12):1872-1880.
PMID: 36054650 DOI: 10.1111/exd.14665

Altered gut microbiota composition has been observed in individuals with hidradenitis suppurutiva (HS) and many other inflammatory diseases, including obesity, type 1 and type 2 diabetes. Here, we addressed whether adalimumab, a systemic anti-inflammatory therapy, may impact the microbiota biochemical profile, particularly on beneficial metabolites such as short-chain fatty acids (SCFAs). We conducted an observational single-arm pilot trial to assess gut microbiota composition by 16S rRNA gene sequence analysis and to detect metabolite signatures by gas chromatography in stool samples from participants with HS prior to and 12 weeks after commencing adalimumab therapy. HS individuals that better responded to adalimumab treatment showed a shift in the composition and function of the gut microbiota with significantly increased SCFA acetate and propionate compared to age, gender and BMI-matched healthy controls. A positive correlation was observed between propionate with Prevotella sp and Faecalibacterium prausnitsii. Increased SCFAs, changes in gut microbiota composition, function and metabolic profile following 12 weeks of adalimumab suggest that targeting SCFAs may be considered a potential biomarker to be evaluated as a complementary protective factor or as a diagnostically relevant signal in HS.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Assessment of pan-Leishmania detection by recombinase polymerase amplification assay

Louizi C, Khan MAA, Faisal K, Chowdhury R, Ghosh P, Hossain F, et al.

Diagn Microbiol Infect Dis, 2023 Feb;105(2):115862.
PMID: 36493571 DOI: 10.1016/j.diagmicrobio.2022.115862

The spread of vector habitats along with increasing human mobility can introduce atypical Leishmania species and hence can challenge existing diagnostic practices for rapid detection of active infection with species outside the narrow target range. Here we assessed the pan-Leishmania detection ability of isothermal recombinase polymerase amplification (RPA) assays targeting 18S rRNA gene, cathepsin L-like cysteine proteinase B (Cpb) gene, and kinetoplast minicircle DNA (kDNA) regions. While the lowest limit of detection of the 18S rRNA-RPA and Cpb-RPA assays were estimated as 12 and 17 standard DNA molecules, respectively, both assays could amplify genomic DNA of 7 pathogenic Leishmania species. Evaluation of 18S rRNA-RPA and our previously developed kDNA-RPA assays on 70 real-time PCR-positive leishmaniasis samples of varying pathologies resulted in sensitivity rates of 35.71% and 88.57%, respectively, while the combined sensitivity was 98.57%. Combinatorial application of 18S rRNA-RPA and kDNA-RPA assays can be recommended for further diagnostic assessments.

Matched MeSH terms: RNA, Ribosomal, 18S/genetics
Fulltext The Roles of Probiotics in the Gut Microbiota Composition and Metabolic Outcomes in Asymptomatic Post-Gestational Diabetes Women: A Randomized Controlled Trial

Hasain Z, Raja Ali RA, Ahmad HF, Abdul Rauf UF, Oon SF, Mokhtar NM

Nutrients, 2022 Sep 19;14(18).
PMID: 36145254 DOI: 10.3390/nu14183878

Probiotics are widely used as an adjuvant therapy in various diseases. Nonetheless, it is uncertain how they affect the gut microbiota composition and metabolic and inflammatory outcomes in women who have recently experienced gestational diabetes mellitus (post-GDM). A randomized, double-blind, placebo-controlled clinical trial involving 132 asymptomatic post-GDM women was conducted to close this gap (Clinical Trial Registration: NCT05273073). The intervention (probiotics) group received a cocktail of six probiotic strains from Bifidobacterium and Lactobacillus for 12 weeks, while the placebo group received an identical sachet devoid of living microorganisms. Anthropometric measurements, biochemical analyses, and 16S rRNA gene sequencing results were evaluated pre- and post-intervention. After the 12-week intervention, the probiotics group’s fasting blood glucose level significantly decreased (mean difference −0.20 mmol/L; p = 0.0021). The HbA1c, total cholesterol, triglycerides, and high-sensitivity C-reactive protein levels were significantly different between the two groups (p < 0.05). Sequencing data also demonstrated a large rise in the Bifidobacterium adolescentis following probiotic supplementation. Our findings suggest that multi-strain probiotics are beneficial for improved metabolic and inflammatory outcomes in post-GDM women by modulating gut dysbiosis. This study emphasizes the necessity for a comprehensive strategy for postpartum treatment that includes probiotics to protect post-GDM women from developing glucose intolerance.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa

Kurina I, Popenko A, Klimenko N, Koshechkin S, Chuprikova L, Filipenko M, et al.

Mol Cell Probes, 2020 Aug;52:101570.
PMID: 32304824 DOI: 10.1016/j.mcp.2020.101570

Nowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods - the platform and high-throughput 16S rRNA sequencing - across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Genomic, metabolomic, and functional characterisation of beneficial properties of Pediococcus pentosaceus ST58, isolated from human oral cavity

Favaro L, Campanaro S, Fugaban JII, Treu L, Jung ES, d'Ovidio L, et al.

Benef Microbes, 2023 Mar 14;14(1):57-72.
PMID: 36815495 DOI: 10.3920/BM2022.0067

Bacteriocins produced by lactic acid bacteria are proteinaceous antibacterial metabolites that normally exhibit bactericidal or bacteriostatic activity against genetically closely related bacteria. In this work, the bacteriocinogenic potential of Pediococcus pentosaceus strain ST58, isolated from oral cavity of a healthy volunteer was evaluated. To better understand the biological role of this strain, its technological and safety traits were deeply investigated through a combined approach considering physiological, metabolomic and genomic properties. Three out of 14 colonies generating inhibition zones were confirmed to be bacteriocin producers and, according to repPCR and RAPD-PCR, differentiation assays, and 16S rRNA sequencing it was confirmed to be replicates of the same strain, identified as P. pentosaceus, named ST58. Based on multiple isolation of the same strain (P. pentosaceus ST58) over the 26 weeks in screening process for the potential bacteriocinogenic strains from the oral cavity of the same volunteer, strain ST58 can be considered a persistent component of oral cavity microbiota. Genomic analysis of P. pentosaceus ST58 revealed the presence of operons encoding for bacteriocins pediocin PA-1 and penocin A. The produced bacteriocin(s) inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp. used to determine the activity spectrum. The highest levels of production (6400 AU/ml) were recorded against L. monocytogenes strains after 24 h of incubation and the antimicrobial activity was inhibited after treatment of the cell-free supernatants with proteolytic enzymes. Noteworthy, P. pentosaceus ST58 also presented antifungal activity and key metabolites potentially involved in these properties were identified. Overall, this strain can be of great biotechnological interest towards the development of effective bio-preservation cultures as well as potential health promoting microbes.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Influence of angiotensin II on the gut microbiome: modest effects in comparison to experimental factors

R Muralitharan R, Nakai ME, Snelson M, Zheng T, Dinakis E, Xie L, et al.

Cardiovasc Res, 2024 Sep 02;120(10):1155-1163.
PMID: 38518247 DOI: 10.1093/cvr/cvae062

AIMS: Animal models are regularly used to test the role of the gut microbiome in hypertension. Small-scale pre-clinical studies have investigated changes to the gut microbiome in the angiotensin II hypertensive model. However, the gut microbiome is influenced by internal and external experimental factors, which are not regularly considered in the study design. Once these factors are accounted for, it is unclear if microbiome signatures are reproduceable. We aimed to determine the influence of angiotensin II treatment on the gut microbiome using a large and diverse cohort of mice and to quantify the magnitude by which other factors contribute to microbiome variations.
METHODS AND RESULTS: We conducted a retrospective study to establish a diverse mouse cohort resembling large human studies. We sequenced the V4 region of the 16S rRNA gene from 538 samples across the gastrointestinal tract of 303 male and female C57BL/6J mice randomized into sham or angiotensin II treatment from different genotypes, diets, animal facilities, and age groups. Analysing over 17 million sequencing reads, we observed that angiotensin II treatment influenced α-diversity (P = 0.0137) and β-diversity (i.e. composition of the microbiome, P < 0.001). Bacterial abundance analysis revealed patterns consistent with a reduction in short-chain fatty acid producers, microbial metabolites that lower blood pressure. Furthermore, animal facility, genotype, diet, age, sex, intestinal sampling site, and sequencing batch had significant effects on both α- and β-diversity (all P < 0.001). Sampling site (6.8%) and diet (6%) had the largest impact on the microbiome, while angiotensin II and sex had the smallest effect (each 0.4%).
CONCLUSION: Our large-scale data confirmed findings from small-scale studies that angiotensin II impacted the gut microbiome. However, this effect was modest relative to most of the other factors studied. Accounting for these factors in future pre-clinical hypertensive studies will increase the likelihood that microbiome findings are replicable and translatable.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Novel Vibrio vulnificus sequence type 540 infection in a hepatitis patient

Chua HS, Soh YH, Ibrahim S, Abdullah NH, Che Mat Seri NAA, AbuBakar S, et al.

Trop Biomed, 2024 Jun 01;41(2):220-223.
PMID: 39154277 DOI: 10.47665/tb.41.2.014

Vibrio vulnificus infection is associated with high morbidity and mortality in high-risk patients. Poor prognoses could lead to >50% mortality rate. The present report describes a case of V. vulnificus bacteremia in a cirrhotic patient with underlying hepatitis C. He presented with generalised abdominal pain associated with distention and could not ambulate for one week. He also complained of fever for six days and pruritus for 10 days. Tea-coloured urine was noted in continuous bag drainage. The abdomen was distended but soft, with mild tenderness palpated over the left lumbar and iliac region. Blood investigation indicated ongoing infection and inflammation. The aerobic blood culture was identified using the matrix-assisted laser desorption/ionisation-time of flight mass spectrometry and confirmed via 16S rDNA sequencing as V. vulnificus. Multilocus sequence typing of the isolated V. vulnificus revealed a novel sequence type, ST540. The patient responded well to the intravenous cefoperazone and was then discharged with a four day-course of oral ciprofloxacin, 500 mg twice daily after completing the intravenous cefoperazone for 10 days. Clinical history and physical examination are important for early antibiotic therapy initiation and appropriate surgical intervention. Furthermore, bacterial strain typing is also essential for epidemiological surveillance and potentially anticipating the pathogen's virulence traits, which are vital in controlling and preventing the spread of infection.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Fulltext Plasmodium cynomolgi Infections Not Found in Microscopy-Diagnosed Malaria Cases across Sabah, Malaysia

Murdiyarso LS, Rajahram GS, Tan AF, Piera KA, William T, Oyong DA, et al.

Am J Trop Med Hyg, 2025 Jan 08;112(1):85-88.
PMID: 39531730 DOI: 10.4269/ajtmh.24-0264

Zoonotic malaria presents a major public health challenge in Southeast Asia. Plasmodium cynomolgi coinfects the same macaque hosts and mosquito vectors as the most common cause of zoonotic malaria, Plasmodium knowlesi. Plasmodium cynomolgi appears morphologically similar to Plasmodium vivax on microscopy and can amplify P. vivax polymerase chain reaction (PCR) assays, confounding transmission estimates. We screened 2,103 samples for P. cynomolgi across all 26 districts in Sabah, Malaysia, from 2010 to 2021. Samples comprised 1,425 P. knowlesi, 256 P. vivax, 293 P. falciparum, and 31 Plasmodium malariae PCR-confirmed malaria cases and 100 malaria microscopy-positive and species-specific PCR-negative samples. A nested PCR assay targeting P. cynomolgi-specific 18S small subunit ribosomal ribonucleic acid with a detection limit of ∼2 parasites/µL was conducted on whole blood samples. No P. cynomolgi infections were detected. Symptomatic P. cynomolgi co-infections appear rare in Malaysia, although prevalence may be underestimated owing to the absence of routine molecular screening and the sensitivity of available assays.

Matched MeSH terms: RNA, Ribosomal, 18S/genetics
Shallow shotgun sequencing of healthcare waste reveals plastic-eating bacteria with broad-spectrum antibiotic resistance genes

Siew SW, Khairi MHF, Hamid NA, Asras MFF, Ahmad HF

Environ Pollut, 2025 Jan 01;364(Pt 1):125330.
PMID: 39551377 DOI: 10.1016/j.envpol.2024.125330

The burgeoning crises of antimicrobial resistance and plastic pollution are converging in healthcare settings, presenting a complex challenge to global health. This study investigates the microbial populations in healthcare waste to understand the extent of antimicrobial resistance and the potential for plastic degradation by bacteria. Our metagenomic analysis, using both amplicon and shallow shotgun sequencing, provided a comprehensive view of the taxonomic diversity and functional capacity of the microbial consortia. The viable bacteria in healthcare waste samples were analyzed employing full-length 16S rRNA sequencing, revealing a diverse bacterial community dominated by Firmicutes and Proteobacteria phyla. Notably, Proteus mirabilis VFC3/3 and Pseudomonas sp. VFA2/3 were detected, while Stenotrophomonas maltophilia VFV3/2 surfaced as the predominant species, holding implications for the spread of hospital-acquired infections and antimicrobial resistance. Antibiotic susceptibility testing identified multidrug-resistant strains conferring antimicrobial genes, including the broad-spectrum antibiotic carbapenem, underscoring the critical need for improved waste management and infection control measures. Remarkably, we found genes linked to the breakdown of plastic that encoded for enzymes of the esterase, depolymerase, and oxidoreductase classes. This suggests that specific bacteria found in medical waste may be able to reduce the amount of plastic pollution that comes from biological and medical waste. The information is helpful in formulating strategies to counter the combined problems of environmental pollution and antibiotic resistance. This study emphasises the importance of monitoring microbial communities in hospital waste in order to influence waste management procedures and public health policy. The findings highlight the need for a multidisciplinary approach to mitigate the risks associated with antimicrobial resistance and plastic waste, especially in hospital settings where they intersect most acutely.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
New host record and redescription of Amblyomma cordiferum nymphs and larvae infesting Malaysian house rats (Rattus rattus diardii) in Peninsular Malaysia, with molecular evidence of Rickettsia, Borrelia, and Bartonella

Kazim AR, Nasir DM, Tan TK, Yin VW, Noh AAM, Heo CC, et al.

Acta Trop, 2025 Jan;261:107496.
PMID: 39667694 DOI: 10.1016/j.actatropica.2024.107496

Nymphal and larval Amblyomma cordiferum ticks, a relatively rare species, were collected from the Malaysian house rat (Rattus rattus diardii) in Peninsular Malaysia. Redescription and molecular analysis of nymphs and larvae, based on the 12S rRNA, 16S rRNA, and COI genes, revealed divergence from A. cordiferum in Taiwan, suggesting that the Taiwanese tick specimens may represent a different taxon. Molecular analysis of the pathogens in these specimens revealed three sequences of Rickettsia closely related or identical to Rickettsia raoultii (99.71-100%), two sequences of relapsing fever Borrelia identical to Borrelia theileri, and four sequences of Bartonella identical to Bartonella phoceensis. This study also identifies a new host record for A. cordiferum in R. r. diardii and reports the first detection of Rickettsia, Borrelia, and Bartonella in this tick species.

Matched MeSH terms: RNA, Ribosomal/genetics
Fulltext Genetic profiling of multidrug-resistant Acinetobacter baumannii from a tertiary care center in Malaysia

Shahari AS, Palanisamy NK, Mohd Nor F

Microbiol Spectr, 2025 Feb 04;13(2):e0087224.
PMID: 39704504 DOI: 10.1128/spectrum.00872-24

Genetic characterization of multidrug-resistant (MDR) Acinetobacter baumannii remains scarce in Malaysia. This study aimed to characterize antibiotic resistance, genomic location, and genetic relatedness among the A. baumannii isolates obtained from a tertiary hospital in Malaysia. A total of 128 MDR A. baumannii isolates were collected from patients admitted to various wards (intensive care unit [ICU], neonatal intensive care unit, coronary care unit, high dependency ward [HDW], and general wards). The isolates were identified by Vitek 2 and PCR amplification of the 16S rRNA gene followed by sequencing. The isolates were tested against imipenem, ceftazidime, amikacin, gentamicin, ampicillin, and ciprofloxacin using disk diffusion, Epsilometer test, and broth microdilution. The antibiotic resistance genes, blaOXA-23, blaOXA-24, blaADC, blaVIM, and blaIMP, were detected in chromosomal and plasmid DNA using PCR. Insertion sequence ISAba1/blaOXA-23 gene was detected on chromosomal DNA only. Isolates with different antibiotic susceptibility patterns and PCR profiles were subjected to multi-locus sequence typing. MDR A. baumannii was predominantly found in HDW (39.84%), general wards (29.69%), and ICU (28.13%). All isolates conferred resistance to carbapenem and more than 90% resistance to the remaining antibiotics. The antibiotic resistance genes blaOXA-23, blaVIM, and blaADC were detected in both chromosomal and plasmid DNA. The ISAba1/blaOXA-23 gene was detected in 99.22% of the isolates. Four sequence types (STs) were distinguished: ST2 (76.67%), ST164 (10%), ST642 (10%), and ST643 (3.33%). ST164 and ST642 were unique and represent a significant finding in Malaysia's surveillance data. These STs are associated with acquired blaOXA-23, indicating an evolutionary adaptation of A. baumannii within the hospital setting.IMPORTANCEAcinetobacter baumannii is a ubiquitous Gram-negative coccobacillus bacterium that is primarily associated with nosocomial infections that can colonize biotic and abiotic surfaces to enhance cell-to-cell adhesion, ensuring the establishment of infections. To date, the spread of multidrug-resistant A. baumannii (MDRAB) has become rampant and a great concern in the hospital setting, as the available antibiotics are insufficient to treat infections. The antibiotic resistance island resides in a mobile element and rapidly evolved. The antibiotic susceptibility data with its resistance mechanisms would contribute to and facilitate the management and infection control caused by MDRAB.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics

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