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Background: Hypermucoviscous carbapenem-resistant Klebsiella pneumoniae (hmCRKp) is emerging globally and approaching the worst-case scenario in health care system. Aims: The main objective in this study was to determine the hypermucoviscous characteristics among the carbapenem-resistant K. pneumoniae (CRKp) isolated from a teaching hospital in Malaysia. The association of hypermucoviscous phenotype with the virulence traits and clinical presentations were also investigated. Methods: A retrospective study was conducted in University Malaya Medical Centre (UMMC). The presence of hypermucoviscous K. pneumoniae was identified among a collection of CRKp clinical isolates (first isolate per patient) from 2014 to 2015 using string test. Correlation between clinical and microbial characteristics of the hmCRKp was investigated. Results: A total of nine (7.5%) hmCRKp were detected among 120 CRKp isolates. Majority of the isolates were hospital acquired or health care-associated infections. None of the patients had typical pyogenic liver abscess. All of the hmCRKp isolates harbored carbapenemase genes and were multidrug resistant. K1/K serotype, peg-344, allS, and magA were not identified among hmCRKp isolates, whereas aerobactin siderophore receptor gene (iutA), iroB, rmpA, and rmpA2 were detected. Only three hmCRKp isolates were resistant to serum bactericidal. Conclusions: All the isolates presented inconclusive evidence for the interpretation of hypervirulence. Therefore, more study should be performed in the future to have a better understanding of the virulence mechanisms in correlation with the clinical and microbial determinants.

Aims: The fluid of Nepenthes gracilis harbors diverse bacterial taxa that could serve as a gene pool for the discovery of the new genre of antimicrobial agents against multidrug-resistant Klebsiella pneumoniae. The aim of this study was to explore the presence of antibacterial genes in the fluids of N. gracilis growing in the wild. Methods: Using functional metagenomic approach, fosmid clones were isolated and screened for antibacterial activity against three strains of K. pneumoniae. A clone that exhibited the most potent antibacterial activity was sent for sequencing to identify the genes responsible for the observed activity. The secondary metabolites secreted by the selected clone was sequentially extracted using hexane, chloroform, and ethyl acetate. The chemical profiles of a clone (C6) hexane extract were determined by gas chromatography/mass spectrometry (GC-MS). Results: Fosmid clone C6 from the fluid of pitcher plant that exhibited antibacterial activity against three strains of K. pneumoniae was isolated using functional metagenome approach. A majority of the open reading frames detected from C6 were affiliated with the largely understudied Acidocella genus. Among them, the gene that encodes for coproporphyrinogen III oxidase in the heme biosynthesis pathway could be involved in the observed antibacterial activity. Based on the GC-MS analysis, the identities of the putative bioactive compounds were 2,5-di-tert-butylphenol and 1-ethyl-2-methyl cyclododecane. Conclusions: The gene that encodes for coproporphyrinogen III oxidase in the heme biosynthesis pathway as well as the secondary metabolites, namely 2,5-di-tert-butylphenol and 1-ethyl-2-methyl cyclododecane could be the potential antibacterial molecules responsible for the antibacterial activity of C6.

Background: Gastrointestinal carriage of multidrug resistant (MDR) Gram-negative bacilli, especially Klebsiella pneumoniae and Escherichia coli, was highly associated with severe nosocomial infections. The main objectives of this study were to determine the clonal relatedness of intestinal carriage and transmission risk factors of MDR E. coli and K. pneumoniae amongst preterm infants admitted to the neonatal intensive care unit (NICU). Methods: A prospective cohort study of preterm infants with gestational age

Obesity is a driving factor in the onset of metabolic disorders. This study aims to investigate the effects of the myricetin derivative-rich fraction (MD) from Syzygium malaccense leaf extract on high-fat diet (HFD)-induced obesity and its associated complications and its influence on uncoupling protein-1 (UCP-1) and gut microbiota in C57BL/6J mice. Mice were randomly assigned into four groups (n = 6) and given a normal diet (ND) or high-fat diet (HFD) for 10 weeks to induce obesity. The HFD groups (continued with HFD) were administered 50 mg kg-1 MD (treatment), 50 mg kg-1 metformin (positive control) and normal saline (HFD and ND controls) daily for four weeks via oral gavage. The ten-week HFD-feeding resulted in hyperglycemia and elevated urinary oxidative indices. The subsequent MD administration caused significant weight reduction without appetite suppression and amelioration of insulin resistance, steatosis and dyslipidemia. Besides, MD significantly reduced lipid hydroperoxides and protein carbonyls in tissue homogenates and urine and elevated Trolox equivalent antioxidant capacity (TEAC), ferric reducing antioxidant power (FRAP) and reduced glutathione (GSH) and thus, alleviated oxidative stress. The weight reduction was correlated with downregulation of inflammatory markers and the increased UCP-1 level, suggesting weight loss plausibly through thermogenesis. The Akkermansia genus (reflects improved metabolic status) in the HFD50 group was more abundant than that in the HFD group while the non-enzymatic antioxidant markers were strongly associated with UCP-1. In conclusion, MD ameliorates obesity and its related complications possibly via the upregulation of UCP-1 and increased abundance of Akkermansia genus and is promising as a therapeutic agent in the treatment of obesity and its associated metabolic disorders.

The emergence of carbapenemase-producing Enterobacteriaceae has become a major global concern. OXA-48-like carbapenemase gene and its variants have been increasingly reported worldwide. This study reported the first OXA-181-producing Klebsiella quasipneumoniae isolate in Malaysia. This bacterium was isolated from blood specimen of a three-year-old boy with Alagille syndrome who had liver biopsy on October 2016. He had undergone liver transplant in India ten months previously. The genotypic and phenotypic characteristics of the strain were elucidated in this study. To our best knowledge, this is the first report of OXA-181-producing K. quasipneumoniae in Malaysia.

Background: Klebsiella pneumoniae is a major opportunistic pathogen frequently associated with nosocomial infections, and often poses a major threat to immunocompromised patients. In our previous s...

Background The rise of nature-based ecotourism in the past decade has introduced unprecedented challenges in managing the increasing interaction between humans and animals. The potential transmission of antibiotic resistant microbes between humans and non-human primate populations is a concern due to their genetic similarity. Malaysia is well known for hotspots of wildlife diversity where non-human primates like monkeys and orangutans have become popular tourist attractions. In this study, we assessed the prevalence of antimicrobial resistant Staphylococcus aureus, Enterococcus species, and other Enterobacteriaceae in the faeces of human (HS) and two non-human primates (NHP) in Malaysia, the Long-tailed macaque (Macaca fascicularis, MF) and Silvered leaf monkey (Trachypithecus cristatus, TC). In addition, the faecal bacterial composition was profiled to evaluate the potential association between antibiotic resistant profiles and composition of gut microbiota. Results We tested the isolated bacteria using a selection of antibiotics. The results showed that both the number of antibiotic resistant strains and resistance level were higher in humans than NHPs. Overall, the composition of gut microbiome and pattern of antibiotic resistance showed that there was higher similarity between MF and TC, the two NHPs, than with HS. In addition, samples with higher levels of antibiotic resistance showed lower bacterial richness. Homo sapiens had the lowest bacterial diversity and yet it had higher abundance of Bacteroides. In contrast, NHPs displayed higher bacterial richness and greater prevalence of Firmicutes such as Ruminococceae and Oscillospira. Conclusion Higher antibiotic susceptibility in NHPs is likely related to low direct exposure to antibiotics. The lack of resistance may also suggest limited antimicrobial resistance transmission between humans and NHP. Nonetheless, continued monitoring over a long period will help mitigate the risk of anthropozoonosis and zooanthroponosis.

Cholera is an acute diarrheal illness caused by the Gram-negative bacterium Vibrio cholerae. The pathogen is known for its ability to form biofilm that confers protection against harsh environmental condition and as part of the colonisation process during infection. Coaggregation is a process that facilitates the formation of biofilm. In a preliminary in vitro study, high coaggregation index and biofilm production were found between V. cholerae with human commensals namely Escherichia coli and Enterobacter cloacae. Building upon these results, the effects of coaggregation were further evaluated using adult BALB/c mouse model. The animal study showed no significant differences in mortality and fluid accumulation ratio between treatment groups infected with V. cholerae alone and those infected with coaggregation partnership (V. cholerae with E. coli or V. cholerae with E. cloacae). However, mild inflammation was detected in both partnering pairs. Higher density of V. cholerae was recovered from faecal samples of mice co-infected with E. coli and V. cholerae in comparison with other groups at 24 h post-infection. This partnership also elicited slightly higher levels of interleukin-5 (IL-5) and interleukin-10 (IL-10). Nonetheless, the involvement of autoinducer-2 (AI-2) as the signalling molecules in quorum sensing system is not evident in this study. Since E. coli is one of the common commensals, our result may suggest the involvement of commensals in cholera development.

Background Singapore and Malaysia are neighbouring countries with similar ethnic make-up: Chinese, Indian, and Malays. However, Singapore is a high-income economy while Malaysia is a middle-income economy. Such a difference has resulted in some levels of dichotomy in diet and lifestyles. In this study, we sought to investigate the gut-ethnic variation across the two neighbouring countries with varying levels of economic development. Methods A total of 439 relatively healthy Malaysian (n=190) and Singaporean (n=249) adults (>18) were included, comprising Chinese (n=240), Indian (n=74), Malay (n=40), and the indigenous Jakun community (n=85). The sequences were processed with DADA2 and annotated using the SILVA database. Results Country of origin explained the most variation in the gut microbiota (PERMANOVA, Pseudo-F=80.798, R2=0.156, p=0.001; IDDF2021-ABS-0150 Figure 1. Ordination). Importantly, ethnicity was still significantly associated with the gut microbiota even after adjusting for the country, age and sex (PERMANOVA, Pseudo-F=4.206, R2=0.019, p=0.001). Several taxa were found to be differentially abundant across ethnicity (ANCOM-BC, q Conclusions Gut-ethnic differences persist across geographical regions, which was likely due to similar lifestyle and cultural practices by individuals sharing similar ancestry. These signals provide potential biomarkers on the role of the gut microbiota in the aetiology of the unequal disease burdens affecting the different ethnic groups in this multicultural region.

Background Psychological stress, which is associated with poor sleep quality, has a profound effect on the gut microbiome. To better elucidate the gut microbiome changes associated with psychological stress, we measured levels of stress and sleep quality among the healthy stool donors recruited through a national campaign, and further assessed their relationship with the gut microbiome. Methods The gut microbial composition of 272 adults residing in Singapore was determined by 16S rRNA V3-V4 amplicon sequencing. Stress and distress levels of participants were assessed using the Perceived Stress Scale (PSS) and Kessler Psychological Distress Scale (K10) respectively, while sleep quality was assessed using the Pittsburgh Sleep Quality Index (PSQI). Multivariate statistical data analyses were conducted to explore the link between the gut microbiome, stress, distress and sleep quality. Results A significant proportion of stool donors exhibited low distress (84.2%) levels. However, nearly one-third of participants reported high-stress levels (33.5%) and poor sleep quality (44.8%) (IDDF2021-ABS-0165 Figure A. Stacked bar plot showing the number of participants under each category of (i) K10 , (ii) PSS and (iii) PSQI). The overall variation in the gut microbiome composition amongst stool donors was predominantly dependent on age and body mass index (BMI), rather than psychosocial stress and sleep quality (IDDF2021-ABS-0165 Figure B. PERMANOVA results of main factors in this study). However, four microbial features (i.e., Streptococcus, Erysipelotrichaceae UCG-003, Sutterella and Parabacteroides) were found to be positively associated with severe distress, of which Erysipelotrichaceae UCG-003 was more abundant in both distressed and stressed donors (DESeq2, p Conclusions One-third of the participants exhibited high stress/distress levels and almost half poor sleep. In this study, we identified several bacterial genera that are significantly altered in the gut microbiome of stressed individuals, with Erysipelotrichaceae UCG-003 being consistently increased across people with high stress and severe distress levels. Erysipelotrichaceae UCG-003 was previously reported to be elevated in individuals with sleep deprivation. Our findings also suggest the need to factor for stress and sleep quality when studying the gut microbiome of healthy individuals.

Background The gut microbiome plays an instrumental role in cardiovascular, metabolic and gastrointestinal health (Valdes et al. 2018). In Traditional Chinese Medicine (TCM), one’s health status can be described by nine body constitutions (BCs) which are broadly classified as ‘Neutral’, indicating optimal health, or ‘Unbalanced’, indicating suboptimal health. Similar to the gut microbiome, BCs are strongly influenced by lifestyle and diet. We evaluated the gut microbial composition of Neutral, Qi-Deficiency (QD), Phlegm-dampness (PD) and Damp Heat (DH) subjects. The latter three are unbalanced BCs, with QD associated with heart disease (Zhu et al. 2017), PD with obesity and metabolic syndrome (Wang et al. 2013), and DH with gastrointestinal disease (Liang et al. 2020). Methods Stool samples were collected from 211 healthy subjects and gut microbial composition was profiled using 16S rRNA amplicon sequencing of the V3-V4 regions. BCs were determined using the Constitution in Chinese Medicine Questionnaire (Wang, 2005). Alpha diversity of QD, PD and DH was inferred and compared against that of Neutral using the Kruskal-Wallis test. Differentially abundant bacterial phyla, family and species were identified by calculating Log2FoldChange of taxa in the unbalanced BCs compared to Neutral. Results There were 135 Neutral, 59 QD, 24 PD and 12 DH subjects. 16 participants exhibited two or more unbalanced BCs. PD exhibited significantly lower alpha diversity (Shannon, Simpson) than Neutral (p Conclusions Varying TCM BCs exhibit unique microbiota signatures. Participants with unbalanced BCs are associated with greater dysbiosis compared to participants with Neutral BC. The lower alpha diversity in PD is consistent with that in obese and metabolic syndrome patients (Stanislawski et al. 2019; Oh et al. 2021). Streptococcus gallolyticus, a species associated with gastrointestinal malignancy (Chand et al. 2016), was significantly higher in all three unbalanced BCs and thus may serve as a potential biomarker for identifying patients with unbalanced BCs.

Background The impact of non-dietary lifestyle factors on the gut microbiota, such as physical activity, has not been frequently reported. Recent studies have suggested that exercise can increase the number of beneficial microbial species which enhance short-chain fatty acid synthesis and carbohydrate metabolism. Therefore, we investigated the relationship between physical activity and gut microbiome composition within a cohort of multi-ethnic healthy Singaporeans. Methods 257 individuals completed the Global Physical Activity Questionnaire (GPAQ) (Armstrong et al. 2006) and Food Frequency Questionnaire (FFQ) (Whitton et al. 2017), to obtain quantitative measures of their physical activity, nutrition and dietary habits, respectively. They also provided paired stool samples, which underwent 16S rRNA V3-4 amplicon sequencing. Community and individual microbial features associated with physical activity were assessed using microbial ecology measures such as α-diversity and principal coordinate analysis (PCA), as well as, multivariate sparse Partial Least Squares analyses, whilst confounding for nutritional and dietary habits. Results Using the GPAQ, 57% of the individuals were deemed to have an active lifestyle. Active individuals have increased microbial α-diversity, although not statistically significant. Unsupervised PCA analysis identified a subset of active individuals with distinct microbiome signatures, whereby these individuals, compared to those with sedentary lifestyles, have increased abundances of Prevotella spp., which is in keeping with their increased fibre intake. Sedentary lifestyle individuals were found to have increased abundance of Lachnoclostridium spp., whereby phylogenetic similar microbial features (such as Roseburia and Subdoligranulum spp.) were significantly correlated with more frequent eating out at hawker stalls and fast-food establishments (IDDF2021-ABS-0169 Figure 1. Correlation between gut microbiome with (a) nutrient intake; and (b) food habit). Studying the metabolic potential of the microbiome, active individuals had increased abundances of gene content related to energy production, whereby sedentary individuals had increased abundances of gene content related to degradation of aromatic compounds. Conclusions Our study reaffirms that increased physical activity is associated with increased microbial diversity and beneficial microbial features. However, the differences in gut microbiota associated with physical activity may be due to differences in dietary intake and practices, rather than the exercise itself. Further studies investigating the link of gut microbiome and physical activity should control and standardize the dietary intake of participants.

Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA R 2=0.005, pseudo-F=2.643, P=0.001). A sparse partial least squares – discriminant analysis model trained using the gut microbiota of individuals from China, India and Indonesia (representation of Chinese, Indian and Malay ethnic group, respectively) showed a better-than-random performance in classifying Malaysian of Chinese descent, although the performance for Indian and Malay were modest (true prediction rate, Chinese=0.60, Indian=0.49, Malay=0.44). Separately, differential abundance analysis singled out Ligilactobacillus as being elevated in Indians. We postulate that despite the strong influence of geographical factors on the gut microbiota, cultural similarity due to a shared ethnic origin drives the presence of a shared gut microbiota composition. The interplay of these factors will likely depend on the circumstances of particular groups of migrants.

Background Gut microbiome alterations have been reported in Parkinson's disease (PD), but with heterogenous findings, likely due to differences in study methodology and population. We investigated the main microbiome alterations in PD, their correlations with disease severity, and the impact of study and geographical differences. Methods After systematic screening, raw 16S rRNA gene sequences were obtained from ten case-control studies totaling 1703 subjects (969 PD, 734 non-PD controls; seven predominantly Caucasian and three predominantly non-Caucasian cohorts). Quality-filtered gene sequences were analyzed using a phylogenetic placement approach, which precludes the need for the sequences to be sourced from similar regions in the 16S rRNA gene, thus allowing a direct comparison between studies. Differences in microbiome composition and correlations with clinical variables were analyzed using multivariate statistics. Results Study and geography accounted for the largest variations in gut microbiome composition. Microbiome composition was more similar for subjects from the same study than those from different studies with the same disease status. Microbiome composition significantly differed between Caucasian and non-Caucasian populations. After accounting for study differences, microbiome composition was significantly different in PD vs. controls (albeit with a marginal effect size), with several distinctive features including increased abundances of Megasphaera and Akkermansia, and reduced Roseburia. Several bacterial genera correlated with PD motor severity, motor response complications and cognitive function. Conclusion Consistent microbial features in PD merit further investigation. The large variations in microbiome findings of PD patients underscore the need for greater harmonization of future research, and personalized approaches in designing microbial-directed therapeutics.

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great concern, as carbapenems are the last-line therapy for multidrug-resistant Gram-negative bacteria infections. This study aims to report the epidemiology of CRKP in a teaching hospital in Malaysia based on the molecular genotypic and clinical characteristics of the isolates. Sixty-three CRKP strains were isolated from a tertiary teaching hospital from January 2016 until August 2017. Carbapenemase genes were detected in 55 isolates, with blaOXA-48 (63.5%) as the predominant carbapenemase gene, followed by blaNDM (36.5%). At least one porin loss was detected in nine isolates. Overall, 63 isolates were divided into 30 clusters at similarity of 80% with PFGE analysis. Statistical analysis showed that in-hospital mortality was significantly associated with the usage of central venous catheter, infection or colonization by CRKP, particularly NDM-producers. In comparison, survival analysis using Cox proportional hazards regression identified a higher hazard ratio for patients with a stoma and patients treated with imipenem but a lower hazard ratio for patients with NDM-producing CRKP. OXA-48 carbapenemase gene was the predominant carbapenemase gene in this study. As CRKP infection could lead to a high rate of in-hospital mortality, early detection of the isolates was important to reduce their dissemination.

No studies have investigated the influence of ethnicity in a multi-ethnic middle-income country with a long-standing history of co-habitation. Stool samples from 214 Malaysian community members (46 Malay, 65 Chinese, 49 Indian, and 54 Jakun) were collected. The gut microbiota of the participants was investigated using 16S amplicon sequencing. Ethnicity exhibited the largest effect size across participants (PERMANOVA Pseudo-F = 4.24, R2 = 0.06, p = 0.001). Notably, the influence of ethnicity on the gut microbiota was retained even after controlling for all demographic, dietary factors and other covariates which were significantly associated with the gut microbiome (PERMANOVA Pseudo-F = 1.67, R2 = 0.02, p = 0.002). Our result suggested that lifestyle, dietary, and uncharacterized differences collectively drive the gut microbiota variation across ethnicity, making ethnicity a reliable proxy for both identified and unidentified lifestyle and dietary variation across ethnic groups from the same community.

Burkholderia pseudomallei, a Gram-negative bacterial pathogen that causes melioidosis, is of public health importance in endemic areas including Malaysia. An investigation of the molecular epidemiology links of B. pseudomallei would contribute to better understanding of the clonal relationships, transmission dynamics and evolutionary change. Multilocus sequence typing (MLST) of 45 clinical B. pseudomallei isolates collected from sporadic melioidosis cases in Malaysia was performed. In addition, a total of 449 B. pseudomallei Malaysian strains submitted to the MLST database from 1964 until 2019 were included in the temporal analysis to determine the endemic sequence types (STs), emergence and re-emergence of ST(s). In addition, strain-specific distribution was evaluated using BURST tool. Genotyping of 45 clinical strains was resolved into 12 STs, and the majority were affiliated with ST46 (n = 11) and ST1342 (n = 7). Concomitantly, ST46 was the most prevalent ST in Malaysia, which was first reported in 1964. All the Malaysian B. pseudomallei strains were resolved into 76 different STs with 36 of them uniquely present only in Malaysia. ST1342 was most closely related to ST1034, in which both STs were unique to Malaysia and first isolated from soil samples in Pahang, a state in Malaysia. The present study revealed a high diversity of B. pseudomallei in Malaysia. Localized evolution giving rise to the emergence of new STs was observed, suggesting that host and environmental factors play a crucial role in the evolutionary changes in B. pseudomallei.

Emerging evidence has shown a link between the perturbations and development of the gut microbiota in infants with their immediate and long-term health. To better understand the assembly of the gut microbiota in preterm infants, faecal samples were longitudinally collected from the preterm (n = 19) and term (n = 20) infants from birth until month 12. 16S rRNA gene sequencing (n = 141) and metabolomics profiling (n = 141) using nuclear magnetic resonance spectroscopy identified significant differences between groups in various time points. A panel of amino acid metabolites and central metabolism intermediates significantly correlated with the relative abundances of 8 species of bacteria were identified in the preterm group. In contrast, faecal metabolites of term infants had significantly higher levels of metabolites which are commonly found in milk such as fucose and β-hydroxybutyrate. We demonstrated that the early-life factors such as gestational age, birth weight and NICU exposures, exerted a sustained effect to the dynamics of gut microbial composition and metabolism of the neonates up to one year of age. Thus, our findings suggest that intervention at this early time could provide ‘metabolic rescue’ to preterm infants from aberrant initial gut microbial colonisation and succession.

Coffee is rich in antioxidant and has been shown to confer various health benefits. Here, we investigated the effect of single-dose coffee consumption in healthy human subjects. About 30 healthy volunteers were recruited and given a serving of sugar free black coffee. Urine and fecal samples were collected and analyzed. Significant changes in urinary metabolites relating to coffee, gut microbial and host energy metabolisms were observed post-coffee consumption. Clear sex differences were also observed in the urinary metabolic profiles pre- and post-coffee consumption. Sex differences in richness and composition of gut microbiota were observed, however, the effect of single-dose coffee consumption on host gut microbiota were unremarkable. These findings indicated that single-dose coffee consumption affects sex-specific host metabolic responses that relates to gut-microbe and energy metabolism. This study demonstrated the utility of systems biology tools to unravel complexity of host-diet biology and gut microbial responses. PRACTICAL APPLICATIONS: This study demonstrated that integrated systems biology approach enabled efficient extractions of host biochemical and microbial information that allows food industry to ascertain the impact of diet and longitudinal assessment of potential functional food in humans.

Background Probiotics are the most recognised alternative to antibiotic growth promoters (AGPs) for poultry production. They adhere to the intestinal epithelial cells to exert their beneficial effects on the host. However, this is often restricted by indigenous gut microbes that compete for adhesion sites and nutrients. Therefore, phage application has been proposed to reduce the competition of probiotics with gut microbiota. The main objective of this study was to investigate the effects of phages on the gut microbiota and their impact on probiotic efficacy in chickens. Results Four best Escherichia coli lytic phages were selected and characterised. The in vivo trial was conducted to investigate the effects of dietary treatments of phage cocktail at 0.1% (1ɸ) and 0.2% (2ɸ), 0.1% PrimaLac ® probiotic (P) and their combinations (1ɸP, 2ɸP) on growth performance and gut microbiota of chickens. The results from the in vivo trial showed that chickens in the 1ɸP group had significantly (P < 0.05) better body weight (BW), body weight gain (BWG), and feed conversion ratio (FCR), lower serum triglycerides and higher ileal villus height than the control. Chickens in the 1ɸP group also had higher (P < 0.05) ileal villus height, and lower crypt depth than those in the probiotic group. The gut microbiota profiles revealed that 1ɸP supplementation significantly (P < 0.05) reduced E. coli population, increased (P < 0.001) short chain fatty acids (SCFAs) producers, and improved (P < 0.001) gene expressions that are related to carbohydrate and amino acid metabolisms, and nutrient uptake. Conclusions The results from this study showed that 1ɸP treatment could modulate the gut microbiota and enhance growth performance in chickens. This finding could be considered as a potential alternative to AGPs for poultry.

OXA-48-like carbapenemase gene remains a hidden threat, as different OXA-48 variants have varying presentations of susceptibility to antibiotics that might affect the treatment decisions. Rapid detection and differentiation of OXA-48-like carbapenemase genes are critical for targeted treatment and infection control. In this study, we aimed to develop high-resolution melting (HRM) analysis for the differentiation of OXA-48 variants. HRM analysis is a post-polymerase chain reaction (post-PCR) method for identification of small variations in nucleic acid sequences based on the PCR dissociation curve. A total of 82 bacterial strains, which consisted of Enterobacteriaceae and non-Enterobacteriaceae, were collected from a tertiary teaching hospital. The sensitivity and specificity of the assay were determined, and the developed assay was evaluated using the collected isolates against conventional-sequencing method. Overall, the developed assay was able to detect isolates that harboured OXA-48 and OXA232/OXA-181 by showing two distinct peaks at 81.1 &plusmn, 0.2 &deg, C and 82.1 &plusmn, C, respectively. The detection limit of the assay was 1.6 x 10-6 ng/&micro, l for OXA-48 and 1.8 x 10-7 ng/&micro, l for OXA-232/OXA-181. This assay showed 100% specificity when evaluated on a panel of 37 isolates comprised of different species of bacteria and yeasts. When the assay with isolates collected in the year 2016 was first evaluated, the assay showed comparable results with conventional PCR-sequencing method where 34 OXA-48 and OXA-232/OXA-181 were detected. By using HRM analysis, the presence of OXA-48-like variants could be easily identified within 3 hours from the pure culture.

It is generally accepted that bacterial diversity in a community confers resistance to environmental perturbation. Communities with high bacterial diversity are less likely to be impacted by environmental changes such as warming. As such, hydrocarbon-contaminated Antarctic soil that are typically characterised by low bacterial diversity and highly selective taxonomic composition are expected to be more sensitive to changes in temperature than uncontaminated Antarctic soil. To test this hypothesis, we evaluated the response of bacterial community structure to warming of hydrocarbon-contaminated and uncontaminated soil collected from Casey Station, Windmill Island, East Antarctica by using microcosms incubated at 5, 10 and 15 °C over a period of 12 weeks. Our results showed that shifts occurred in the bacterial community in relation to the incubation temperatures in both the hydrocarbon-contaminated and uncontaminated soil, with a stronger response observed in the contaminated soil. Taxa referred as comprising hydrocarbon-degrading genera such as Rhodococcus, was the most prevalent genus in the contaminated soil after incubation at 15 °C, accounting for approximately 32–50% of the total detected genera. However, there were no significant differences in the selected functional genes, potentially suggesting high levels of metabolic plasticity in the studied soil bacterial communities. Overall, we showed that hydrocarbon contamination in soil might lead to lower bacterial community stability against environmental perturbation such as temperature variation.

Background: The giant amoebal viruses of Mimivirus and Marseillevirus are large DNA viruses and have been documented in water, soil, and sewage samples. The trend of discovering these giant amoebal viruses has been increasing throughout Asia with Japan, India, and Saudi Arabia being the latest countries to document the presence of these viruses. To date, there have been no reports of large amoebal viruses being isolated in South East Asia. Objective: In this study, we aim to discover these viruses from soil samples in an aboriginal village (Serendah village) in Peninsular ­Malaysia. Method and Results: We successfully detected and isolated both Mimivirus-like and Marseillevirus-like viruses using Acanthamoeba castellanii. Phylogeny analysis identified them as Mimivirus and Marseillevirus, respectively. Conclusion: The ubiquitous nature of both Mimivirus and Marseillevirus is further confirmed in our study as they are detected in higher quantity in soil that is near to water vicinities in an aboriginal village in Peninsular Malaysia. However, this study is limited by our inability to investigate the impact of Mimivirus and Marseillevirus on the aboriginal villagers. More studies on the potential impact of these viruses on human health, especially on the aborigines, are warranted.

The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) has now become a global sentinel event. CRAB infections often instigate severe clinical complications and are potentially fatal, especially for debilitated patients. The present study aimed to conduct molecular characterization on CRAB isolated from patients in the intensive care unit from 2015 to 2016 and determine the risk factors associated with patients’ mortality. One hundred CRAB isolates were retrospectively selected and included in this study. Antimicrobial susceptibility testing showed that all isolates remained susceptible to colistin, even though 62% of them conferred resistance to all other classes of antibiotics tested. OXA carbapenemase gene was found to be the predominant carbapenemase gene, with 99% of the isolates coharbouring blaOXA-23-like and blaOXA-51-like carbapenemase genes. All isolates were carrying intact CarO genes, with the presence of various degree of nucleotide insertion, deletion and substitution. Overall, PFGE subtyped the isolates into 13 distinct pulsotypes, with the presence of 2 predominant pulsotypes. Univariate analysis implied that age, infection/colonization by CRAB, ethnicity, comorbidity and CRAB specimen source were significantly associated with in-hospital mortality. Multivariate analysis identified a higher risk of mortality for patients who are of Chinese ethnicity with diabetes as an underlying disease. As CRAB infection could lead to high rate of mortality, comprehensive infection control measures are needed to minimize the spread of this pathogen.

The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.

The community dynamics of environmental bacteria is dependent on micro-climatic factors such as temperature and water potentials. A shift in any one of these factors can have a major impact on the richness and composition of the microbes in the soil. However, microbial responses towards these climate stressors are poorly characterised. Here, we undertook a microcosm study to assess the effect of temperature and water content on the bacterial community structure in a tropical soil over a four week period. The microcosms were incubated at three different temperatures (25 °C, 30 °C, and 35 °C) and maintained under two different water levels (2 and 5 mL). Using a combination of molecular assessment tools and numerical inference, we showed that short-term variation in both temperature and water content induced significant changes to the soil bacterial community composition. The greatest difference in community structure between treatments was observed in the Week 2 microcosms, but in the Week 4 microcosms, the community structure between treatments became more similar. Compared to temperature, water content exerted a greater effect on the bacterial diversity. Firmicutes was the most abundant phylum in all the analysed samples, and its relative abundance increased with elevation in temperature and water content. Out of six functional genes analysed, the nitrogen fixation gene (nifH) and denitrification gene (nosZ) showed significant correlations to the bacterial community structures.

The prevalence and antibiotic susceptibility of intestinal carriage of Gram-negative bacteria among preterm infants admitted to the neonatal intensive care unit (NICU) in a tertiary teaching hospital in Malaysia were determined. A total of 34 stool specimens were obtained from preterm infants upon admission and once weekly up to two weeks during hospitalization. The presumptive colonies of Escherichia coli and Klebsiella pneumoniae were selected for identification, antibiotic susceptibility testing, and subtyping by using pulsed-field gel electrophoresis (PFGE). Out of 76 Gram-negative isolates, highest resistance was detected for amoxicillin/clavulanate (30.8%, n = 16), ceftriaxone (42.3%, n = 22), ceftazidime (28.8%, n = 15), cefoxitin (28.8%, n = 15), aztreonam (36.5%, n = 19), and polymyxin B (23.1%, n = 12). Three colistin resistant K. pneumoniae have also been detected based on E-test analysis. Thirty-nine isolates of K. pneumoniae and 20 isolates of E. coli were resistant to more than three antimicrobial classes and were categorized as multidrug resistant (MDR). PFGE analysis revealed a higher diversity in pulsotypes for K. pneumoniae (18 pulsotypes) in comparison to E. coli (four pulsotypes). In addition, a total of fifteen pulsotypes was observed from 39 MDR K. pneumoniae. The risk factors for antibiotic resistance were assessed using random forest analysis. Gender was found to be the most important predictor for colistin resistant while length, OFC, and delivery mode were showing greater predictive power in the polymyxin B resistance. This study revealed worrying prevalence rates of intestinal carriage of multidrug-resistant K. pneumoniae and E. coli of hospitalized preterm infants in Malaysia, particularly high resistance to polymyxins.

The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae has greatly affected the clinical efficacy of β-lactam antibiotics in the management of urinary tract infections (UTIs). The limited treatment options have resulted in the increased use of carbapenem. However, flomoxef could be a potential carbapenem-sparing strategy for UTIs caused by ESBL-producers. Here, we compared the in vitro susceptibility of UTI-associated ESBL-producers to flomoxef and established β-lactam antibiotics. Fifty Escherichia coli and Klebsiella pneumoniae strains isolated from urine samples were subjected to broth microdilution assay, and the presence of ESBL genes was detected by polymerase chain reactions. High rates of resistance to amoxicillin-clavulanate (76–80%), ticarcillin-clavulanate (58–76%), and piperacillin-tazobactam (48–50%) were observed, indicated by high minimum inhibitory concentration (MIC) values (32 µg/mL to 128 µg/mL) for both species. The ESBL genes blaCTX-M and blaTEM were detected in both E. coli (58% and 54%, respectively) and K. pneumoniae (88% and 74%, respectively), whereas blaSHV was found only in K. pneumoniae (94%). Carbapenems remained as the most effective antibiotics against ESBL-producing E. coli and K. pneumoniae associated with UTIs, followed by flomoxef and cephamycins. In conclusion, flomoxef may be a potential alternative to carbapenem for UTIs caused by ESBL-producers in Malaysia.

Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p < .05) and T2 diets (p < .05), demonstrating the efficiency of MJ as a supplement to low aP diet. Nevertheless, MJ did not significantly affect the microbial population and diversity in broilers' caeca, which mainly consists of members from Bacteroidetes, Firmicutes, and Proteobacteria. Regardless, significant variations in the caecal bacterial composition were observed over time, probably due to succession as the broilers aged. This is the first reported study on the effect of MJ on the microbial diversity of broiler's caeca.

The increasing prevalence of antibiotic resistant pathogens poses a serious threat to global health. However, less emphasis has been placed to co-relate the gene expression and metabolism of antibiotic resistant pathogens. This study aims to elucidate gene expression and variations in metabolism of multidrug resistant Klebsiella pneumoniae after exposure to antibiotics. Phenotypic responses of three genotypically distinct carbapenem resistant Klebsiella pneumoniae (CRKP) strains untreated and treated with sub-lethal concentrations of imipenem were investigated via phenotype microarrays (PM). The gene expression and metabolism of the strain harboring blaNDM-1 before and after exposure to sub-lethal concentration of imipenem were further investigated by RNA-sequencing (RNA-Seq) and 1H NMR spectroscopy respectively. Most genes related to cell division, central carbon metabolism and nucleotide metabolism were downregulated after imipenem treatment. Similarly, 1H NMR spectra obtained from treated CRKP showed decrease in levels of bacterial end products (acetate, pyruvate, succinate, formate) and metabolites involved in nucleotide metabolism (uracil, xanthine, hypoxanthine) but elevated levels of glycerophosphocholine. The presence of anserine was also observed for the treated CRKP while FAPγ-adenine and methyladenine were only present in untreated bacterial cells. As a conclusion, the studied CRKP strain exhibited decrease in central carbon metabolism, cell division and nucleotide metabolism after exposure to sub-lethal concentrations of imipenem. The understanding of the complex biological system of this multidrug resistant bacterium may help in the development of novel strategies and potential targets for the management of the infections.

Human toxocariasis which is caused mainly by the larvae of Toxocara canis and Toxocara cati, is a worldwide zoonotic disease that can be a potentially serious human infection. The enzyme-linked immunosorbent assay (ELISA) using T. canis excretory-secretory (TES) antigens harvested from T. canis larvae is currently the serological test for confirming toxocariasis. An alternative to producing large amounts of Toxocara TES and improved diagnosis for toxocariasis is through the development of highly specific recombinant antigens such as the T. canis second stage larva excretory-secretory 30 kDa protein (recTES-30). The aim of this study was to evaluate the sensitivity and specificity of a rapid diagnostic kit (RDT, named as iToxocara kit) in comparison to recTES-30 ELISA in Serendah Orang Asli village in Selangor, Malaysia. A total of 133 subjects were included in the study. The overall prevalence rates by ELISA and RDT were 29.3% and 33.1%, respectively, with more positive cases detected in males than females. However, no association was found between toxocariasis and gender or age. The percentage sensitivity, specificity, positive predictive value and negative predictive value of RDT were 85.7%, 90.1%, 80% and 93.2%, respectively. The prevalence for toxocariasis in this population using both ELISA and RDT was 27.1% (36/133) and the K-concordance test suggested good agreement of the two tests with a Cohen's kappa of 0.722, P

Understanding the basal gut bacterial community structure and the host metabolic composition is pivotal for the interpretation of laboratory treatments designed to answer questions pertinent to host-microbe interactions. In this study, we report for the first time the underlying gut microbiota and systemic metabolic composition in BALB/c mice during the acclimatisation period. Our results showed that stress levels were reduced in the first three days of the study when the animals were subjected to repetitive handling daily but the stress levels were increased when handling was carried out at lower frequencies (weekly). We also observed a strong influence of stress on the host metabolism and commensal compositional variability. In addition, temporal biological compartmental variations in the responses were observed. Based on these results, we suggest that consistency in the frequency and duration of laboratory handling is crucial in murine models to minimise the impact of stress levels on the commensal and host metabolism dynamics. Furthermore, caution is advised in consideration of the temporal delay effect when integrating metagenomics and metabonomics data across different biological matrices (i.e. faeces and urine).

Genotype and metabolomic variation are important for bacterial survival and adaptation to environmental changes. In this study, we compared the relationship among Klebsiella pneumoniae strains based on their genotypic and metabolic profiles. In addition, we also evaluated the association of the relationship with beta-lactamase production. A total of 53 K. pneumoniae strains isolated in 2013–2014 from a tertiary teaching hospital in Malaysia were subjected to antimicrobial susceptibility testing (AST) via disk diffusion method and beta-lactamase production confirmation. The bacterial strains were also typed genotypically and metabolically via REP-PCR and 1H-NMR spectroscopy respectively. The concordance of the matrices derived based on genotypic and metabolic characterization was measured based on Spearman’s rank correlation. Spearman’s correlation rank showed that there is a weak but significant negative correlation between the genetic fingerprints and metabolic profiles of K. pneumoniae. Specifically, K. pneumoniae strains were clustered into five major clusters based on REP-PCR where most of the carbapenem resistant K. pneumoniae (CRKP) strains made up the major cluster. In contrast, metabolic patterns of the three groups (i.e. CRKP, extended spectrum beta-lactamase producing K. pneumoniae (ESBL), susceptible) of K. pneumoniae were clearly differentiated on PLS-DA score plots derived from 1H-NMR spectroscopy. Overall, this study showed that metabolomic profiling using 1H-NMR spectroscopy is able to discriminate K. pneumoniae strains based on their beta-lactamase production status.

Since the advent of 16S rRNA gene-based molecular analysis, an increasing amount of work has been conducted on the Antarctic soil bacterial community. The majority of such studies suggest that the Antarctic soil environment may harbour a greater diversity of bacteria than was previously thought, and indeed that a proportion of the bacterial species found might be unique to the Antarctic. However, few have looked at the distribution of soil sequence types from different biogeographic regions of the continent. Here, we assess the taxonomic distribution of soil bacteria from different regions and latitudes in Antarctica by integrating 16S rRNA gene sequence information from 13 independent studies that, together, obtained samples from 35 locations ranging from 51°S to 78°S. The majority of these formed a transect across the continent, representing most of the ice-free regions of the Antarctic Peninsula and Scott Sector. Using detailed phylogenetic analysis, we found that most of the Antarctic soil environments contained a narrow range of bacterial species when compared to the overall number of sequences available. Further, patterns in the taxonomic distribution of Antarctic soil bacterial communities were significantly correlated to both the underlying soil parameters and geographic (regional) origins.

BackgroundEnterococcus faecalisandEnterococcus faeciumare ubiquitous opportunistic pathogens found in the guts of humans and farmed animals. This study aimed to determine the occurrence, antimicrobial resistance, virulence, biofilm-forming ability and genotypes ofE. faecalisandE. faeciumfrom swine farms. Correlations between the genotypes, virulotypes, antibiotic resistance, and the environmental factors such as locality of farms and farm hygiene practice were explored.MethodsE. faecalisandE. faeciumstrains were isolated from the oral, rectal and fecal samples of 140 pigs; nasal, urine and fecal samples of 34 farmers working in the farms and 42 environmental samples collected from seven swine farms located in Peninsular Malaysia. Antibiotic susceptibility test was performed using the disk diffusion method, and the antibiotic resistance and virulence genes were detected by Polymerase Chain Reaction. Repetitive Extragenic Palindromic-Polymerase Chain Reaction and Pulsed-Field Gel Electrophoresis were performed to determine the clonality of the strains. Crosstab/Chi-square test and DistLM statistical analyses methods were used to determine the correlations between the genotypes, virulence factors, antibiotic resistance, and the environmental factors.ResultsA total of 211E. faecalisand 42E. faeciumwere recovered from 140 pigs, 34 farmers and 42 environmental samples collected from seven swine farms in Peninsular Malaysia. Ninety-eight percent of the strains were multidrug-resistant (resistant to chloramphenicol, tetracycline, ciprofloxacin and erythromycin). Fifty-two percent of the strains formed biofilms. Virulence genesefa, asaI, gelE,esp,cylandacegenes were detected. Virulence genesefaandasaI were most prevalent inE. faecalis(90%) andE. faecium(43%), respectively. Cluster analyses based on REP-PCR and PFGE showed the strains were genetically diverse. Overall, the strains isolated from pigs and farmers were distinct, except for three highly similar strains found in pigs and farmers. The strains were regional- and host-specific.DiscussionThis study revealed alarming high frequencies of multidrug-resistant enterococci in pigs and swine farmers. The presence of resistance and virulence genes and the ability to form biofilm further enhance the persistence and pathogenicity of the strains. Although the overall clonality of the strains were regionals and host-specific, strains with high similarity were found in different hosts. This study reiterates a need of a more stringent regulation to ensure the proper use of antibiotics in swine husbandry to reduce the wide spread of multidrug-resistant strains.

Soil bacterial diversity at environmentally distinct locations on Signy Island, South Orkney Islands was examined using the denaturing gradient gel profiling approach. A range of chemical variables in soils at each site was determined in order to describe variation between locations. No apparent differences in Shannon Diversity Index (H′) were observed. However, as revealed in an analysis of similarity (ANOSIM), the dominant bacterial communities of all eight studied locations were significantly different. Within this, higher levels of similarity were observed between penguin rookeries, seal wallows and vegetated soils, all of which share varying levels of impact from vertebrate activity, in contrast with more barren soil. In addition, the lowest H′ value was detected from the latter soil which also has the most extreme environmental conditions, and its bacterial community has the greatest genetic distance from the other locations. DGGE analyses indicated that the majority of the excised and sequenced bands were attributable to the Bacteroidetes. Across a range of ten environmental variables, multivariate correlation analysis suggested that a combination of pH, conductivity, copper and lead content potentially contributed explanatory value to the measured soil bacterial diversity.

SUMMARYToxoplasmosis affects a third of the global population and is of particular concern for immunologically compromised individuals. Toxoplasmosis induces host physiological events ranging from immunological to metabolic responses across multiple biological compartments. To understand the sequence of host responses during acute and chronicToxoplasma gondiiinfection, eight male BALB/c mice were infected with 2000T. gondiiME49 tachyzoites with a further eight uninfected mice used as controls. Plasma cytokines status, urinary metabolic profiling and fecal microbial profiles were characterized to monitor temporal variation related toT. gondiiinfection. The results showed elevated serum interferon-γ(IFN-γ), interleukin-12p40 and necrosis factor-αduring acute phase of infection with concomitant perturbation in host energy metabolism and host-gut microbiome co-metabolism of phenolics and a shift in microbial composition. However, the differences were less pronounced during the putative chronic phase of infection with elevated IFN-γ, differences in urinaryN-acetyls andO-acetyls of glycoproteins with no shift in gut microbial composition. Structural equation modelling on the current data showed host immune responses as the main driver for changes observed in urinary metabolites and gut microbial composition. Such an approach can be applied to other models of infectious diseases to aid understanding of host–pathogen interactions and potential biomarker discovery.

Background Intestinal parasitic infections (IPIs) among indigenous people have been widely documented in Malaysia, however, the prevalence of these infections remains high. In the past, most studies have focused on specific species of parasites but polyparasitism has received limited attention. In addition, epidemiology studies on indigenous people tend to consider them as a homogenous group, whereas in reality different sub-ethnic groups have different cultural and living practices. Variations in living habits such as personal hygiene practices may predispose different groups to different parasitic infections. To better understand prevalence and risk factors of intestinal parasitism among different sub-ethnic groups, the present study was conducted among two sub-ethnic groups of indigenous people (Temuan and Mah Meri) residing in Selangor state, Malaysia. Methods A cross-sectional study that focused on two distinct sub-ethnic groups was carried out from February to September 2014. Faecal samples were collected from 186 participants and examined using the formalin-ether sedimentation technique. A molecular approach was adopted to conduct a genetic characterisation of the parasites. Additionally, questionnaires were administered to obtain information on the demographics, socio-economic backgrounds and behavioural risks relating to the participants, as well as information about their environments. Statistical analyses (i.e. binary and multivariate logistic regression analyses) were performed to measure risk factors. Results For Temuan communities, trichuriasis (64.2 %) was the most common infection found, preceding hookworm infection (34 %), ascariasis (7.5 %), giardiasis (14.2 %) and amoebiasis (7.5 %). As for the Mah Meri communities, trichuriasis (77.5 %) prevailed over ascariasis (21.3 %), hookworm (15 %), giardiasis (7.5 %) and amoebiasis (3.8 %). Significant differences in proportions of trichuriasis, ascariasis and hookworm infections were observed between the Temuan and Mah Meri sub-ethnic groups. Polyparasitism was more common among the Temuan sub-ethnic group (41.5 %) compared to the Mah Meri sub-ethnic group (32.5 %), with the majority of participants harbouring two parasites concurrently (Temuan: 33 %, Mah Meri: 20 %). Trichuris trichiura and Ascaris lumbricoides co-infections were most prevalent (10 %) among the Mah Meri communities, while a co-infection of T. trichiura with hookworm (19.8 %) was most common among the Temuan communities. Multivariate analyses showed that being unemployed, having a large family and drinking unboiled water were found to be significantly associated with intestinal parasitism. Conclusion The present study highlights substantial polyparasitism and risk factors for infections in the Temuan and Mah Meri sub-ethnic groups. The high prevalence of IPIs among these two sub-ethnic groups indicates that parasitic infections are important health issues in these communities. Hence, it is imperative to implement sound intervention strategies such as periodic preventive chemotherapy coupled with health education in order to reduce and eradicate these infections. Electronic supplementary material The online version of this article (doi:10.1186/s40249-016-0168-z) contains supplementary material, which is available to authorized users.

Background Chicken gut microbiota has paramount roles in host performance, health and immunity. Understanding the topological difference in gut microbial community composition is crucial to provide knowledge on the functions of each members of microbiota to the physiological maintenance of the host. The gut microbiota profiling of the chicken was commonly performed previously using culture-dependent and early culture-independent methods which had limited coverage and accuracy. Advances in technology based on next-generation sequencing (NGS), offers unparalleled coverage and depth in determining microbial gut dynamics. Thus, the aim of this study was to investigate the ileal and caecal microbiota development as chicken aged, which is important for future effective gut modulation. Material and methods Ileal and caecal contents of broiler chicken were extracted from 7, 14, 21 and 42-day old chicken. Genomic DNA was then extracted and amplified based on V3 hyper-variable region of 16S rRNA. Bioinformatics, ecological and statistical analyses such as Principal Coordinate Analysis (PCoA) was performed in mothur software and plotted using PRIMER 6. Additional analyses for predicted metagenomes were performed through PICRUSt and STAMP software package based on Greengenes databases. Results A distinctive difference in bacterial communities was observed between ilea and caeca as the chicken aged (P

Gut microbiota plays an important role in mammalian host metabolism and physiological functions. The functions are particularly important in young children where rapid mental and physical developments are taking place. Nevertheless, little is known about the gut microbiome and the factors that contribute to microbial variation in the gut of South East Asian children. Here, we compared the gut bacterial richness and composition of pre-adolescence in Northern Malaysia. Our subjects covered three distinct ethnic groups with relatively narrow range of socioeconomic discrepancy. These included the Malays (n = 24), Chinese (n = 17) and the Orang Asli (indigenous) (n = 20). Our results suggested a strong ethnicity and socioeconomic-linked bacterial diversity. Highest bacterial diversity was detected from the economically deprived indigenous children while the lowest diversity was recorded from the relatively wealthy Chinese children. In addition, predicted functional metagenome profiling suggested an over-representation of pathways pertinent to bacterial colonisation and chemotaxis in the former while the latter exhibited enriched gene pathways related to sugar metabolism.

Background.Central intermediary metabolism (CIM) in bacteria is defined as a set of metabolic biochemical reactions within a cell, which is essential for the cell to survive and respond to environmental perturbations. The genes associated with CIM are commonly found in both pathogenic and non-pathogenic strains. As these genes are involved in vital metabolic processes of bacteria, we explored the efficiency of the genes in genotypic characterization ofBurkholderia pseudomalleiisolates, compared with the established pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) schemes.Methods.Nine previously sequencedB. pseudomalleiisolates from Malaysia were characterized by PFGE, MLST and CIM genes. The isolates were later compared to the other 39B. pseudomalleistrains, retrieved from GenBank using both MLST and sequence analysis of CIM genes. UniFrac and hierachical clustering analyses were performed using the results generated by both MLST and sequence analysis of CIM genes.Results.Genetic relatedness of nine MalaysianB. pseudomalleiisolates and the other 39 strains was investigated. The nine Malaysian isolates were subtyped into six PFGE profiles, four MLST profiles and five sequence types based on CIM genes alignment. All methods demonstrated the clonality of OB and CB as well as CMS and THE. However, PFGE showed less than 70% similarity between a pair of morphology variants, OS and OB. In contrast, OS was identical to the soil isolate, MARAN. To have a better understanding of the genetic diversity ofB. pseudomalleiworldwide, we further aligned the sequences of genes used in MLST and genes associated with CIM for the nine Malaysian isolates and 39B. pseudomalleistrains from NCBI database. Overall, based on the CIM genes, the strains were subtyped into 33 profiles where majority of the strains from Asian countries were clustered together. On the other hand, MLST resolved the isolates into 31 profiles which formed three clusters. Hierarchical clustering using UniFrac distance suggested that the isolates from Australia were genetically distinct from the Asian isolates. Nevertheless, statistical significant differences were detected between isolates from Malaysia, Thailand and Australia.Discussion.Overall, PFGE showed higher discriminative power in clustering the nine MalaysianB. pseudomalleiisolates and indicated its suitability for localized epidemiological study. Compared to MLST, CIM genes showed higher resolution in distinguishing those non-related strains and better clustering of strains from different geographical regions. A closer genetic relatedness of Malaysian isolates with all Asian strains in comparison to Australian strains was observed. This finding was supported by UniFrac analysis which resulted in geographical segregation between Australia and the Asian countries.