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Kombucha is a fermented tea traditionally known for its health-enhancing properties owing to the bioactive compounds generated by acetic acid bacteria (AAB) and lactic acid bacteria (LAB). We compared the distribution of AAB and LAB and their functional pathways across nine commercial kombucha products in Singapore using shotgun metagenomic sequencing. A high prevalence ofKomagataeibacterspecies includingKomagataeibacter saccharivorans(82.93% in B),Komagataeibacter xylinus(93.38% in D) andKomagataeibacter rhaeticus(92.20% and 30.62% in G and I) was detected in AAB-dominant kombucha. LAB-dominant kombucha was largely represented byBacillus coagulans(~99% in E and F) andLactobacillus nagelii(~60% in H). Despite differences in bacterial composition, both LAB-and AAB-dominant kombucha harbour pathways involved in the biosynthesis of short-chain fatty acids (SCFAs), amino and organic acids and vitamin B12. “Fatty acid and beta-oxidation II (peroxisome)” and “fatty acid and beta-oxidation I” were detected in the LAB but not the AAB-dominant kombucha.

BackgroundDiabetes is one of the leading causes of chronic kidney disease (CKD) and end-stage renal disease. This study aims to develop and validate different risk predictive models for incident CKD and CKD progression in people with type 2 diabetes (T2D).MethodsWe reviewed a cohort of people with T2D seeking care from two tertiary hospitals in the metropolitan cities of the state of Selangor and Negeri Sembilan from January 2012 to May 2021. To identify the 3-year predictor of developing CKD (primary outcome) and CKD progression (secondary outcome), the dataset was randomly split into a training and test set. A Cox proportional hazards (CoxPH) model was developed to identify predictors of developing CKD. The resultant CoxPH model was compared with other machine learning models on their performance using C-statistic.ResultsThe cohorts included 1992 participants, of which 295 had developed CKD and 442 reported worsening of kidney function. Equation for the 3-year risk of developing CKD included gender, haemoglobin A1c, triglyceride and serum creatinine levels, estimated glomerular filtration rate, history of cardiovascular disease and diabetes duration. For risk of CKD progression, the model included systolic blood pressure, retinopathy and proteinuria. The CoxPH model was better at prediction compared with other machine learning models examined for incident CKD (C-statistic: training 0.826; test 0.874) and CKD progression (C-statistic: training 0.611; test 0.655). The risk calculator can be found at https://rs59.shinyapps.io/071221/.ConclusionsThe Cox regression model was the best performing model to predict people with T2D who will develop a 3-year risk of incident CKD and CKD progression in a Malaysian cohort.

Objective Converging evidence suggests that intestinal inflammation is involved in the pathogenesis of neurodegenerative diseases. Previous studies on fecal calprotectin in Parkinson’s disease (PD) were limited by small sample sizes, and literature regarding intestinal inflammation in multiple system atrophy (MSA) is very scarce. We investigated the levels of fecal calprotectin, a marker of intestinal inflammation, in PD and MSA.Methods We recruited 169 subjects (71 PD, 38 MSA, and 60 age-similar nonneurological controls). Clinico-demographic data were collected. PD and MSA were subtyped and the severity assessed using the MDS-UPDRS and UMSARS, respectively. Fecal calprotectin and blood immune markers were analyzed.Results Compared to controls (median: 35.7 [IQR: 114.2] μg/g), fecal calprotectin was significantly elevated in PD (median: 95.6 [IQR: 162.1] μg/g, p = 0.003) and even higher in MSA (median: 129.5 [IQR: 373.8] μg/g, p = 0.002). A significant interaction effect with age was observed; between-group differences were significant only in older subjects (i.e., ≥ 61 years) and became more apparent with increasing age. A total of 28.9% of MSA and 18.3% of PD patients had highly abnormal fecal calprotectin levels (≥ 250 μg/g); however, this difference was only significant for MSA compared to controls. Fecal calprotectin correlated moderately with selected blood immune markers in PD, but not with clinical features of PD or MSA.Conclusions Elevated fecal calprotectin suggests a role for intestinal inflammation in PD and MSA. A more complete understanding of gut immune alterations could open up new avenues of research and treatment for these debilitating diseases.

Phages, which are often used therapeutically, have begun to receive interest as alternatives to antibiotic growth promoters (AGPs) for enhancing chicken growth. Another option that has been extensively studied as a growth promoter in chickens is probiotics. To the best of our knowledge, there is currently no study available on the use of phages and probiotics in combination as potential feed additives for broiler chickens. Therefore, this study demonstrated the effects of a phage cocktail, probiotics, and their combination on the growth performance and gut microbiota of broiler chickens. A total of 288 one-day-old male Cobb 500 broilers were randomly allotted to one of six treatments in a completely randomised design. The treatments were (i) C (basal diet (BD) only), (ii) 1ϕ (BD + 0.1% phage cocktail), (iii) 2ϕ (BD + 0.2% phage cocktail), (iv) P (BD + 0.1% probiotic), (v) 1ϕP (BD + 0.1% phage cocktail + 0.1% probiotic), and (vi) 2ϕP (BD + 0.2% phage cocktail + 0.1% probiotic). The 1ϕP treatment had significantly (p < 0.05) better BW (35 days), BWG (22–35 days, 1–35 days), and FCR (1–21 days, 22–35 days, 1–35 days) compared to C. Unique gut microbiota diversity was also found between the ϕP (1ϕP and 2ϕP) and non-ϕP groups (C, 1ϕ, 2ϕ, and P) in ilea, particularly in the 35-day-old chickens. Microorganisms associated with short-chain fatty acid (SCFA) producers were significantly (p < 0.05) more present in the ϕP group than in the non-ϕP group. The predicted genes related to carbohydrate and amino acid metabolism were significantly upregulated in ϕP groups compared to non-ϕP groups. These genes were involved in the digestion and absorption of nutrients, as well as the production of energy. Our findings showed that the 1ϕP treatment could be a potential alternative to AGPs for poultry, as growth performance was enhanced, and gut microbiota was positively modulated.

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.

Non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae (NC-CRKP) confers carbapenem resistance through a combination of chromosomal mutations and acquired non-carbapenemase resistance mechanisms. In this study, we aimed to evaluate the clinical and molecular profiles of NC-CRKP isolated from patients in a tertiary teaching hospital in Malaysia from January 2013 to October 2019. During the study period, 54 NC-CRKP-infected/colonised patients’ isolates were obtained. Clinical parameters were assessed in 52 patients. The all-cause in-hospital mortality rate among NC-CRKP patients was 46.2% (24/52). Twenty-three (44.2%) patients were infected, while others were colonised. Based on the Charlson Comorbidity Index (CCI) score, 92.3% (48/52) of the infected/colonised patients had a score of ≥ 1. Resistance genes found among the 54 NC-CRKP isolates were blaTEM, blaSHV, blaCTX-M, blaOXA, and blaDHA. Porin loss was detected in 25/54 (46.3%) strains. None of the isolated strains conferred carbapenem resistance through the efflux pumps system. In conclusion, only 25/54 (46.3%) NC-CRKP conferred carbapenem resistance through a combination of porin loss and the acquisition of non-carbapenemase resistance mechanisms. The carbapenem resistance mechanisms for the remaining strains (53.7%) should be further investigated as rapid identification and distinction of the NC-CRKP mechanisms enable optimal treatment and infection control efforts.

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.

Non-carbapenemase-producing carbapenem-resistant

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.

Background Knowledge on the epidemiology, genotypic and phenotypic features of antimicrobial-resistant (AMR) ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) and their association with hospital-acquired infections (HAIs) are limited in Malaysia. Therefore, we evaluated the AMR features and resistance mechanisms of the ESKAPEE pathogens collected in a tertiary hospital located in the capital of Malaysia. Methods A total of 378 AMR-ESKAPEE strains were obtained based on convenience sampling over a nine-month study period (2019–2020). All strains were subjected to disk diffusion and broth microdilution assays to determine the antimicrobial susceptibility profiles. Polymerase chain reaction (PCR) and DNA sequence analyses were performed to determine the AMR genes profiles of the non-susceptible strains. Chi-square test and logistic regression analyses were used to correlate the AMR profiles and clinical data to determine the risk factors associated with HAIs. Results High rates of multidrug resistance (MDR) were observed in A. baumannii, K. pneumoniae, E. coli, and S. aureus (69–89%). All organisms except E. coli were frequently associated with HAIs (61–94%). Non-susceptibility to the last-resort drugs vancomycin (in Enterococcus spp. and S. aureus), carbapenems (in A. baumannii, P. aeruginosa, and Enterobacteriaceae), and colistin (in Enterobacteriaceae) were observed. Both A. baumannii and K. pneumoniae harbored a wide array of extended-spectrum β-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA). Metallo-β-lactamase genes (blaVEB, blaVIM, blaNDM) were detected in carbapenem-resistant strains, at a higher frequency compared to other local reports. We detected two novel mutations in the quinolone-resistant determining region of the gyrA in fluoroquinolone-resistant E. coli (Leu-102-Ala; Gly-105-Val). Microbial resistance to ampicillin, methicillin, and cephalosporins was identified as important risk factors associated with HAIs in the hospital. Conclusion Overall, our findings may provide valuable insight into the microbial resistance pattern and the risk factors of ESKAPEE-associated HAIs in a tertiary hospital located in central Peninsular Malaysia. The data obtained in this study may contribute to informing better hospital infection control in this region.

The gut–brain axis is a hot topic in Parkinson's disease (PD). It has been postulated that gut pathogens and dysbiosis can contribute to peripheral inflammatory states or trigger downstream metabolic effects that exacerbate the neurodegenerative process in PD. Several preclinical and clinical studies have demonstrated disrupted intestinal permeability, intestinal inflammation, altered gut microbiome, and reduced fecal short‐chain fatty acids in PD. In this regard, microbial‐directed therapies such as probiotics are emerging as potential therapeutic options. Probiotic supplementation is postulated to confer a variety of health benefits due to the diverse functions of these live microorganisms, including inhibition of pathogen colonization, modulation/“normalization” of the microbiome and/or its function, immunomodulatory effects (e.g. reducing inflammation), and improved host epithelial barrier function. Interestingly, several PD animal model studies have demonstrated the potential neuroprotective effects of probiotics in reducing dopaminergic neuronal degeneration. Notably, two randomized placebo‐controlled trials have provided class I evidence for probiotics as a treatment for constipation in PD. However, the effects of probiotics on other PD aspects, such as motor disability and cognitive function, and its long‐term efficacy (including effects on PD drug absorption in the gut) have not been investigated adequately. Further targeted animal and human studies are also warranted to understand the mechanisms of actions of probiotics in PD and to tailor probiotic therapy based on individual host profiles to improve patient outcomes in this disabling disorder., This review introduces readers to the gut–brain axis theory in Parkinson's disease (PD) and summarizes relevant literature regarding alterations of gut microbiome/physiology in PD. This is then followed by a focused review on the potential roles of probiotics in PD, with critical appraisals of published clinical and preclinical evidence. Importantly, current knowledge gaps and leads for future research are highlighted.

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.

Staphylococcus aureus expresses diverse proteins at different stages of growth. The immunodominant staphylococcal antigen A (IsaA) is one of the proteins that is constitutively produced by S. aureus during colonisation and infection. SACOL2584 (or isaA) is the gene that encodes this protein. It has been suggested that IsaA can hydrolyse cell walls, and there is still need to study isaA gene disruption to analyse its impact on staphylococcal phenotypes and on alteration to its transcription and protein profiles. In the present study, the growth curve in RPMI medium (which mimics human plasma), autolytic activity, cell wall morphology, fibronectin and fibrinogen adhesion and biofilm formation of S. aureus SH1000 (wildtype) was compared to that of S. aureus MS001 (isaA mutant). RNA sequencing and liquid chromatography–tandem mass spectrometry were carried out on samples of both S. aureus strains taken during the exponential growth phase, followed by bioinformatics analysis. Disruption of isaA had no obvious effect on the growth curve and autolysis ability or thickness of cell walls, but this study revealed significant strength of fibronectin adherence in S. aureus MS001. In particular, the isaA mutant formed less biofilm than S. aureus SH1000. In addition, proteomics and transcriptomics showed that the adhesin/biofilm-related genes and hemolysin genes, such as sasF, sarX and hlgC, were consistently downregulated with isaA gene disruption. The majority of the upregulated genes or proteins in S. aureus MS001 were pur genes. Taken together, this study provides insight into how isaA disruption changes the expression of other genes and has implications regarding biofilm formation and biological processes.

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.

Typhoid fever is a disease caused by Salmonella Typhi that was implicated in millions of illnesses worldwide annually. Individuals that do not recover fully from typhoid fever can become asymptomatic carriers of the disease. Host antibodies against the S. Typhi antigens, HlyE (for acute typhoid) and YncE (for carriers) were previously reported to be useful biomarkers for the disease. Here, we expressed and purified recombinant HlyE and YncE antigens and tested the IgG, IgA and IgM responses in 422 sera samples retrieved from acute typhoid patients, other febrile, food handlers, and healthy individuals. The results showed that HlyE-IgG, -IgA and -IgM ELISAs have a collective sensitivity of 83% while YncE-IgG and -IgA ELISAs identified 16 possible carriers based on their antibody profiles. The identification of sensitive biomarkers for typhoid carrier detection is crucial for disease eradication.

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.

To compare the cardiovascular, renal and safety outcomes of second-line glucose-lowering agents used in the management of people with type 2 diabetes.MEDLINE, EMBASE and CENTRAL were searched from inception to 13 July 2021 for randomised controlled trials comparing second-line glucose lowering therapies with placebo, standard care or one another. Primary outcomes included cardiovascular and renal outcomes. Secondary outcomes were non-cardiovascular adverse events. Risk ratios (RRs) and corresponding confidence intervals (CI) or credible intervals (CrI) were reported within pairwise and network meta-analysis. The quality of evidence was evaluated using the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) criteria. Number needed to treat (NNT) and number needed (NNH) to harm were calculated at 5 years using incidence rates and RRs. PROSPERO (CRD42020168322).We included 38 trials from seven classes of glucose-lowering therapies. Both sodium-glucose co-transporter-2 inhibitors (SGLT2i) and glucagon-like peptide 1 receptor agonists (GLP1RA) showed moderate to high certainty in reducing risk of 3-point major adverse cardiovascular events, 3P-MACE (network estimates: SGLT2i [RR 0.90; 95% CrI 0.84-0.96; NNT, 59], GLP1RA [RR 0.88; 95% CrI 0.83-0.93; NNT, 50]), cardiovascular death, all-cause mortality, renal composite outcome and macroalbuminuria. SGLT2i also showed high certainty in reducing risk of hospitalization for heart failure (hHF), ESRD, acute kidney injury, doubling in serum creatinine and decline in eGFR. GLP1RA were associated with lower risk of stroke (high certainty) while glitazone use was associated with an increased risk of hHF (very low certainty). The risk of developing ESRD was lower with the use of sulphonylureas (low certainty). For adverse events, sulphonylureas and insulin were associated with increased hypoglycaemic events (very low to low certainty), while GLP1RA increased the risk of gastrointestinal side effects leading to treatment discontinuation (low certainty). DPP-4i increased risk of acute pancreatitis (low certainty). SGLT2i were associated with increased risk of genital infection, volume depletion (high certainty), amputation and ketoacidosis (moderate certainty). Risk of fracture was increased with the use of glitazones (moderate certainty).SGLT2i and GLP1RA were associated with lower risk for different cardiorenal end points, when used as an adjunct to metformin in people with type 2 diabetes. Additionally, SGLT2i demonstrated benefits in reducing risk for surrogate end points in kidney disease progression. Safety outcomes differ among the available pharmacotherapies.

The prevalence of pre-diabetes is increasing globally, affecting an estimated 552 million people by 2030. While lifestyle interventions are the first line of defense against progression toward diabetes, information on barriers toward pre-diabetes management and how to overcome these barriers are scarce. This systematic review describes the publics’ and healthcare professionals’ knowledge, attitude and practice (KAP) toward pre-diabetes and determines the barriers toward pre-diabetes management. A systematic search for studies examining KAP towards pre-diabetes was conducted in six databases from inception to September 2022. Studies that quantitatively assessed at least two KAP elements using questionnaires were included. The quality of studies was assessed using the NIH Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. Barriers and enablers were identified and mapped onto the Capability, Motivation, and Behaviour model to identify factors that influence behavior change. Twenty-one articles that surveyed 8876 participants were included in this review. Most of the reviews (n=13) were directed to healthcare professionals. Overall, positive attitudes toward diabetes prevention efforts were observed, although there were still knowledge deficits and poor behavior toward pre-diabetes management. Barriers and enablers were detected at patients (eg, goals and intention), healthcare professionals (eg, clinical judgement) and system (eg, access and resources) levels. The use of different survey instruments to assess KAP prevented a head-to-head comparison between studies. Most studies conducted among patients were from middle-income countries, while among healthcare professionals (HCPs) were from high-income countries, which may produce some biasness. Nevertheless, the development of pre-diabetes intervention should focus on: (1) increasing knowledge on pre-diabetes and its management; (2) imparting practical skills to manage pre-diabetes; (3) providing resources for lifestyle management; (4) improving the accessibility of lifestyle management programs; and (5) other HCPs and human support to pre-diabetes management.

The rise of antimicrobial resistance (AMR) among clinically important bacteria, including respiratory pathogens, is a growing concern for public health worldwide. Common causative bacteria for upper respiratory tract infections (URTIs) include Streptococcus pneumoniae and Haemophilus influenzae, and sometimes Staphylococcus aureus. We assessed the β-lactam resistant trends and mechanisms of 150 URTI strains isolated in a tertiary care hospital in Kuala Lumpur Malaysia. High rates of non-susceptibility to penicillin G (38%), amoxicillin-clavulanate (48%), imipenem (60%), and meropenem (56%) were observed in S. pneumoniae. Frequent mutations at STMK and SRNVP motifs in PBP1a (41%), SSNT motif in PBP2b (32%), and STMK and LKSG motifs in PBP2x (41%) were observed in S. pneumoniae. H. influenzae remained highly susceptible to most β-lactams, except for ampicillin. Approximately half of the ampicillin non-susceptible H. influenzae harboured PBP3 mutations (56%) and only blaTEM was detected in the ampicillin-resistant strains (47%). Methicillin-susceptible S. aureus (MSSA) strains were mostly resistant to penicillin G (92%), with at least two-fold higher median minimum inhibitory concentrations (MIC) for all penicillin antibiotics (except ticarcillin) compared to S. pneumoniae and H. influenzae. Almost all URTI strains (88–100%) were susceptible to cefcapene and flomoxef. Overall, β-lactam antibiotics except penicillins remained largely effective against URTI pathogens in this region.

Inappropriate use of antibiotics has been shown to contribute to the occurrence of multidrug-resistant organisms (MROs). A surveillance study was performed in the largest tertiary care hospital in Kuala Lumpur, Malaysia, from 2018 to 2020 to observe the trends of broad-spectrum antibiotics (beta-lactam/beta-lactamases inhibitors (BL/BLI), extended-spectrum cephalosporins (ESC), and fluoroquinolones (FQ)) and antibiotics against MRO (carbapenems, polymyxins, and glycopeptides) usage and the correlation between antibiotic consumption and MROs. The correlation between 3-year trends of antibiotic consumption (defined daily dose (DDD)/100 admissions) with MRO infection cases (per 100 admissions) was determined using a Jonckheere-Terpstra test and a Pearson’s Correlation coefficient. The antimicrobial resistance trend demonstrated a positive correlation between ESC and FQ towards the development of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Klebsiella spp, ESBL-producing Escherichia coli (E. coli), and MRO Acinetobacter baumannii (A. baumannii). Increasing carbapenem consumption was positively correlated with the occurrence of ESBL-producing Klebsiella spp and E. coli. Polymyxin use was positively correlated with ESBL-producing Klebsiella spp, MRO A. baumannii, and carbapenem-resistant Enterobacteriaceae. The findings reinforced concerns regarding the association between MRO development, especially with a surge in ESC and FQ consumption. Stricter use of antimicrobials is thus crucial to minimise the risk of emerging resistant organisms.

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.

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.

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 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.

Carbapenem resistantA total of 168 CRE strains isolated from a tertiary teaching hospital from 2014-2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistantThe predominant CRE species isolated was

BACKGROUND Prediabetes, where an individual’s glycaemic variables are significantly higher than normal but lower than the threshold for diabetes, is a major health problem. People with prediabetes experience a higher risk of developing chronic kidney disease, neuropathy, diabetic retinopathy, cardiac events, and stroke. The implementation of lifestyle-changing interventions or programs designed to monitor and adjust a prediabetic person’s lifestyle, daily activities, and diet has been demonstrated to substantially reduce the risk of developing diabetes.[4] Implementing these interventions, however, is not without its challenges. One way to overcome these challenges would be the use of distal technologies such as telehealth, mobile health, game‐based support, social platforms, patient portals, as well as wearable devices. To the best of our knowledge, no reviews have attempted to summarise the published research related to the use of distal technologies for the prevention of diabetes. OBJECTIVE The aim of this systematic review is to critically appraise studies where distal technologies have been applied in a prediabetic population. The systematic review also aimed to synthesize the evidence to determine the effectiveness of lifestyle interventions utilizing distal technologies in people with prediabetes. METHODS The systematic review was conducted on articles from database inception till 31st December 2020 within the PubMed/MEDLINE, EMBASE, SCOPUS, and The Cochrane Library databases. The databases were searched for published articles describing the use of distal technologies in prediabetes. The search terms related to digital health and prediabetes were used. The reference lists of included articles were also reviewed to identify any relevant articles that may have been missed. This study was registered with PROSPERO: CRD42020188051. Articles which met the following inclusion criteria were included: 1) the study included prediabetic individuals, 2) was a randomised controlled trial, 3) the intervention included the use of any distal technology, and 4) published in peer-reviewed journals. RESULTS The initial search identified a total of 364 articles. After the removal of duplicates and ineligible articles, 29 articles were selected for inclusion in this review. Meta-analysis of 15 of the studies showed that distal technologies was effective in reducing participants’ body weight by 1.24 kg [95% CI: -1.92, -0.56], their BMIs (MD: -0.64; -0.93 to -0.35) and waist circumference (MD: -1.27; -2.22 to -0.32), when compared to usual care/control. HbA1c levels were lowered marginally by 0.05% (95% CI: -0.09% to -0.02%) in the intervention group compared to the control group. However, distal technologies had limited impact on FPG (-0.11 mmol/l; -0.25 to 0.02), total cholesterol (-0.06 mmol/l; 95% CI: -0.14 to 0.03), low density lipoprotein (-0.04; -0.09 to 0.02), high density lipoprotein (0.03; -0.01 to 0.07) and triglyceride levels (-0.05; -0.13 to 0.02) compared to control group. CONCLUSIONS The evidence reviewed suggests that lifestyle interventions incorporating distal technologies can be effective in helping prediabetics reduce their body weight, body mass index, waist circumference, and blood glucose. The effectiveness of these interventions in improving lipid profile, blood pressure, and quality of life remains unclear. While the results are encouraging, more work is required to improve the evaluation and implementation of these complex interventions.

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.

Phytase enzyme is supplemented to poultry feed to improve phosphorus (P) availability. Mitsuokella jalaludinii, bacteria isolated from the rumen of cattle, has been reported as a cheaper alternative source of phytase. As much nutrients are trapped within the phytate complex, we hypothesized that the supplementation of M. jalaludinii phytase to poultry feed would enhance nutrient utilization by poultry. In the current study, the efficacy of freeze-dried M. jalaludinii cells (Mj) as feed supplement for broilers fed low-available phosphorus (low-aP) diet was evaluated. Day-old male Cobb raised in battery cages were assigned to three treatment groups [normal-available phosphorus diet with heat-deactivated Mj (DMj); low-aP diet with DMj; and low-aP diet with Mj], each consisting of four replicates (10 birds per replicate) for a 3-weeks feeding period. Feed intake was recorded daily from day 1-21, whereas broilers were weighted at day 1, 7, 14, and 21. Total excreta were collected at day 11-13 and 18-20. At day 21, twelve broilers from each treatment group were slaughtered to collect plasma and tibia. The results showed that Mj significantly enhanced broilers’ live weight and feed conversion ratio compared to the control groups (p

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.

Objective Gut microbiome alterations in Parkinson disease (PD) have been reported repeatedly, but their functional relevance remains unclear. Fecal metabolomics, which provide a functional readout of microbial activity, have scarcely been investigated. We investigated fecal microbiome and metabolome alterations in PD, and their clinical relevance. Methods Two hundred subjects (104 patients, 96 controls) underwent extensive clinical phenotyping. Stool samples were analyzed using 16S rRNA gene sequencing. Fecal metabolomics were performed using two platforms, nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry. Results Fecal microbiome and metabolome composition in PD was significantly different from controls, with the largest effect size seen in NMR-based metabolome. Microbiome and NMR-based metabolome compositional differences remained significant after comprehensive confounder analyses. Differentially abundant fecal metabolite features and predicted functional changes in PD versus controls included bioactive molecules with putative neuroprotective effects (eg, short chain fatty acids [SCFAs], ubiquinones, and salicylate) and other compounds increasingly implicated in neurodegeneration (eg, ceramides, sphingosine, and trimethylamine N-oxide). In the PD group, cognitive impairment, low body mass index (BMI), frailty, constipation, and low physical activity were associated with fecal metabolome compositional differences. Notably, low SCFAs in PD were significantly associated with poorer cognition and low BMI. Lower butyrate levels correlated with worse postural instability-gait disorder scores. Interpretation Gut microbial function is altered in PD, characterized by differentially abundant metabolic features that provide important biological insights into gut-brain pathophysiology. Their clinical relevance further supports a role for microbial metabolites as potential targets for the development of new biomarkers and therapies in PD. ANN NEUROL 2021;89:546-559.

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.

Objective:To determine whether probiotics are effective for constipation, a common and often difficult-to-treat problem, in Parkinson’s disease (PD).Methods:In this double-blind, randomized placebo-controlled single-centre trial, 280 PD patients were screened and 72 eligible patients were block-randomized (1:1) to receive either multi-strain probiotics capsules (n=34), or identical-appearing placebo (n=38), for four weeks. The primary endpoint was the change in the average number of spontaneous bowel movements (SBM) per week during the last two weeks of intervention, compared with the two-week pre-intervention phase, recorded by daily stool diary. Secondary outcome measures included changes in stool consistency, constipation severity score, and quality of life related to constipation. Satisfaction with intervention received was assessed. Change in levels of fecal calprotectin, a marker of intestinal inflammation, was an exploratory outcome.Results:SBM increased by 1.0±1.2/week after treatment with probiotics, and decreased by 0.3±1.0/week in the placebo group (mean difference 1.3, 95%CI: 0.8-1.8, PConclusions:Multi-strain probiotics treatment was effective for constipation in PD. Further studies are needed to investigate the long-term efficacy and safety of probiotics in PD, as well as their mechanisms of action.Classification of evidence:This study provides Class I evidence that for people with PD, multi-strain probiotics significantly increased the average number of spontaneous bowel movements per week.Clinicaltrials.gov identifier:NCT03377322

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.