1
|
Hanafiah A, Sukri A, Yusoff H, Chan CS, Hazrin-Chong NH, Salleh SA, Neoh HM. Insights into the Microbiome and Antibiotic Resistance Genes from Hospital Environmental Surfaces: A Prime Source of Antimicrobial Resistance. Antibiotics (Basel) 2024; 13:127. [PMID: 38391513 PMCID: PMC10885873 DOI: 10.3390/antibiotics13020127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/20/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
Hospital environmental surfaces are potential reservoirs for transmitting hospital-associated pathogens. This study aimed to profile microbiomes and antibiotic resistance genes (ARGs) from hospital environmental surfaces using 16S rRNA amplicon and metagenomic sequencing at a tertiary teaching hospital in Malaysia. Samples were collected from patient sinks and healthcare staff counters at surgery and orthopaedic wards. The samples' DNA were subjected to 16S rRNA amplicon and shotgun sequencing to identify bacterial taxonomic profiles, antibiotic resistance genes, and virulence factor pathways. The bacterial richness was more diverse in the samples collected from patient sinks than those collected from staff counters. Proteobacteria and Verrucomicrobia dominated at the phylum level, while Bacillus, Staphylococcus, Pseudomonas, and Acinetobacter dominated at the genus level. Staphylococcus epidermidis and Staphylococcus aureus were prevalent on sinks while Bacillus cereus dominated the counter samples. The highest counts of ARGs to beta-lactam were detected, followed by ARGs against fosfomycin and cephalosporin. We report the detection of mcr-10.1 that confers resistance to colistin at a hospital setting in Malaysia. The virulence gene pathways that aid in antibiotic resistance gene transfer between bacteria were identified. Environmental surfaces serve as potential reservoirs for nosocomial infections and require mitigation strategies to control the spread of antibiotic resistance bacteria.
Collapse
Affiliation(s)
- Alfizah Hanafiah
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia
| | - Asif Sukri
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Hamidah Yusoff
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia
| | | | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Sharifah Azura Salleh
- Infection Control Unit, Hospital Canselor Tuanku Muhriz, Cheras, Kuala Lumpur 56000, Malaysia
| | - Hui-Min Neoh
- UKM Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur 56000, Malaysia
| |
Collapse
|
2
|
Roslan MAM, Omar MN, Sharif NAM, Raston NHA, Arzmi MH, Neoh HM, Ramzi AB. Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment. NPJ Biofilms Microbiomes 2023; 9:95. [PMID: 38065982 PMCID: PMC10709320 DOI: 10.1038/s41522-023-00463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The human microbiome has emerged as a key player in maintaining skin health, and dysbiosis has been linked to various skin disorders. Amidst growing concerns regarding the side effects of antibiotic treatments, the potential of live biotherapeutic products (LBPs) in restoring a healthy microbiome has garnered significant attention. This review aims to evaluate the current state of the art of the genetically or metabolically engineered LBPs, termed single-cell engineered LBPs (eLBPs), for skin repair and disease treatment. While some studies demonstrate promising outcomes, the translation of eLBPs into clinical applications remains a significant hurdle. Substantial concerns arise regarding the practical implementation and scalability of eLBPs, despite the evident potential they hold in targeting specific cells and delivering therapeutic agents. This review underscores the need for further research, robust clinical trials, and the exploration of current advances in eLBP-based bioengineered bacterial chassis and new outlooks to substantiate the viability and effectiveness of eLBPs as a transformative approach in skin repair and disease intervention.
Collapse
Affiliation(s)
| | - Mohd Norfikri Omar
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Nur Azlina Mohd Sharif
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Nurul Hanun Ahmad Raston
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Mohd Hafiz Arzmi
- Department of Fundamental Dental & Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, 25200, Kuantan, Pahang, Malaysia
- Melbourne Dental School, The University of Melbourne, 3053, Melbourne, Victoria, Australia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| |
Collapse
|
3
|
Salawudeen A, Raji YE, Jibo GG, Desa MNM, Neoh HM, Masri SN, Di Gregorio S, Jamaluddin TZMT. Epidemiology of multidrug-resistant Klebsiella pneumoniae infection in clinical setting in South-Eastern Asia: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2023; 12:142. [PMID: 38062531 PMCID: PMC10704709 DOI: 10.1186/s13756-023-01346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
The rising prevalence of multidrug-resistant (MDR) and extended-spectrum beta lactamase-resistant (ESBL) Klebsiella pneumoniae (K. pneumoniae) is an important global public health challenge. This threat is even more pertinent in clinical settings. Morbidity and mortality associated with this condition are alarming particularly in the developing regions of the world. A comprehensive evaluation of the epidemiology of this phenomenon will assist towards the global effort of reducing its burden. So, this systematic review and meta-analysis was conducted to evaluate the epidemiology of MDR K. pneumoniae in South-Eastern Asia (SEA). The study was done under the PRISMA guidelines and was preceded by the development of a priori protocol. The protocol was then registered in PROSPERO-the public registry for systematic reviews. Seven important outcomes which include the assessment of the overall MDR K. pneumoniae prevalence were designed to be evaluated. A literature search was carried out in five selected electronic databases and 4389 were screened. Of these articles, 21 studies that met the eligibility criteria were included in the review. Relevant data were extracted from the included studies. By conducting a quality effect meta-analysis, the pooled prevalence for MDR and ESBL K. pneumoniae in SEA was estimated at 55% (CI 9-96) and 27% (CI 32-100) respectively. The review also identified ESBL genes types of allodemic situations occurring mostly in respiratory tract infections. The high prevalence of MDR and ESBL K. pneumoniae in this subregion is highly significant and of both public health and clinical relevance. Overall, the findings of this review will assist in the effective prevention and control of this threat in SEA.
Collapse
Affiliation(s)
- Adamu Salawudeen
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Microbiology, Faculty of Science, Gombe State University, Tudun Wada, Gombe, 760214, Gombe State, Nigeria
| | - Yakubu Egigogo Raji
- Department of Pathology, Clinical Microbiology Unit, College of Health Sciences, Ibrahim Badamasi Babangida University Lapai, Lapai, 911101, Nigeria
| | - Garba Gidandawa Jibo
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Microbiology, Faculty of Life Sciences, Kebbi State University of Science and Technology, Aliero, 863104, Nigeria
| | - Mohd Nasir Mohd Desa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Jalan Ya'acob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - Siti Norbaya Masri
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Medical Microbiology, Hospital Sultan Abdul Aziz Shah, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Sabrina Di Gregorio
- Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Postal Code 1113, Buenos Aires, Argentina
- CONICET, National Scientific and Technical Research Council - Argentina, Postal Code 1425, Buenos Aires, Argentina
| | - Tengku Zetty Maztura Tengku Jamaluddin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia.
- Infection Control Unit, Department of Medical Microbiology, Hospital Sultan Abdul Aziz Shah, Universiti Putra Malaysia, 43400, Serdang, Malaysia.
| |
Collapse
|
4
|
Navarathinam SD, Neoh HM, Tan TL, Wahab AA, Mohd Nizam Tzar MN, Ding CH. Antifungal susceptibility profile and biofilm-producing capability of Candida tropicalis isolates in a tertiary medical centre. Malays J Pathol 2023; 45:417-424. [PMID: 38155383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
BACKGROUND Candida tropicalis is a globally distributed yeast that has been popping up in the medical literature lately, albeit for unenviable reasons. C. tropicalis is associated with substantial morbidity, mortality as well as drug resistance. The aims of this study were to ascertain the antifungal susceptibility profile and the biofilm-producing capability of this notorious yeast in our centre. METHODS C. tropicalis isolates from sterile specimens were collected over a 12-month period. Conclusive identification was achieved biochemically with the ID 32 C kit. Susceptibility to nine antifungal agents was carried out using the colourimetric broth microdilution kit Sensititre YeastOne YO10. Biofilm-producing capability was evaluated by quantifying biomass formation spectrophotometrically following staining with crystal violet. RESULTS Twenty-four non-repetitive isolates of C. tropicalis were collected. The resistance rates to the triazole agents were 29.2% for fluconazole, 16.7% for itraconazole, 20.8% for voriconazole and 8.3% for posaconazole-the pan-azole resistance rate was identical to that of posaconazole. No resistance was recorded for amphotericin B, flucysosine or any of the echinocandins tested. A total of 16/24 (66.7%) isolates were categorized as high biomass producers and 8/24 (33.3%) were moderate biomass producers. None of our isolates were low biomass producers. CONCLUSION The C. tropicalis isolates from our centre were resistant only to triazole agents, with the highest resistance rate being recorded for fluconazole and the lowest for posaconazole. While this is not by itself alarming, the fact that our isolates were prolific biofilm producers means that even azole-susceptible isolates can be paradoxically refractory to antifungal therapy.
Collapse
Affiliation(s)
- S D Navarathinam
- Universiti Kebangsaan Malaysia, Faculty of Medicine, Department of Medical Microbiology and Immunology, Kuala Lumpur, Malaysia
| | - H M Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - T L Tan
- Universiti Kebangsaan Malaysia, Faculty of Medicine, Department of Emergency Medicine, Kuala Lumpur, Malaysia
| | - A A Wahab
- Universiti Kebangsaan Malaysia, Faculty of Medicine, Department of Medical Microbiology and Immunology, Kuala Lumpur, Malaysia
| | - M N Mohd Nizam Tzar
- Universiti Kebangsaan Malaysia, Faculty of Medicine, Department of Medical Microbiology and Immunology, Kuala Lumpur, Malaysia
| | - C H Ding
- Universiti Kebangsaan Malaysia, Faculty of Medicine, Department of Medical Microbiology and Immunology, Kuala Lumpur, Malaysia.
| |
Collapse
|
5
|
Hatta MNA, Mohamad Hanif EA, Chin SF, Low TY, Neoh HM. Parvimonas micra Infection Enhances Proliferation, Wound Healing, and Inflammation of a Colorectal Cancer Cell Line. Biosci Rep 2023:233081. [PMID: 37218575 DOI: 10.1042/bsr20230609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023] Open
Abstract
The gut microbiota Parvimonas micra has been found to be enriched in gut mucosal tissues and fecal samples of colorectal cancer (CRC) patients compared to non-CRC controls. In this study, we investigated the tumorigenic potential of P. micra and its regulatory pathways in CRC using HT-29, a low-grade CRC intestinal epithelial cell. For every P. micra-HT-29 interaction assay, HT-29 was co-cultured anaerobically with P. micra at an MOI of 100:1 (bacteria: cells) for 2 hr. We found that P. micra increased HT-29 cell proliferation by 38.45% (P=0.008), with the highest wound healing rate at 24 hr post-infection (P=0.02). In addition, inflammatory marker expression (IL-5, IL-8, CCL20, CSF2) was also significantlyinduced. Shotgun proteomics profiling analysis revealed that P. micra affects the protein expression of HT-29 (157 up-regulated; 214 down-regulated proteins). Upregulation of PSMB4 protein and its neighbouring subunits revealed association of the ubiquitin-proteasome pathway in CRC carcinogenesis; whereas downregulation of CUL1, YWHAH, and MCM3 signified cell cycle dysregulation. Moreover, 22 clinically relevant epithelial-mesenchymal transition (EMT)-markers were expressed in HT-29 infected with P. micra. Overall, this study elucidated exacerbated oncogenic properties of P. micra in HT-29 via aberrant cell proliferation, enhanced wound healing, inflammation, upregulation of ubiquitin-proteasome pathway (UPPs) and activation of EMT pathways.
Collapse
Affiliation(s)
| | | | - Siok-Fong Chin
- Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| |
Collapse
|
6
|
Azami NAM, Moi ML, Salleh SA, Neoh HM, Kamaruddin MA, Jalal NA, Ismail N, Takasaki T, Kurane I, Jamal R. Dengue epidemic in Malaysia: urban versus rural comparison of dengue immunoglobulin G seroprevalence among Malaysian adults aged 35-74 years. Trans R Soc Trop Med Hyg 2021; 114:798-811. [PMID: 32735681 DOI: 10.1093/trstmh/traa056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND A periodic serosurvey of dengue seroprevalence is vital to determine the prevalence of dengue in countries where this disease is endemic. This study aimed to determine the prevalence of dengue immunoglobulin G (IgG) seropositivity among healthy Malaysian adults living in urban and rural areas. METHODS A total of 2598 serum samples (1417 urban samples, 1181 rural samples) were randomly collected from adults ages 35-74 y. The presence of the dengue IgG antibody and neutralising antibodies to dengue virus (DENV) 1-4 was determined using enzyme-linked immunosorbent assay and the plaque reduction neutralisation test assay, respectively. RESULTS The prevalence of dengue IgG seropositivity was 85.39% in urban areas and 83.48% in rural areas. The seropositivity increased with every 10-y increase in age. Ethnicity was associated with dengue seropositivity in urban areas but not in rural areas. The factors associated with dengue seropositivity were sex and working outdoors. In dengue IgG-positive serum samples, 98.39% of the samples had neutralising antibodies against DENV3, but only 70.97% of them had neutralising antibodies against DENV4. CONCLUSION The high seroprevalence of dengue found in urban and rural areas suggests that both urban and rural communities are vital for establishing and sustaining DENV transmission in Malaysia.
Collapse
Affiliation(s)
- Nor Azila Muhammad Azami
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| | - Meng Ling Moi
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Sharifah Azura Salleh
- Department of Medical Microbiology and Immunology, University Kebangsaan Malaysia Medical Centre, Kuala Lumpur, 56000, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| | - Mohd Arman Kamaruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| | - Nazihah Abdul Jalal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| | - Norliza Ismail
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, Kanagawa, 253-0087, Japan
| | - Ichiro Kurane
- National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, 56000, Malaysia
| |
Collapse
|
7
|
Sugurmar ANK, Mohd R, Shah SA, Neoh HM, Cader RA. Gut microbiota in Immunoglobulin A Nephropathy: a Malaysian Perspective. BMC Nephrol 2021; 22:145. [PMID: 33882859 PMCID: PMC8060124 DOI: 10.1186/s12882-021-02315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 03/11/2021] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The alteration of the gut microbiome in the gut-kidney axis has been associated with a pro-inflammatory state and chronic kidney disease (CKD). A small-scaled Italian study has shown an association between the gut microbiome and Immunoglobulin A Nephropathy (IgAN). However, there is no data on gut microbiota in IgAN in the Asian population. This study compares the gut microbial abundance and diversity between healthy volunteers and Malaysian IgAN cohort. METHODS A comparative cross-sectional study was conducted involving biopsy-proven IgAN patients in clinical remission with matched controls in a Malaysian tertiary centre. Demographic data, routine blood and urine results were recorded. Stool samples were collected and their DNA was extracted by 16S rRNA gene sequencing to profile their gut microbiota. RESULTS Thirty-six IgAN patients (13 male; 23 female) with the mean age of 45.5 ± 13.4 years and median estimated glomerular filtration rate (eGFR) of 79.0 (62.1-92.2) mls/min/1.73m2 with median remission of 7 years were analysed and compared with 12 healthy controls (4 male; 8 female) with the mean age of 46.5 ± 13.5 years and eGFR of 86.5 (74.2-93.7) mls/min/1.73m2. Other demographic and laboratory parameters such as gender, ethnicity, body mass index (BMI), haemoglobin, serum urea and serum albumin were comparable between the two groups. There were no significant differences seen in the Operational Taxonomic Unit (OTU) and alpha diversity (Shannon index) between IgAN and healthy controls. Alpha diversity increased with increasing CKD stage (p = 0.025). Firmicutes/Bacteroidetes (F/B) ratio was low in both IgAN and healthy cohort. Fusobacteria phylum was significantly increased (p = 0.005) whereas Euryarchaoeota phylum was reduced (p = 0.016) in the IgAN group as compared to the control cohort. CONCLUSION Although we found no differences in OTU and alpha diversity between IgAN in remission and control cohort, there were some differences between the two groups at phylum level.
Collapse
Affiliation(s)
- Agni Nhirmal Kumar Sugurmar
- Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia.
| | - Rozita Mohd
- Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - Shamsul Azhar Shah
- Department of Community Health, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Molecular Biology Institute, Kuala Lumpur, Malaysia
| | - Rizna Abdul Cader
- Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia.,ParkCity Medical Centre, No.2, Jalan Intisari Perdana, Desa ParkCity, Kuala Lumpur, 52200, Malaysia
| |
Collapse
|
8
|
Sapri HF, Ismail MAH, Sani NAM, Noordin A, Tan TL, Hussin S, Neoh HM. Molecular surveillance of methicillin-susceptible Staphylococcus aureus (MSSA) isolated over a one-year period from a Malaysian Teaching Hospital. Germs 2020; 10:104-111. [PMID: 32656107 DOI: 10.18683/germs.2020.1191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/19/2020] [Accepted: 05/31/2020] [Indexed: 11/08/2022]
Abstract
Introduction We report the results of a molecular surveillance study carried out on methicillin-susceptible Staphylococcus aureus (MSSA) isolated in a one-year duration from Hospital Canselor Tuanku Muhriz (HCTM), a tertiary hospital located in Kuala Lumpur, Malaysia. Methods The first strain isolated from each MSSA infection in HCTM during the year 2009 was included into the study. Antimicrobial susceptibility testing and agr group typing were carried out for all strains; virulence gene (cna, seh, TSST-1 and PVL) typing results of the strains were obtained from a previous study. Pulsed-field gel electrophoresis (PFGE) was done on selected strains from the orthopedic ward. Relationship(s) between different typing methods used in the study was investigated, where a p value of <0.05 indicated significant association between typing methods. Results A total of 880 MSSA strains were included into the study. The strains were generally susceptible to most antibiotics, with most of them carrying cna and agr-I (51.6%, n=454; 39.8%, n=350, respectively). A total of 17 PFGE pulsotypes were identified using an 80% similarity cut-off value, where the main pulsotype (pulsotype E) consisted of 24 isolates (23.5%). agr-III strains were found to be usually positive for both cna and seh (p<0.05). In addition, some PFGE pulsotypes were also characteristic of certain virulence genes or agr groups. Conclusions We did not identify a dominant MSSA clone circulating in HCTM in 2009. Nevertheless, results from this molecular surveillance will provide good baseline data for the hospital's second S. aureus surveillance planned for the year 2020.
Collapse
Affiliation(s)
- Hassriana Fazilla Sapri
- PhD, Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Mohd Azrul Hisham Ismail
- MSc, UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Nurul Azirah Mohamad Sani
- PhD, Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Ainihayati Noordin
- MSc, Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Toh Leong Tan
- MD, DrEmMed, Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Salasawati Hussin
- MD, MPath; Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Medical Science Division, Faculty of Medicine, University of Cyberjaya, Cyberjaya, 63000, Selangor, Malaysia
| | - Hui-Min Neoh
- PhD, UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras, 56000 Kuala Lumpur, Malaysia
| |
Collapse
|
9
|
Neoh HM, Tan XE, Sapri HF, Tan TL. Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives. Infect Genet Evol 2019; 74:103935. [PMID: 31233781 DOI: 10.1016/j.meegid.2019.103935] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/01/2022]
Abstract
Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.
Collapse
Affiliation(s)
- Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.
| | - Xin-Ee Tan
- Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Hassriana Fazilla Sapri
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
| | - Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
| |
Collapse
|
10
|
Kaku Y, Park ES, Noguchi A, Inoue S, Lunt R, Malbas FF, Demetria C, Neoh HM, Jamal R, Morikawa S. Establishment of an immunofluorescence assay to detect IgM antibodies to Nipah virus using HeLa cells expressing recombinant nucleoprotein. J Virol Methods 2019; 269:83-87. [PMID: 30954461 DOI: 10.1016/j.jviromet.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/05/2019] [Accepted: 03/17/2019] [Indexed: 11/17/2022]
Abstract
A novel indirect fluorescent antibody test (IFAT) for detection of IgM against Nipah virus (NiV) was developed using HeLa 229 cells expressing recombinant NiV nucleocapsid protein (NiV-N). The NiV IFAT was evaluated using three panels of sera: a) experimentally produced sera from NiV-N-immunized/pre-immunized macaques, b) post-infection human sera associated with a Nipah disease outbreak in the Philippines in 2014, and c) human sera from a non-exposed Malaysian population. Immunized macaque sera showed a characteristic granular staining pattern of the NiV-N expressed antigen in HeLa 229 cells, which was readily distinguished from negative-binding results of the pre-immunized macaque sera. The IgM antibody titers in sequential serum samples (n = 7) obtained from three Nipah patients correlated well with previously published results using conventional IgM capture ELISA and SNT serology. The 90 human serum samples from unexposed persons were unreactive by IFAT. The IFAT utilizing NiV-N-expressing HeLa 229 cells to detect IgM antibody in an early stage of NiV infection is an effective approach, which could be utilized readily in local laboratories to complement other capabilities in NiV-affected countries.
Collapse
Affiliation(s)
- Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan.
| | - Eun-Sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Akira Noguchi
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Satoshi Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Ross Lunt
- Australian Animal Health Laboratory, 5 Portarlington Road, East Geelong, Vic, 3220, Australia
| | - Fedelino F Malbas
- Research Institute for Tropical Medicine, 9002 Research Dr, Alabang, Muntinlupa, 1781, Metro Manila, Philippines
| | - Catalino Demetria
- Research Institute for Tropical Medicine, 9002 Research Dr, Alabang, Muntinlupa, 1781, Metro Manila, Philippines
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Pusat Perubatan UKM, Jalan Yaacob Latiff, Bandar Tun Razak, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Pusat Perubatan UKM, Jalan Yaacob Latiff, Bandar Tun Razak, Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640, Japan
| |
Collapse
|
11
|
Tee LF, Tan TL, Neoh HM, Jamal R. Rapid Detection of Sepsis using CESDA: the Caenorhabditis elegans Sepsis Detection Assay. Rev Soc Bras Med Trop 2019; 52:e20180300. [PMID: 30892548 DOI: 10.1590/0037-8682-0300-2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/31/2018] [Indexed: 03/14/2023] Open
Abstract
INTRODUCTION The nematode Caenorhabditis elegans was used as a biological sensor to detect the urine of sepsis patients (CESDA assay). METHODS C. elegans was aliquoted onto the center of assay plates and allowed to migrate towards sepsis (T) or control (C) urine samples spotted on the same plate. The number of worms found in either (T) or (C) was scored at 10-minute intervals over a 60-minute period. RESULTS The worms were able to identify the urine (<48 hours) of sepsis patients rapidly within 20 minutes (AUROC=0.67, p=0.012) and infection within 40 minutes (AUROC=0.80, p=0.016). CONCLUSIONS CESDA could be further explored for sepsis diagnosis.
Collapse
Affiliation(s)
- Ling Fei Tee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| |
Collapse
|
12
|
Megat Mohd Azlan PIH, Chin SF, Low TY, Neoh HM, Jamal R. Analyzing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer. Proteomics 2019; 19:e1800176. [PMID: 30557447 DOI: 10.1002/pmic.201800176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 12/02/2018] [Indexed: 12/20/2022]
Abstract
Dysbiosis of gut microbiome can contribute to inflammation, and subsequently initiation and progression of colorectal cancer (CRC). Throughout these stages, various proteins and metabolites are secreted to the external environment by microorganisms or the hosts themselves. Studying these proteins may help enhance our understanding of the host-microorganism relationship or they may even serve as useful biomarkers for CRC. However, secretomic studies of gut microbiome of CRC patients, until now, are scarcely performed. In this review article, the focus is on the roles of gut microbiome in CRC, the current findings on CRC secretome are highlighted, and the emerging challenges and strategies to drive forward this area of research are addressed.
Collapse
Affiliation(s)
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia
| |
Collapse
|
13
|
Tan TL, Tang YJ, Ching LJ, Abdullah N, Neoh HM. Comparison of Prognostic Accuracy of the quick Sepsis-Related Organ Failure Assessment between Short- & Long-term Mortality in Patients Presenting Outside of the Intensive Care Unit - A Systematic Review & Meta-analysis. Sci Rep 2018; 8:16698. [PMID: 30420768 PMCID: PMC6232181 DOI: 10.1038/s41598-018-35144-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/30/2018] [Indexed: 12/29/2022] Open
Abstract
The purpose of this meta-analysis was to compare the ability of the qSOFA in predicting short- (≤30 days or in-hospital mortality) and long-term (>30 days) mortality among patients outside the intensive care unit setting. Studies reporting on the qSOFA and mortality were searched using MEDLINE and SCOPUS. Studies were included if they involved patients presenting to the ED with suspected infection and usage of qSOFA score for mortality prognostication. Data on qSOFA scores and mortality rates were extracted from 36 studies. The overall pooled sensitivity and specificity for the qSOFA were 48% and 86% for short-term mortality and 32% and 92% for long-term mortality, respectively. Studies reporting on short-term mortality were heterogeneous (Odd ratio, OR = 5.6; 95% CI = 4.6-6.8; Higgins's I2 = 94%), while long-term mortality studies were homogenous (OR = 4.7; 95% CI = 3.5-6.1; Higgins's I2 = 0%). There was no publication bias for short-term mortality analysis. The qSOFA score showed poor sensitivity but moderate specificity for both short and long-term mortality, with similar performance in predicting both short- and long- term mortality. Geographical region was shown to have nominal significant (p = 0.05) influence on qSOFA short-term mortality prediction.
Collapse
Affiliation(s)
- Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
- Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Ying Jing Tang
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Ling Jing Ching
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Noraidatulakma Abdullah
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
- Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000, Cheras, Kuala Lumpur, Malaysia
| |
Collapse
|
14
|
Chin SF, Megat Mohd Azlan PIH, Mazlan L, Neoh HM. Identification of Schizosaccharomyces pombe in the guts of healthy individuals and patients with colorectal cancer: preliminary evidence from a gut microbiome secretome study. Gut Pathog 2018; 10:29. [PMID: 30008808 PMCID: PMC6040075 DOI: 10.1186/s13099-018-0258-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/03/2018] [Indexed: 12/01/2022] Open
Abstract
Over the years, genetic profiling of the gut microbiome of patients with colorectal cancer (CRC) using genome sequencing has suggested over-representation of several bacterial taxa. However, little is known about the protein or metabolite secretions from the microbiota that could lead to CRC pathology. Proteomic studies on the role of microbial secretome in CRC are relatively rare. Here, we report the identification of proteins from Schizosaccharomyces pombe found in the stool samples of both healthy individuals and patients with CRC. We found that distinctive sets of S. pombe proteins were present exclusively and in high intensities in each group. Our finding may trigger a new interest in the role of gut mycobiota in carcinogenesis.
Collapse
Affiliation(s)
- Siok-Fong Chin
- 1UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | | | - Luqman Mazlan
- 2Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- 1UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| |
Collapse
|
15
|
Osman MA, Neoh HM, Ab Mutalib NS, Chin SF, Jamal R. 16S rRNA Gene Sequencing for Deciphering the Colorectal Cancer Gut Microbiome: Current Protocols and Workflows. Front Microbiol 2018; 9:767. [PMID: 29755427 PMCID: PMC5934490 DOI: 10.3389/fmicb.2018.00767] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/04/2018] [Indexed: 12/15/2022] Open
Abstract
The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.
Collapse
Affiliation(s)
- Muhammad-Afiq Osman
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| |
Collapse
|
16
|
Tee LF, Neoh HM, Then SM, Murad NA, Asillam MF, Hashim MH, Nathan S, Jamal R. Effects of simulated microgravity on gene expression and biological phenotypes of a single generation Caenorhabditis elegans cultured on 2 different media. Life Sci Space Res (Amst) 2017; 15:11-17. [PMID: 29198309 DOI: 10.1016/j.lssr.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/15/2017] [Accepted: 06/22/2017] [Indexed: 06/07/2023]
Abstract
Studies of multigenerational Caenorhabditis elegans exposed to long-term spaceflight have revealed expression changes of genes involved in longevity, DNA repair, and locomotion. However, results from spaceflight experiments are difficult to reproduce as space missions are costly and opportunities are rather limited for researchers. In addition, multigenerational cultures of C. elegans used in previous studies contribute to mixture of gene expression profiles from both larvae and adult worms, which were recently reported to be different. Usage of different culture media during microgravity simulation experiments might also give rise to differences in the gene expression and biological phenotypes of the worms. In this study, we investigated the effects of simulated microgravity on the gene expression and biological phenotype profiles of a single generation of C. elegans worms cultured on 2 different culture media. A desktop Random Positioning Machine (RPM) was used to simulate microgravity on the worms for approximately 52 to 54 h. Gene expression profile was analysed using the Affymetrix GeneChip® C. elegans 1.0 ST Array. Only one gene (R01H2.2) was found to be downregulated in nematode growth medium (NGM)-cultured worms exposed to simulated microgravity. On the other hand, eight genes were differentially expressed for C. elegans Maintenance Medium (CeMM)-cultured worms in microgravity; six were upregulated, while two were downregulated. Five of the upregulated genes (C07E3.15, C34H3.21, C32D5.16, F35H8.9 and C34F11.17) encode non-coding RNAs. In terms of biological phenotype, we observed that microgravity-simulated worms experienced minimal changes in terms of lifespan, locomotion and reproductive capabilities in comparison with the ground controls. Taking it all together, simulated microgravity on a single generation of C. elegans did not confer major changes to their gene expression and biological phenotype. Nevertheless, exposure of the worms to microgravity lead to higher expression of non-coding RNA genes, which may play an epigenetic role in the worms during longer terms of microgravity exposure.
Collapse
Affiliation(s)
- Ling Fei Tee
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Malaysia.
| | - Sue Mian Then
- Department of Biomedical Sciences, The University of Nottingham, Malaysia
| | - Nor Azian Murad
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Malaysia
| | - Mohd Fairos Asillam
- National Space Agency, Ministry of Science, Technology & Innovation, Malaysia
| | - Mohd Helmy Hashim
- National Space Agency, Ministry of Science, Technology & Innovation, Malaysia
| | - Sheila Nathan
- Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Malaysia.
| |
Collapse
|
17
|
Abstract
The human gut is home to complex microbial populations that change dynamically in response to various internal and external stimuli. The gut microbiota provides numerous functional benefits that are crucial for human health but in the setting of a disturbed equilibrium, the microbial community can cause deleterious outcomes such as diseases and cancers. Characterization of the functional activities of human gut microbiota is fundamental to understand their roles in human health and disease. Metaproteomics, which refers to the study of the entire protein collection of the microbial community in a given sample is an emerging area of research that provides informative details concerning functional aspects of the microbiota. In this mini review, we present a summary of the progress of metaproteomic analysis for studying the functional role of gut microbiota. This is followed by an overview of the experimental approaches focusing on fecal specimen for metaproteomics and is concluded by a discussion on the challenges and future directions of metaproteomic research.
Collapse
Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia.
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Cheras, Kuala Lumpur, Malaysia
| |
Collapse
|
18
|
Neoh HM, Yieng CY, Raja Abd Rahman RMFB, Hussin S, Jamal R. Simplified protocol of gel-based multiple locus variable number of tandem repeats analysis (MLVA) for Staphylococcus aureus typing. Germs 2017. [PMID: 28626740 DOI: 10.18683/germs.2017.1114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hui-Min Neoh
- PhD, UKM Medical Molecular Biology Institute (UMBI), University Kebangsaan Malaysia, Pusat Perubatan UKM, Jalan Yaacob Latiff, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Choi-Ying Yieng
- BSc, Faculty of Biosciences and Medical Engineering, University Teknologi Malaysia, Skudai, 81310 Johor, Malaysia
| | - Raja Mohd Fadhil B Raja Abd Rahman
- Dip. Lab Tech, UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Pusat Perubatan UKM, Jalan Yaacob Latiff, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Salasawati Hussin
- MD, MPath, Department of Medical Microbiology & Immunology, Faculty of Medicine, University Kebangsaan Malaysia, Pusat Perubatan UKM, Jalan Yaacob Latiff, Cheras, 56000 Kuala Lumpur, Malaysia
| | - Rahman Jamal
- MD, PhD, UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Pusat Perubatan UKM, Jalan Yaacob Latiff, Cheras, 56000 Kuala Lumpur, Malaysia
| |
Collapse
|
19
|
Noordin A, Sapri HF, Mohamad Sani NA, Leong SK, Tan XE, Tan TL, Mohamad Zin N, Neoh HM, Hussin S. Antimicrobial resistance profiling and molecular typing of methicillin-resistant Staphylococcus aureus isolated from a Malaysian teaching hospital. J Med Microbiol 2016; 65:1476-1481. [PMID: 27902380 DOI: 10.1099/jmm.0.000387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The annual prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Malaysia has been estimated to be 30 % to 40 % of all S. aureus infections. Nevertheless, data on the antimicrobial resistance and genetic diversity of Malaysian MRSAs remain few. In 2009, we collected 318 MRSA strains from various wards of our teaching hospital located in Kuala Lumpur, the capital city of Malaysia, and performed antimicrobial susceptibility testing on these strains. The strains were then molecularly characterized via staphylococcal cassette chromosome (SCC) mec and virulence gene (cna, sea, seb, sec, sed, see, seg, seh, sei, eta, etb, Panton-Valentine leukocidin and toxic shock syndrome toxin-1) typing; a subset of 49 strains isolated from the intensive care unit was also typed using PFGE. Most strains were found to be resistant to ciprofloxacin (92.5 %), erythromycin (93.4 %) and gentamicin (86.8 %). The majority (72.0 %) of strains were found to harbour SCCmec type III-SCCmercury with the presence of ccrC, and carried the sea+cna gene combination (49.3 %), with cna as the most prevalent virulence gene (94.0 %) detected. We identified four PFGE clusters, with pulsotype C (n=19) as the dominant example in the intensive care unit, where this pulsotype was found to be associated with carriage of SCCmec type III and the sea gene (P=0.05 and P=0.02, respectively). In summary, the dominant MRSA circulating in our hospital in 2009 was a clone that was ciprofloxacin, erythromycin and gentamicin resistant, carried SCCmec type III-SCCmercury with ccrC and also harboured the sea+cna virulence genes. This clone also appears to be the dominant MRSA circulating in major hospitals in Kuala Lumpur.
Collapse
Affiliation(s)
- Ainihayati Noordin
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hassriana Fazzila Sapri
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurul Azirah Mohamad Sani
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Shih Kei Leong
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Xin-Ee Tan
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Noraziah Mohamad Zin
- Programme of Biomedical Science, School of Diagnostic and Applied Health Sciences, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Salasawati Hussin
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| |
Collapse
|
20
|
Tan XE, Neoh HM, Looi ML, Chin SF, Cui L, Hiramatsu K, Hussin S, Jamal R. Activated ADI pathway: the initiator of intermediate vancomycin resistance in Staphylococcus aureus. Can J Microbiol 2016; 63:260-264. [PMID: 28059579 DOI: 10.1139/cjm-2016-0439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Comparative proteomic profiling between 2 vancomycin-intermediate Staphylococcus aureus (VISA) strains, Mu50Ω-vraSm and Mu50Ω-vraSm-graRm, and vancomycin-susceptible S. aureus (VSSA) strain Mu50Ω revealed upregulated levels of catabolic ornithine carbamoyltransferase (ArcB) of the arginine catabolism pathway in VISA strains. Subsequent analyses showed that the VISA strains have higher levels of cellular ATP and ammonia, which are by-products of arginine catabolism, and displayed thicker cell walls. We postulate that elevated cytoplasmic ammonia and ATP molecules, resulting from activated arginine catabolism upon acquisition of vraS and graR mutations, are important requirements facilitating cell wall biosynthesis, thereby contributing to thickened cell wall and consequently reduced vancomycin susceptibility in VISA strains.
Collapse
Affiliation(s)
- Xin-Ee Tan
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Hui-Min Neoh
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.,b Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Mee-Lee Looi
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.,c Taylor's University Lakeside Campus, School of Biosciences, Malaysia
| | - Siok Fong Chin
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| | - Longzhu Cui
- d Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Keiichi Hiramatsu
- b Department of Bacteriology, School of Medicine, Juntendo University, Japan
| | - Salasawati Hussin
- e Department of Medical Microbiology and Immunology, Universiti Kebangsaan Malaysia, Malaysia
| | - Rahman Jamal
- a UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia
| |
Collapse
|
21
|
Abdul Samat MN, Hussin S, Neoh HM, Noordin A, Chuan HD, Abdul Wahab A, Rahman MM. Clonal Diversity of Methicillin-resistant Staphylococcus aureus in UKM Medical Centre: Characterisation by Multilocus Sequence Typing of Different SCCmec Type Representatives. SAINS MALAYS 2015. [DOI: 10.17576/jsm-2015-4409-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
22
|
Shah SA, Neoh HM, Syed Abdul Rahim SS, Azhar ZI, Hassan MR, Safian N, Jamal R. Spatial Analysis of Colorectal Cancer Cases in Kuala Lumpur. Asian Pac J Cancer Prev 2014; 15:1149-54. [DOI: 10.7314/apjcp.2014.15.3.1149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
23
|
Ramli SR, Neoh HM, Aziz MN, Hussin S. Screening and detection of heterogenous vancomycin intermediate Staphylococcus aureus in Hospital Kuala Lumpur Malaysia, using the glycopeptide resistance detection Etest and population analysis profiling. Infect Dis Rep 2012; 4:e20. [PMID: 24470927 PMCID: PMC3892648 DOI: 10.4081/idr.2012.e20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 12/19/2011] [Accepted: 01/08/2012] [Indexed: 11/22/2022] Open
Abstract
In a 3-month study done in Hospital Kuala Lumpur (HKL), 7 out of 320 methicillin resistant Staphylococcus aureus isolates were confirmed as heterogeneous vancomycin intermediate S. aureus (hVISA) using the glycopeptide resistance detection e-test and population analysis, giving a prevalence rate of 2.19%. This is the first report of hVISA in Malaysia.
Collapse
Affiliation(s)
- Siti Roszilawati Ramli
- Department of Microbiology and Immunology, University Kebangsaan Malaysia Medical Centre; ; Institute for Medical Research, MalaysiaJalan Pahang
| | - Hui-Min Neoh
- UKM Medical Molecular Biology Institute,University Kebangsaan Malaysia
| | | | - Salasawati Hussin
- Department of Microbiology and Immunology, University Kebangsaan Malaysia Medical Centre
| |
Collapse
|
24
|
Muhammad Azami NA, Salleh SA, Neoh HM, Syed Zakaria SZ, Jamal R. Dengue epidemic in Malaysia: Not a predominantly urban disease anymore. BMC Res Notes 2011; 4:216. [PMID: 21714858 PMCID: PMC3154160 DOI: 10.1186/1756-0500-4-216] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 06/29/2011] [Indexed: 11/10/2022] Open
Abstract
Background Dengue infection has been an important and serious public health concern in Malaysia ever since its first reported case here in 1902. Nevertheless, to our knowledge, no nationwide investigation has been carried out to determine the actual magnitude of dengue endemicity in the Malaysian population. In this study, we describe a cross sectional seroepidemiology study of dengue IgG seroprevalence in the Malaysian adult population. Findings From 1000 subjects (35-74 years old), 91.6% subjects were found to be dengue seropositive. Age is found to be a significant risk factor associated with dengue seroposivity, where the seroprevalence increased with every 10 year increase in age. Nevertheless, gender and ethnicity did not have an effect. Interestingly, there were similar seroprevalence rates between urban and rural samples, showing that dengue is presently not confined to urban areas in Malaysia. Conclusions High dengue IgG seropositivity found in the population is an indication that dengue might be endemic in Malaysia for a long time into the future. Public awareness, proper vector control and vigilant surveillance are critical to keep the infection rates low and to prevent outbreaks.
Collapse
|
25
|
Cui L, Tominaga E, Neoh HM, Hiramatsu K. Correlation between Reduced Daptomycin Susceptibility and Vancomycin Resistance in Vancomycin-Intermediate Staphylococcus aureus. Antimicrob Agents Chemother 2006; 50:1079-82. [PMID: 16495273 PMCID: PMC1426436 DOI: 10.1128/aac.50.3.1079-1082.2006] [Citation(s) in RCA: 324] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present here findings of a strong positive correlation between reduced daptomycin susceptibility and vancomycin resistance in vancomycin-intermediate Staphylococcus aureus (VISA). This correlation is related to cell wall thickening, suggesting that, similar to the case with vancomycin resistance in VISA, the physical barrier of a thickened cell wall may contribute to daptomycin resistance in S. aureus.
Collapse
Affiliation(s)
- Longzhu Cui
- Department of Bacteriology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, Japan 113-8421.
| | | | | | | |
Collapse
|
26
|
Cui L, Lian JQ, Neoh HM, Reyes E, Hiramatsu K. DNA microarray-based identification of genes associated with glycopeptide resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2005; 49:3404-13. [PMID: 16048954 PMCID: PMC1196288 DOI: 10.1128/aac.49.8.3404-3413.2005] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Six pairs of transcription profiles between glycopeptide-intermediate S. aureus (GISA [or vancomycin-intermediate S. aureus; VISA]) and glycopeptide-susceptible S. aureus (vancomycin-susceptible S. aureus [VSSA], including glycopeptide-susceptible isogenic mutants from VISA) strains were compared using a microarray. Ninety-two open reading frames which were or tended to be increased in transcription in VISA in at least five out of six array combination pairs were evaluated for their effects on glycopeptide susceptibility by introducing these genes one by one into VSSA strain N315 to construct an overexpression library. By screening the library, 17 genes including 8 novel genes were identified as associated with glycopeptide resistance since their experimental overexpression reduced vancomycin and/or teicoplanin susceptibility of N315. The raised MICs of vancomycin and teicoplanin were 1.25 to 3.0 and 1.5 to 6.0 mg/liter, respectively, as compared to 1.0 mg/liter of N315. Three of these genes, namely graF, msrA2, and mgrA, also raised the oxacillin MIC from 8.0 mg/liter for N315 to 64 to approximately 128 mg/liter when they were overexpressed in N315. Their contribution to vancomycin and beta-lactam resistance was further supported by gene knockout and trans-complementation assay. By using a plasmid-based promoter-green fluorescent protein gene (gfp) transcriptional fusion system, graF promoter-activated cells were purified, and subsequent susceptibility tests and Northern blot analysis demonstrated that the cells with up-regulated activity of graF promoter showed reduced susceptibility to vancomycin, teicoplanin, and oxacillin. In addition, cell morphology studies showed that graF and msrA2 overexpression increased cell wall thickness of N315 by factors of 23.91 and 22.27%, respectively, accompanied by glycopeptide MIC increments of 3- to 6-fold, when they were overexpressed in N315. Moreover, extended experiments and analyses indicate that many of the genes identified above are related to the cell wall biosynthetic pathway, including active nutrient transport systems. We propose that the genes which raise glycopeptide resistance in S. aureus function toward altering the cell wall metabolic pathway.
Collapse
Affiliation(s)
- Longzhu Cui
- Department of Bacteriology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan.
| | | | | | | | | |
Collapse
|