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Farva K, Sattar H, Ullah H, Raziq A, Mehmood MD, Tareen AK, Sultan IN, Zohra Q, Khan MW. Phenotypic Analysis, Molecular Characterization, and Antibiogram of Caries-Causing Bacteria Isolated from Dental Patients. Microorganisms 2023; 11:1952. [PMID: 37630520 PMCID: PMC10457851 DOI: 10.3390/microorganisms11081952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Dental caries is a biofilm-mediated, sugar-driven, multifactorial, dynamic disease that results in the phasic demineralization and remineralization of dental hard tissues. Despite scientific advances in cariology, dental caries remains a severe global concern. The aim of this study was to determine the optimization of microbial and molecular techniques for the detection of cariogenic pathogens in dental caries patients, the prevalence of cariogenic bacteria on the basis of socioeconomic, climatological, and hygienic factors, and in vitro evaluation of the antimicrobial activity of selected synthetic antibiotics and herbal extracts. In this study, oral samples were collected from 900 patients for bacterial strain screening on a biochemical and molecular basis. Plant extracts, such as ginger, garlic, neem, tulsi, amla, and aloe vera, were used to check the antimicrobial activity against the isolated strains. Synthetic antimicrobial agents, such as penicillin, amoxicillin, erythromycin, clindamycin, metronidazole, doxycycline, ceftazidime, levofloxacin, and ciprofloxacin, were also used to access the antimicrobial activity. Among 900 patients, 63% were males and 37% were females, patients aged between 36 and 58 (45.7%) years were prone to disease, and the most common symptom was toothache (61%). For oral diseases, 21% used herbs, 36% used antibiotics, and 48% were self-medicated, owing to sweets consumption (60.66%) and fizzy drinks and fast food (51.56%). Staphylococcus mutans (29.11%) and Streptococcus sobrinus (28.11%) were found as the most abundant strains. Seven bacterial strains were successfully screened and predicted to be closely related to genera S. sobrinus, S. mutans, Actinomyces naeslundii, Lactobacillus acidophilus, Eubacterium nodatum, Propionibacterium acidifaciens, and Treponema Pallidum. Among plant extracts, the maximum zone of inhibition was recorded by ginger (22.36 mm) and amla (20.01 mm), while among synthetic antibiotics, ciprofloxacin and levofloxacin were most effective against all microbes. This study concluded that phyto extracts of ginger and amla were considered suitable alternatives to synthetic antibiotics to treat dental diseases.
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Affiliation(s)
- Khushbu Farva
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Huma Sattar
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Hayat Ullah
- Metabolic Engineering Lab, Department of Biological Engineering, Utah State University, Logan, UT 84322, USA
| | - Abdur Raziq
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Muhammad Danish Mehmood
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Afrasiab Khan Tareen
- Department of Biotechnology, Balochistan University of Information Technology Engineering and Management Sciences, Quetta 87300, Pakistan
| | - Imrana Niaz Sultan
- Department of Biotechnology, Balochistan University of Information Technology Engineering and Management Sciences, Quetta 87300, Pakistan
| | - Quratulaain Zohra
- Department of Biotechnology, Project of Sahara for Life Trust, The Sahara College Narowal, Punjab 51601, Pakistan
| | - Muhammad Waseem Khan
- Department of Biotechnology, Balochistan University of Information Technology Engineering and Management Sciences, Quetta 87300, Pakistan
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Selvam K, Ahmad Najib M, Khalid MF, Ozsoz M, Aziah I. CRISPR-Cas Systems-Based Bacterial Detection: A Scoping Review. Diagnostics (Basel) 2022; 12:diagnostics12061335. [PMID: 35741144 PMCID: PMC9221980 DOI: 10.3390/diagnostics12061335] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Recently, CRISPR-Cas system-based assays for bacterial detection have been developed. The aim of this scoping review is to map existing evidence on the utilization of CRISPR-Cas systems in the development of bacterial detection assays. A literature search was conducted using three databases (PubMed, Scopus, and Cochrane Library) and manual searches through the references of identified full texts based on a PROSPERO-registered protocol (CRD42021289140). Studies on bacterial detection using CRISPR-Cas systems that were published before October 2021 were retrieved. The Critical Appraisal Skills Programme (CASP) qualitative checklist was used to assess the risk of bias for all the included studies. Of the 420 studies identified throughout the search, 46 studies that met the inclusion criteria were included in the final analysis. Bacteria from 17 genera were identified utilising CRISPR-Cas systems. Most of the bacteria came from genera such as Staphylococcus, Escherichia, Salmonella, Listeria, Mycobacterium and Streptococcus. Cas12a (64%) is the most often used Cas enzyme in bacterial detection, followed by Cas13a (13%), and Cas9 (11%). To improve the signal of detection, 83% of the research exploited Cas enzymes’ trans-cleavage capabilities to cut tagged reporter probes non-specifically. Most studies used the extraction procedure, whereas only 17% did not. In terms of amplification methods, isothermal reactions were employed in 66% of the studies, followed by PCR (23%). Fluorescence detection (67%) was discovered to be the most commonly used method, while lateral flow biosensors (13%), electrochemical biosensors (11%), and others (9%) were found to be less commonly used. Most of the studies (39) used specific bacterial nucleic acid sequences as a target, while seven used non-nucleic acid targets, including aptamers and antibodies particular to the bacteria under investigation. The turnaround time of the 46 studies was 30 min to 4 h. The limit of detection (LoD) was evaluated in three types of concentration, which include copies per mL, CFU per mL and molarity. Most of the studies used spiked samples (78%) rather than clinical samples (22%) to determine LoD. This review identified the gap in clinical accuracy evaluation of the CRISPR-Cas system in bacterial detection. More research is needed to assess the diagnostic sensitivity and specificity of amplification-free CRISPR-Cas systems in bacterial detection for nucleic acid-based tests.
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Affiliation(s)
- Kasturi Selvam
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
| | - Mehmet Ozsoz
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
- Correspondence:
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Blondeau JM, Rankin SC. Diagnostic clinical microbiology. J Vet Pharmacol Ther 2021; 44:250-269. [PMID: 33686661 DOI: 10.1111/jvp.12962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/27/2021] [Accepted: 02/09/2021] [Indexed: 01/07/2023]
Abstract
Technological advancements have changed the way clinical microbiology laboratories are detecting and identifying bacterial, viral, parasitic, and yeast/fungal pathogens. Such advancements have improved sensitivity and specificity and reduce turnaround time to reporting of clinically important results. This article discusses and reviews some traditional methodologies along with some of the technological innovations introduced into diagnostic microbiology laboratories. Some insight to what might be available in the coming years is also discussed.
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Affiliation(s)
- Joseph M Blondeau
- Division of Clinical Microbiology, Royal University Hospital and Saskatchewan Health Authority, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Ophthalmology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Shelley C Rankin
- Department of Pathobiology, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, USA
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Olawale SI, Busayo OOM, Olatunji OI, Mariam M, Olayinka OS. Plasmid profiles and antibiotic susceptibility patterns of bacteria isolated from abattoirs wastewater within Ilorin, Kwara, Nigeria. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 12:547-555. [PMID: 33613909 PMCID: PMC7884279 DOI: 10.18502/ijm.v12i6.5029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background and Objectives: Waste water from abattoirs could harbour bacteria some of which are pathogenic. Therefore, this study aimed to assess the quality of wastewater from some abattoirs in Ilorin, Nigeria. Materials and Methods: The counts of viable bacteria, total coliform, faecal coliform, enterococci, S. aureus, P. aeruginosa and Salmonella/Shigella spp. of the wastewater was determined using selective media. The sanitary condition appraisal, antibiotic susceptibility test and plasmid profile of the isolates were assessed using standard methods. Results: The highest count of viable bacteria and total coliform obtained were 9.0 × 107 and 3.0 × 107 CFU/ml respectively. Faecal coliform and enterococcal count had the same highest value of 3.0 × 105 CFU/ml. The highest count of pathogenic bacteria: Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella spp. were 2.5 × 108, 1.9 × 107 and 3.0 × 104 CFU/ml respectively. The abattoirs sanitary scores ranged from 28.6–57.1%. The isolates showed multiple antibiotic resistance (MAR) index ranging from 0.5–1.0. Plasmid curing with 0.1 mg/ml of acridine orange solution led to reduction in the MAR index of most of the Gram negative bacteria. Pseudomonas stutzeri was susceptible to all the antibiotics while Proteus vulgaris was resistant to all the antibiotics after curing. Most of the Gram negative bacteria isolated belong to the families Enterobacteriaceae and Pseudomonadaceae while the Gram positive bacteria belong to the families Staphylococcaceae, Enterococcaceae and Streptococcaceae. Conclusion: It was concluded from this study that wastewaters from the abattoirs were contaminated by bacteria with high MAR index. Most of these bacteria borne their antibiotic resistant factors in their plasmid.
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Affiliation(s)
- Sule Ismaila Olawale
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara, Nigeria
| | | | | | - Muhammed Mariam
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara, Nigeria
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Tien N, You BJ, Lin HJ, Chang CY, Chou CY, Lin HS, Chang CT, Wang CCN, Chen HC. Repeated centrifuging and washing concentrates bacterial samples in peritoneal dialysis for optimal culture: an original article. BMC Microbiol 2020; 20:365. [PMID: 33246404 PMCID: PMC7694434 DOI: 10.1186/s12866-020-02044-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Bacterial cultures allow the identification of infectious disease pathogens. However, obtaining the results of conventional culture methods is time-consuming, taking at least two days. A more efficient alternative is the use of concentrated bacterial samples to accelerate culture growth. Our study focuses on the development of a high-yield sample concentrating technique. Results A total of 71 paired samples were obtained from patients on peritoneal dialysis (PD). The peritoneal dialysates were repeat-centrifuged and then washed with saline, namely the centrifuging and washing method (C&W method). The concentrated samples were Gram-stained and inoculated into culture plates. The equivalent unprocessed dialysates were cultured as the reference method. The times until culture results for the two methods were compared. The reference method yielded no positive Gram stain results, but the C&W method immediately gave positive Gram stain results for 28 samples (p < 0.001). The culture-negative rate was lower in the C&W method (5/71) than in the reference method (13/71) (p = 0.044). The average time for bacterial identification achieved with the C&W method (22.0 h) was shorter compared to using the reference method (72.5 h) (p < 0.001). Conclusions The C&W method successfully concentrated bacterial samples and superseded blood culture bottles for developing adequate bacterial cultures. The C&W method may decrease the culture report time, thus improving the treatment of infectious diseases.
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Affiliation(s)
- Ni Tien
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Bang-Jau You
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, Taichung, Taiwan.,China Medical University, Taichung, Taiwan
| | - Hsuan-Jen Lin
- Division of Nephrology, Asia University Hospital, Taichung, Taiwan
| | - Chieh-Ying Chang
- College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Che-Yi Chou
- Division of Nephrology, Asia University Hospital, Taichung, Taiwan
| | - Hsiu-Shen Lin
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Chiz-Tzung Chang
- College of Medicine, China Medical University, Taichung, Taiwan. .,Division of Nephrology, China Medical University Hospital, No. 2, Yu-der Road, North District, Taichung, 40447, Taiwan.
| | - Charles C N Wang
- Department of Bioinformatics and Medical Engineering Asia University, Taichung, 41354, Taiwan.,Center for Artificial Intelligence and Precision Medicine Research, Asia University, 500, Lioufeng Rd., Wufeng, Taichung, Taiwan
| | - Hung-Chih Chen
- Department of Bioinformatics and Medical Engineering Asia University, Taichung, 41354, Taiwan. .,Division of Nephrology, Asia University Hospital, No. 222, Fuxin Road, Wufeng District, Taichung, 41354, Taiwan.
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Pavlicek RL, Crane NJ, Ghebremedhin M, Cilwa KE, Elster EA. Diagnostic Bacteriology: Raman Spectroscopy. Methods Mol Biol 2018; 1616:249-261. [PMID: 28600775 DOI: 10.1007/978-1-4939-7037-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Current clinical methodology for identification of bacterial infections relies predominantly on culturing microbes from patient material and performing biochemical tests. This can often be an inefficient and lengthy process, which has a significant detrimental effect upon patient care. Techniques used in other aspects of molecular research have the potential to revolutionize the way in which diagnostic tests are used and delivered in the clinical setting. The need for rapid, accurate, and cost-effective molecular techniques in the diagnostic laboratory is imperative to improving patient care, preventing the spread of drug resistance and decreasing the overall burden associated with nosocomial infections. Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) are powerful vibrational spectroscopy techniques that are being developed for highly sensitive pathogen identification in complex clinical samples. Raman spectroscopy is a molecular technique that is capable of probing samples noninvasively and nondestructively. It has been used with high specificity to assess tissue and bacterial samples at the molecular level with diverse clinical and diagnostic applications. SERS has recently developed out of the advances in the Raman spectroscopy arena. This technique is designed to amplify Raman scattering and allows for better differentiation of bacterial isolates. Although the current parameters for the use of SERS require a pure culture and are relatively monoparametric, current breakthroughs and testing are pushing the technology to new levels and thus changing the face of modern bacterial diagnostics.
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Affiliation(s)
| | - Nicole J Crane
- The Department of Surgery at Uniformed Services University of the Health Sciences & The Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Meron Ghebremedhin
- Department of Regenerative Medicine, Naval Medical Research Center, Silver Spring, MD, USA
| | - Katherine E Cilwa
- Department of Regenerative Medicine, Naval Medical Research Center, Silver Spring, MD, USA
| | - Eric A Elster
- The Department of Surgery at Uniformed Services University of the Health Sciences & The Walter Reed National Military Medical Center, Bethesda, MD, USA.
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