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Perri K, Abdelhaseib M, Fricker AD. Increasing student interest with the Bacterial Unknown Identification Project: using mixed cultures to create real-world applications. J Microbiol Biol Educ 2023; 24:e00070-23. [PMID: 38108012 PMCID: PMC10720552 DOI: 10.1128/jmbe.00070-23] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/14/2023] [Indexed: 12/19/2023]
Abstract
Many introductory-level classes teach fundamental concepts, as they are prerequisites for upper-division courses. Therefore, the student body in these classes has diverse interests. To address this breadth of career trajectory, introductory-level laboratory courses often include experiments that demonstrate a wide range of microbiological techniques and processes. One of the experiments that is a standard component of many microbiology classes, the Bacterial Unknown Identification Project (BUIP), is often limited to isolated organisms or a specific environment. Here, we describe an updated method for the BUIP that incorporates the projected student career diversity through the implementation of multiple mixed cultures of microorganisms associated with different environments. This update can be utilized in any microbiology laboratory classroom. We maintained the learning objectives, including applying appropriate microbiological methods to analyze and interpret results, and effectively communicate scientific findings, while modifying the sample composition. Assessment of the modification demonstrated that upon completion of the BUIP, students felt that the project applied to their career and it did not take too much of their free time to complete.
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Affiliation(s)
- Kayla Perri
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana, USA
| | - Maha Abdelhaseib
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ashwana D. Fricker
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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Panwar S, Duggirala KS, Yadav P, Debnath N, Yadav AK, Kumar A. Advanced diagnostic methods for identification of bacterial foodborne pathogens: contemporary and upcoming challenges. Crit Rev Biotechnol 2023; 43:982-1000. [PMID: 35994308 DOI: 10.1080/07388551.2022.2095253] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 01/14/2022] [Accepted: 06/09/2022] [Indexed: 11/03/2022]
Abstract
It is a public health imperative to have safe food and water across the population. Foodborne infections are one of the primary causes of sickness and mortality in both developed and developing countries. An estimated 100 million foodborne diseases and 120 000 foodborne illness-related fatalities occur each year in India. Several factors affect foodborne illness, such as improper farming methods, poor sanitary and hygienic conditions at all levels of the food supply chain, the lack of preventative measures in the food processing industry, the misuse of food additives, as well as improper storage and handling. In addition, chemical and microbiological combinations also play a key role in disease development. But recent disease outbreaks indicated that microbial pathogens played a major role in the development of foodborne diseases. Therefore, prompt, rapid, and accurate detection of high-risk food pathogens is extremely vital to warrant the safety of the food items. Conventional approaches for identifying foodborne pathogens are labor-intensive and cumbersome. As a result, a range of technologies for the rapid detection of foodborne bacterial pathogens have been developed. Presently, many methods are available for the instantaneous detection, identification, and monitoring of foodborne pathogens, such as nucleic acid-based methods, biosensor-based methods, and immunological-based methods. The goal of this review is to provide a complete evaluation of several existing and emerging strategies for detecting food-borne pathogens. Furthermore, this review outlines innovative methodologies and their uses in food testing, along with their existing limits and future possibilities in the detection of live pathogens in food.
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Affiliation(s)
- Surbhi Panwar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | | | - Pooja Yadav
- Centre for Molecular Biology, Central University of Jammu, Jammu, India
| | - Nabendu Debnath
- Centre for Molecular Biology, Central University of Jammu, Jammu, India
| | - Ashok Kumar Yadav
- Centre for Molecular Biology, Central University of Jammu, Jammu, India
| | - Ashwani Kumar
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, India
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Radenkovs V, Valdovska A, Galina D, Cairns S, Jakovlevs D, Gaidukovs S, Cinkmanis I, Juhnevica-Radenkova K. Elaboration of Nanostructured Levan-Based Colloid System as a Biological Alternative with Antimicrobial Activity for Applications in the Management of Pathogenic Microorganisms. Nanomaterials (Basel) 2023; 13:2969. [PMID: 37999323 PMCID: PMC10674346 DOI: 10.3390/nano13222969] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Considering the documented health benefits of bacterial exopolysaccharides (EPSs), specifically of bacterial levan (BL), including its intrinsic antimicrobial activity against certain pathogenic species, the current study concentrated on the development of active pharmaceutical ingredients (APIs) in the form of colloid systems (CoSs) containing silver nanoparticles (AgNPs) employing in-house biosynthesized BL as a reducing and capping agent. The established protocol of fermentation conditions implicating two species of lactic acid bacteria (LAB), i.e., Streptococcus salivarius K12 and Leuconostoc mesenteroides DSM 20343, ensured a yield of up to 25.7 and 13.7 g L-1 of BL within 72 h, respectively. An analytical approach accomplished by Fourier-transform infrared (FT-IR) spectroscopy allowed for the verification of structural features attributed to biosynthesized BL. Furthermore, scanning electron microscopy (SEM) revealed the crystalline morphology of biosynthesized BL with a smooth and glossy surface and highly porous structure. Molecular weight (Mw) estimated by multi-detector size-exclusion chromatography (SEC) indicated that BL biosynthesized using S. salivarius K12 has an impressively high Mw, corresponding to 15.435 × 104 kilodaltons (kDa). In turn, BL isolated from L. mesenteroides DSM 20343 was found to have an Mw of only 26.6 kDa. Polydispersity index estimation (PD = Mw/Mn) of produced BL displayed a monodispersed molecule isolated from S. salivarius K12, corresponding to 1.08, while this was 2.17 for L. mesenteroides DSM 20343 isolate. The presence of fructose as the main backbone and, to a lesser extent, glucose and galactose as side chain molecules in EPS hydrolysates was supported by HPLC-RID detection. In producing CoS-BL@AgNPs within green biosynthesis, the presence of nanostructured objects with a size distribution from 12.67 ± 5.56 nm to 46.97 ± 20.23 was confirmed by SEM and energy-dispersive X-ray spectroscopy (EDX). The prominent inhibitory potency of elaborated CoS-BL@AgNPs against both reference test cultures, i.e., Pseudomonas aeruginosa, Escherichia coli, Enterobacter aerogenes, and Staphylococcus aureus and those of clinical origin with multi-drug resistance (MDR), was confirmed by disc and well diffusion tests and supported by the values of the minimum inhibitory and bactericidal concentrations. CoS-BL@AgNPs can be treated as APIs suitable for designing new antimicrobial agents and modifying therapies in controlling MDR pathogens.
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Affiliation(s)
- Vitalijs Radenkovs
- Processing and Biochemistry Department, Institute of Horticulture, LV-3701 Dobele, Latvia;
- Research Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia; (A.V.); (D.G.); (D.J.)
| | - Anda Valdovska
- Research Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia; (A.V.); (D.G.); (D.J.)
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia
| | - Daiga Galina
- Research Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia; (A.V.); (D.G.); (D.J.)
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia
| | - Stefan Cairns
- Malvern Panalytical Ltd., Worcestershire, Malvern WR14 1XZ, UK
| | - Dmitrijs Jakovlevs
- Research Laboratory of Biotechnology, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia; (A.V.); (D.G.); (D.J.)
| | - Sergejs Gaidukovs
- Institute of Polymer Materials, Faculty of Materials Science and Applied Chemistry, Riga Technical University, LV-1048 Riga, Latvia;
| | - Ingmars Cinkmanis
- Faculty of Agriculture and Food Technology, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia;
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Panhwar S, Keerio HA, Ilhan H, Boyacı IH, Tamer U. Principles, Methods, and Real-Time Applications of Bacteriophage-Based Pathogen Detection. Mol Biotechnol 2023:10.1007/s12033-023-00926-5. [PMID: 37914863 DOI: 10.1007/s12033-023-00926-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023]
Abstract
Bacterial pathogens in water, food, and the environment are spreading diseases around the world. According to a World Health Organization (WHO) report, waterborne pathogens pose the most significant global health risks to living organisms, including humans and animals. Conventional bacterial detection approaches such as colony counting, microscopic analysis, biochemical analysis, and molecular analysis are expensive, time-consuming, less sensitive, and require a pre-enrichment step. However, the bacteriophage-based detection of pathogenic bacteria is a robust approach that utilizes bacteriophages, which are viruses that specifically target and infect bacteria, for rapid and accurate detection of targets. This review shed light on cutting-edge technologies about the novel structure of phages and the immobilization process on the surface of electrodes to detect targeted bacterial cells. Similarly, the purpose of this study was to provide a comprehensive assessment of bacteriophage-based biosensors utilized for pathogen detection, as well as their trends, outcomes, and problems. This review article summaries current phage-based pathogen detection strategies for the development of low-cost lab-on-chip (LOC) and point-of-care (POC) devices using electrochemical and optical methods such as surface-enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- Sallahuddin Panhwar
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
- Department of Civil Engineering, National University of Sciences and Technology, Quetta, 24090, Balochistan, Pakistan.
| | - Hareef Ahmed Keerio
- Department of Civil and Environmental Engineering, Hanyang University, Seoul, Republic of Korea
| | - Hasan Ilhan
- Department of Chemistry, Faculty of Science, Ordu University, Altinordu, 52200, Ordu, Turkey
| | - Ismail Hakkı Boyacı
- Department of Food Engineering, Faculty of Engineering, Hacettepe University, Beytepe, 06800, Ankara, Turkey
| | - Ugur Tamer
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey.
- Metu MEMS Center, Ankara, Turkey.
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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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Li J, Li Y. Detect feature edges for diagnosis of bacterial vaginosis. PeerJ 2023; 11:e14667. [PMID: 36684669 PMCID: PMC9854373 DOI: 10.7717/peerj.14667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023] Open
Abstract
One of the most common diseases among women of reproductive age is bacterial vaginosis (BV). However, the etiology of BV remains unknown. In this study, we modeled the temporal sample of the vaginal microbiome as a network and investigated the relationship between the network edges and BV. Furthermore, we used feature selection algorithms including decision tree (DT) and ReliefF (RF) to select the network feature edges associated with BV and subsequently validated these feature edges through logistic regression (LR) and support vector machine (SVM). The results show that: machine learning can distinguish vaginal community states (BV, ABV, SBV, and HEA) based on a few feature edges; selecting the top five feature edges of importance can achieve the best accuracy for the feature selection and classification model; the feature edges selected by DT outperform those selected by RF in terms of classification algorithm LR and SVM, and LR with DT feature edges is more suitable for diagnosing BV; two feature selection algorithms exhibit differences in the importance of ranking of edges; the feature edges selected by DT and RF cannot construct sub-network associated with BV. In short, the feature edges selected by our method can serve as indicators for personalized diagnosis of BV and aid in the clarification of a more mechanistic interpretation of its etiology.
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Dumigan A, Gonzalez RC, Morris B, Sá-Pessoa J. Visualisation of Host-Pathogen Communication. Adv Exp Med Biol 2023; 1406:19-39. [PMID: 37016109 DOI: 10.1007/978-3-031-26462-7_2] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The core of biomedical science is the use of laboratory techniques to support the diagnosis and treatment of disease in clinical settings. Despite tremendous advancement in our understanding of medicine in recent years, we are still far from having a complete understanding of human physiology in homeostasis, let alone the pathology of disease states. Indeed medical advances over the last two hundred years would not have been possible without the invention of and continuous development of visualisation techniques available to research scientists and clinicians. As we have all learned from the recent COVID pandemic, despite advances in modern medicine we still have much to learn regarding infection biology. Indeed antimicrobial resistant (AMR) bacteria are a global threat to human health, meaning research into bacterial pathogenesis is vital. In this chapter, we will briefly describe the nature of microbes and host immune responses before delving into some of the visualisation techniques utilised in the field of biomedical research with a focus on host-pathogen interactions. We will give a brief overview of commonly used techniques from gold standard staining methods, in situ hybridisation, microscopy, western blotting, microbial characterisation, to cutting-edge image flow cytometry and mass spectrometry. Specifically, we will focus on techniques utilised to visualise interactions between the host, our own bodies, and invading organisms including bacteria. We will touch on in vitro and ex vivo modelling methodology with examples utilised to delineate pathogenicity in disease. A better understanding of bacterial biology, immunology and how these fields interact (host-pathogen communications) in biomedical research is integral to developing novel therapeutic approaches which circumvent the need for antibiotics, an important issue as we enter a post-antibiotic era.
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Affiliation(s)
- Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.
| | | | - Brenda Morris
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
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Xu X, Zhu R, Lian S, Zhang H, Chen X, Fan L, Chen P, Cao Y. Risk Factors and Molecular Mechanism of Polymyxin B Resistance in Carbapenem-Resistant Klebsiella pneumoniae Isolates from a Tertiary Hospital in Fujian, China. Infect Drug Resist 2022; 15:7485-7494. [PMID: 36544993 PMCID: PMC9762268 DOI: 10.2147/idr.s391674] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Background The emergence of polymyxin B resistance among carbapenem-resistant Klebsiella pneumoniae (CRKP) causes clinical treatment to be more difficult. We aimed to investigate the risk factors and resistance mechanisms in the polymyxin resistant CRKP (PR-CRKP) strains. Methods From January 2021 to January 2022, 239 CRKP strains were selected, all of which were analyzed using antimicrobial susceptibility testing and clinical data. Polymerase chain reaction (PCR) was performed for the detection of resistance genes. RT-qPCR was used to quantify transcriptional levels of polymyxin resistance genes. Risk factors for polymyxin B resistant isolates were identified by logistic regression analysis. Results The resistance rate of polymyxin B was 5.02%. In all CRKP strains, 41.84% came from the ICU. The percentage of carbapenemase producing strains was 93.72%. The main carbapenem resistance gene was blaKPC (90.79%). In the 12 strains of PR-CRKP screened, pmrB and pmrK were overexpressed in all samples which were linked with polymyxin B resistance. Multivariate analysis showed that coronary heart disease may be an independent risk factor predisposing patients to polymyxin B resistance. Conclusion We determine the multifaceted mechanism and risk factors of polymyxin B resistance in CRKP. Polymyxin resistance is a complex and changing problem, and more research is required.
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Affiliation(s)
- Xiaohong Xu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, Fujian, People’s Republic of China
| | - Rongping Zhu
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, Fujian, People’s Republic of China
| | - Siyan Lian
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, Fujian, People’s Republic of China
| | - Hui Zhang
- Medical Technology and Engineering, Fujian Medical University, Fuzhou, Fujian, People’s Republic of China
| | - Xin Chen
- Medical Technology and Engineering, Fujian Medical University, Fuzhou, Fujian, People’s Republic of China
| | - Lingfang Fan
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, Fujian, People’s Republic of China
| | - Peisong Chen
- Medical Technology and Engineering, Fujian Medical University, Fuzhou, Fujian, People’s Republic of China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, Fujian, People’s Republic of China,Correspondence: Yingping Cao, Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, Fujian, People’s Republic of China, Tel +86-133-6591-0806, Email
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Chanthasena P, Hua Y, Rosyidah A, Pathom-Aree W, Limphirat W, Nantapong N. Isolation and Identification of Bioactive Compounds from Streptomyces actinomycinicus PJ85 and Their In Vitro Antimicrobial Activities against Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2022; 11:antibiotics11121797. [PMID: 36551454 PMCID: PMC9774200 DOI: 10.3390/antibiotics11121797] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/28/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Antibiotic-resistant strains are a global health-threatening problem. Drug-resistant microbes have compromised the control of infectious diseases. Therefore, the search for a novel class of antibiotic drugs is necessary. Streptomycetes have been described as the richest source of bioactive compounds, including antibiotics. This study was aimed to characterize the antibacterial compounds of Streptomyces sp. PJ85 isolated from dry dipterocarp forest soil in Northeast Thailand. The 16S rRNA gene sequence and phylogenetic analysis showed that PJ85 possessed a high similarity to Streptomyces actinomycinicus RCU-197T of 98.90%. The PJ85 strain was shown to produce antibacterial compounds that were active against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA). The active compounds of PJ85 were extracted and purified using silica gel column chromatography. Two active antibacterial compounds, compound 1 and compound PJ85_F39, were purified and characterized with spectroscopy, including liquid chromatography and mass spectrometry (LC-MS). Compound 1 was identified as actinomycin D, and compound PJ85_F39 was identified as dihomo-γ-linolenic acid (DGLA). To the best of our knowledge, this is the first report of the purification and characterization of the antibacterial compounds of S. actinomycinicus.
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Affiliation(s)
- Panjamaphon Chanthasena
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Yanling Hua
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - A’liyatur Rosyidah
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wanwisa Limphirat
- Synchrotron Light Research Institute, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Nawarat Nantapong
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Correspondence: ; Tel.: +66-442-242-82
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Bolzon V, Pesando M, Bulfoni M, Nencioni A, Nencioni E. An Integrated Analytical Approach for the Characterization of Probiotic Strains in Food Supplements. Nutrients 2022; 14:nu14235085. [PMID: 36501115 PMCID: PMC9736879 DOI: 10.3390/nu14235085] [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: 11/03/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Research surrounding health benefits from probiotics is becoming popular because of the increasing demand for safer products with protective and therapeutic effects. Proven benefits are species- or genus-specific; however, no certified assays are available for their characterization and quantification at the strain level in the food supplement industry. The objective of this study was to develop a strain-specific Real-time quantitative polymerase chain reaction (RT-qPCR)-based method to be implemented in routine tests for the identification and quantification of Bifidobacterium longum, Bifidobacterium animalis spp. lactis, Lactobacillus paracasei, Lactobacillus rhamnosus, Lactobacillus casei, Bifidobacterium breve, Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus helveticus, starting from a powder mixture of food supplements. The method optimization was carried out in combination with flow cytometry to compare results between the two strategies and implement the analytical workflow with the information also regarding cell viability. These assays were validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) criteria using the plate count enumeration as the gold standard reference. Briefly, probiotic DNAs were extracted from two powder food supplements. Strain-specific primers targeting unique sequence regions of 16S RNA were identified and amplified by RT-qPCR. Primers were tested for specificity, sensitivity, and efficiency. Both RT-qPCR and flow-cytometry methods described in our work for the quantification and identification of Lactobacillus and Bifidobacterium strains were specific, sensitive, and precise, showing better performances with respect to the morphological colony identification. This work demonstrated that RT-qPCR can be implemented in the quality control workflow of commercial probiotic products giving more standardized and effective results regarding species discrimination.
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Affiliation(s)
| | | | - Michela Bulfoni
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Alessandro Nencioni
- IBSA Institut Biochimique SA, Via del Piano 29, CH-6915 Pambio Noranco, Switzerland
| | - Emanuele Nencioni
- Biofarma Group Srl., Via Castelliere 2, 33036 Udine, Italy
- Correspondence:
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Xing G, Shan Y, Wang X, Lin H, Chen S, Pu Q, Lin L. Multiplexed detection of foodborne pathogens using one-pot CRISPR/Cas12a combined with recombinase aided amplification on a finger-actuated microfluidic biosensor. Biosens Bioelectron 2022; 220:114885. [DOI: 10.1016/j.bios.2022.114885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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Shaaban M, Elshaer SL, Abd El-Rahman OA. Prevalence of extended-spectrum β-lactamases, AmpC, and carbapenemases in Proteus mirabilis clinical isolates. BMC Microbiol 2022; 22:247. [PMID: 36221063 PMCID: PMC9552493 DOI: 10.1186/s12866-022-02662-3] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Proteus mirabilis is an opportunistic pathogen, causing a variety of community-acquired and nosocomial illnesses. It poses a potential threat to patients via the production of β-lactamases, which decrease the efficacy of antimicrobial treatment and impair the management of its pathogenicity. Hence, this study was established to determine the prevalence of extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases of P. mirabilis isolated from various clinical specimens. Results Proteus mirabilis was identified in 20.7% (58/280) of specimens. ESBL producers were present at a rate of 51.7% (30/58). All AmpC-positive isolates (n = 20) produced ESBLs as well, so 66.7% of ESBL-producing isolates coproduced AmpC enzymes. The modified Hodge test confirmed carbapenemase production in six out of seven imipenem nonsusceptible isolates. Of these, only two (5.7%) isolates were also ESBL-and AmpC-positive. Antibiotic resistance reached the highest level for cotrimoxazole (62.1%, n = 36/58 isolates) and the lowest for imipenem (12.1%, n = 7/58 isolates). The levels of multidrug-resistant (MDR) was 41.4% among the tested isolates. The blaSHV (83.3%), blaAmpC (80%), and blaVIM-1 (50%) were the most detected genes in phenotypically confirmed ESBL-, AmpC-, and carbapenemase-producing isolates, respectively. Besides, more than a half of the tested P. mirabilis strains (53%) coproduced ESBLs and AmpC. Moreover, two isolates coproduced ESBLs and AmpC together with carbapenemases. Furthermore, dendrogram analysis showed great genetic divergence based on the 21 different enterobacterial repetitive intergenic consensus (ERIC) patterns (P1–P21) through the 34 β-lactamase producers. ERIC analysis distinguished clonal similarities between isolates 21 and 22 in P2 and 9 and 10 in P4, which were isolated from the same clinical source and possessed similar patterns of β-lactamase-encoding genes. Conclusion Hence, there is an urgent need to monitor hospitalized patients and improve healthcare in order to reduce the incidence of infection and outbreaks of infection with antibiotic-resistant Proteus. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02662-3.
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Affiliation(s)
- Mona Shaaban
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Soha Lotfy Elshaer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Ola A Abd El-Rahman
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, 11651, Egypt
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Dendani Chadi Z, Dib L, Zeroual F, Benakhla A. Usefulness of molecular typing methods for epidemiological and evolutionary studies of Staphylococcus aureus isolated from bovine intramammary infections. Saudi J Biol Sci 2022; 29:103338. [PMID: 35813112 PMCID: PMC9257419 DOI: 10.1016/j.sjbs.2022.103338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 05/10/2022] [Accepted: 06/10/2022] [Indexed: 12/05/2022] Open
Abstract
In cattle, Staphylococcus aureus is a major pathogen of increasing importance due to its association with intramammary infections (IMIs), which are a primary cause of antibiotic use on farms and thus of the rise in antibiotic resistance. Methicillin-resistant S. aureus (MRSA), which are frequently isolated from cases of bovine mastitis, represent a public health problem worldwide. Understanding the epidemiology and the evolution of these strains relies on typing methods. Such methods were phenotypic at first, but more recently, molecular methods have been increasingly utilized. Multiple-locus variable number tandem repeat analysis (MLVA), a high-throughput molecular method for determining genetic diversity and the emergence of host- or udder-adapted clones, appears to be the most useful PCR-based method. Despite the difficulties present in reproducibility, interlaboratory reliability, and hard work, it is agreed that pulsed-field gel electrophoresis (PFGE) remains the gold standard, particularly for short-term surveillance. Multilocus sequence typing (MLST) is a good typing method for long-term and global epidemiological investigations, but it is not suitable for outbreak investigations. Staphylococcal protein A (spa) typing is the most widely used method today for first-line typing in the study of molecular evolution, and outbreaks investigations. Staphylococcal cassette chromosome mec (SCCmec) typing has gained popularity for the evolutionary analysis of MRSA strains. Whole-genome sequencing (WGS) and DNA microarrays that represent relatively new DNA-based technologies, provide more information for tracking antibioresistant and virulent outbreak strains. They offer a higher discriminatory power, but are not suitable for routine use in clinical veterinary medicine at this time. Descriptions of the evolution of these methods, their advantages, and limitations are given in this review.
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Gana J, Gcebe N, Pierneef R, Moerane R, Adesiyun AA. Multiple-Locus Variable-Number Tandem Repeat Analysis Genotypes of Listeria monocytogenes Isolated from Farms, Abattoirs, and Retail in Gauteng Province, South Africa. J Food Prot 2022; 85:1249-1257. [PMID: 35588459 DOI: 10.4315/jfp-22-081] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/29/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT The use of multiple-locus variable-number analysis (MLVA) of tandem repeats (TRs) for subtyping Listeria monocytogenes has proven to be reliable and fast. This study determined the MLVA genotypes of 60 isolates of L. monocytogenes recovered from cattle farms, abattoirs, and retail outlets in Gauteng province, South Africa. The distribution of the 60 L. monocytogenes isolates analyzed by type of sample was as follows: raw beef (28, 46.7%), ready-to-eat beef products (9, 15.0%), beef carcass swabs (9, 15.0%), cattle environment (6, 10.0%), and cattle feces (8, 13.3%). The serogroups of the isolates were determined using PCR and the MLVA genotypes based on six selected loci. The frequency of the 60 serogroups detected was as follows: 1/2a-3a (IIa) (27, 45.0%); 4b-4d-4e (1Vb) (24, 40.0%); 1/2c-3c (IIc) (8, 13.3%); and 1/2b-3b (IIb) (1, 1.7%). MLVA successfully clustered genetically related isolates and differentiated nonrelated isolates, irrespective of their sources, sample types, and serogroups, as demonstrated by 16 MLVA pattern types detected. For serogroup 4b-4d-4e (IVb), there was no variation in TRs LM-TR2, LM-TR4, and LM-TR6, which each contained only one allele (02, 00, and 93, respectively). However, across the sources and sample types of isolates, there was variation in serogroup 4b-4d-4e (IVb): LM-TR1 contained 00, 03, and 05; LM-TR3 contained 14, 20, and 22; and LM-TR5 contained 14, 21, and 25. Similar patterns of variation in the TRs were detected in the other serogroups (1/2a-3a, 1/2b-3b, and 1/2c-3c). BioNumeric data analysis identified at least five types in Gauteng province. MLVA epidemiologically clustered the related isolates and differentiated unrelated isolates. HIGHLIGHTS
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Affiliation(s)
- James Gana
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa.,Department of Agricultural Education, Federal College of Education, Kontagora, Niger State, Nigeria
| | - Nomakorinte Gcebe
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, South Africa
| | - Rian Pierneef
- Agricultural Research Council-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
| | - Rebone Moerane
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Abiodun A Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa.,Department of Paraclinical Sciences, School of Veterinary Medicine, The University of West Indies, St. Augustine, Trinidad and Tobago
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Arabzadeh B, Ahmadi Z, Ranjbar R. Molecular Characterization of Antibiotic Resistance and Genetic Diversity of Klebsiella pneumoniae Strains. Canadian Journal of Infectious Diseases and Medical Microbiology 2022; 2022:1-7. [PMID: 35774246 PMCID: PMC9239796 DOI: 10.1155/2022/2156726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/13/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022]
Abstract
The aims of this study were the molecular characterization of antibiotic resistance and genotyping of Klebsiella pneumoniae strains isolated from clinical cases in Tehran, Iran. A total of 100 different types of clinical human samples were collected from a major teaching hospital in Tehran, Iran. Bacterial isolates were identified using standard microbiological tests. Antimicrobial susceptibility testing was done according to the latest CLSI guidelines. PCR was used to amplify the gyrA gene in quinolone-resistant isolates and sequencing was performed for the detection of probable mutations between the isolates. The occurrence of plasmid-mediated quinolone resistance genes (qnrA, qnrB, and qnrS) was also investigated by PCR. Finally, genotyping of the strains was performed by PFGE in a standard condition. The susceptibility pattern revealed a high and low level of resistance against meropenem (20%) and trimethoprim (37%), respectively. PCR and sequencing detected mutation in the gyrA gene in 51% of quinolone-resistant K. pneumoniae. According to the susceptibility report, among nalidixic acid-resistant strains, 60.5%, 50%, and 42.9% of isolates contained qnrA, qnrB, and qnrS, respectively. Among ciprofloxacin-resistant strains, qnrA was the most frequent PMQR gene. The PFGE differentiated the strains into 31 different genetic clusters so that the highest number (7/66) was in category A. Our results indicated that the frequency of resistance to various antibiotics particularly trimethoprim, nalidixic acid, and cefoxitin are increasing. The presence of qnr (S and A) genes and point mutation of the gyrA gene were likely to be responsible for the resistance toward nalidixic acid and ciprofloxacin in our strains. Also, the results obtained from genotyping indicated that the K. pneumoniae strains isolated in this study belonged to the diverse clones.
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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Bhattacharjee R, Nandi A, Mitra P, Saha K, Patel P, Jha E, Panda PK, Singh SK, Dutt A, Mishra YK, Verma SK, Suar M. Theragnostic application of nanoparticle and CRISPR against food-borne multi-drug resistant pathogens. Mater Today Bio 2022; 15:100291. [PMID: 35711292 PMCID: PMC9194658 DOI: 10.1016/j.mtbio.2022.100291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/25/2022] Open
Abstract
Foodborne infection is one of the leading sources of infections spreading across the world. Foodborne pathogens are recognized as multidrug-resistant (MDR) pathogens posing a significant problem in the food industry and healthy consumers resulting in enhanced economic burden, and nosocomial infections. The continued search for enhanced microbial detection tools has piqued the interest of the CRISPR-Cas system and Nanoparticles. CRISPR-Cas system is present in the bacterial genome of some prokaryotes and is repurposed as a theragnostic tool against MDR pathogens. Nanoparticles and composites have also emerged as an efficient tool in theragnostic applications against MDR pathogens. The diagnostic limitations of the CRISPR-Cas system are believed to be overcome by a synergistic combination of the nanoparticles system and CRISPR-Cas using nanoparticles as vehicles. In this review, we have discussed the diagnostic application of CRISPR-Cas technologies along with their potential usage in applications like phage resistance, phage vaccination, strain typing, genome editing, and antimicrobial. we have also elucidated the antimicrobial and detection role of nanoparticles against foodborne MDR pathogens. Moreover, the novel combinatorial approach of CRISPR-Cas and nanoparticles for their synergistic effects in pathogen clearance and drug delivery vehicles has also been discussed. Bacterial CRISPR Cas system are repurposed as a thergodiganostic tool against MDR pathogen. Combinatorial approach of CRISPR-Cas and Nanoparticle is used as delivery vehicle and clearing pathogens. CRISPR-Cas and Nanoparticles is a tool for the food safety profiling of MDR food-borne pathogen.
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Affiliation(s)
- Rahul Bhattacharjee
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Aditya Nandi
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Priya Mitra
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Koustav Saha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Paritosh Patel
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Ealisha Jha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
- Corresponding author.
| | - Sushil Kumar Singh
- DBT- NECAB, Department of Agricultural Biotechnology, Assam Agriculture University, Jorhat, 785013, Assam, India
| | - Ateet Dutt
- Instituto de Investigaciones en Materiales, UNAM, CDMX, Mexico
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alsion 2, DK-6400, Sønderborg, Denmark
- Corresponding author.
| | - Suresh K. Verma
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
- Corresponding author. KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India.
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
- Corresponding author.
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Ramatla T, Tawana M, Onyiche TE, Lekota KE, Thekisoe O, Callaway TR. One Health Perspective of Salmonella Serovars in South Africa Using Pooled Prevalence: Systematic Review and Meta-Analysis. Int J Microbiol 2022; 2022:1-12. [PMID: 35498396 PMCID: PMC9046003 DOI: 10.1155/2022/8952669] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/12/2022] [Accepted: 04/01/2022] [Indexed: 11/18/2022] Open
Abstract
Salmonella is a bacterium that is commonly associated with food-borne infections and is regarded as one of the most important pathogens in public health. Salmonella serovars, particularly Typhimurium and Enteritidis, which are widely distributed globally, mainly result in outbreaks commonly linked to the consumption of animal products. This study is a systematic review and meta-analysis of studies reporting the prevalence of Salmonella serovars from one health perspective that included human, environmental, and animal samples in South Africa. PubMed, ScienceDirect, African Journals Online, and Scopus databases were used to conduct extensive searches of articles which were ultimately included or excluded following the Systematic Reviews and Meta-Analysis (PRISMA) guidelines. According to the data obtained in this review, the overall pooled prevalence estimates (PPE) of Salmonella serovars detection were 79.6%, 61.6%, 56.5%, and 43.2% for human, environment, animal, and environment/animal samples in South Africa, respectively. The majority of the studies (50%) used the polymerase chain reaction (PCR) technique for the detection of Salmonella serovars, followed by culture methods (26.7%), while 20% used serotyping. The PPE for nontyphoidal Salmonellae (NTS) was 65.6% and 34.4% for Salmonella Typhimurium and Salmonella Enteritidis, respectively. Our data further shows that 3 serovars, namely, Salmonella Typhimurium, Salmonella Enteriditis, and Salmonella Hadar, have been isolated from animals, humans, and the environment in South Africa. Our results highlight the ongoing spread of Salmonella spp. especially on animals which might end up infecting humans via direct contact with infected animals or eating infected animal products. This calls for deliberate “One Health” epidemiological studies in order to document information on the transmission between humans, animals, and the environment. This will ultimately result in the formulation of a consolidated salmonellosis control policy by the environmental, human, and veterinary health sectors.
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Aghamohammad S, Nikbin VS, Badmasti F, Shahcheraghi F. High heterogeneity of fecal carriage extended-spectrum beta-lactamase-producing E. coli isolated from iranian community and clinical settings. BMC Infect Dis 2022; 22:318. [PMID: 35361158 PMCID: PMC8973555 DOI: 10.1186/s12879-022-07304-7] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/23/2022] [Indexed: 11/21/2022] Open
Abstract
Background Extended-spectrum beta-lactamase-producing enterobacteria (ESBL-PE) in carriers have become a global health problem. Using molecular typing techniques, including PFGE, could be useful to determine the source of bacterial dissemination. The current study aimed to investigate the intestinal carriage of ESBL-producing E. coli (ESBL-EC) and clonal relatedness among ESBL-EC isolated from hospitalized and outpatient fecal carriers in Iran. Methods A total of 120 rectal swabs were collected; 50.8% (61/120) from intensive care unit (ICU) inpatients and 49.2% (59/120) from outpatients. MacConkey agar enriched with cefotaxime was used to screen the ESBL-EC. PCR assays were performed to detect ESBL and carbapenemase genes. Pulse-fields gel electrophoresis (PFGE) was performed to assess clonal relatedness. Results Totally, 60.0% (72/120) were carrier for ESBL-EC. The rates of resistance against ceftazidime and cefepime were 90.2% (65/72) and 93.0% (67/72), respectively. The rates of blaCTX-M-15, blaTEM, blaSHV, blaNDM-1, blaOXA-48 and blaIMP was 90.2% (65/72), 50.0% (36/72), 5.5% (4/72), 4.1% (3/72), 4.1% (3/72) and 1.3% (1/72), respectively. Based on a cut-off 80%, 69 ESBL-EC isolates could be categorized in 10 mini-cluster and 47 isolates were considered as singletons. Discussion High heterogeneity among isolates from ESBL-EC suggests that this bacterium probably has a different source of dissemination. Screening of carriers in hospitals and communities could help the infection control program in public health. Supplementary information The online version contains supplementary material available at 10.1186/s12879-022-07304-7.
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Affiliation(s)
| | | | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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Kontopodi E, Hettinga K, Stahl B, van Goudoever JB, M van Elburg R. Testing the effects of processing on donor human Milk: Analytical methods. Food Chem 2022; 373:131413. [PMID: 34700038 DOI: 10.1016/j.foodchem.2021.131413] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 01/01/2023]
Abstract
Holder pasteurization is the current recommended method for donor human milk treatment. This method effectively eliminates most life-threatening contaminants in donor milk, but it also greatly reduces some of its biological properties. Consequently, there is a growing interest for developing novel processing methods that can ensure both microbial inactivation and a higher retention of the functional components of donor milk. Our aim was to offer a comprehensive overview of the analytical techniques available for the evaluation of such methods. To suggest an efficient workflow for the analysis of processed donor milk, a safety analytical panel as well as a nutritional value and functionality analytical panel are discussed, together with the principles, benefits, and drawbacks of the available techniques. Concluding on the suitability of a novel method requires a multifactorial approach which can be achieved by a combination of analytical targets and by using complementary assays to cross-validate the obtained results.
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Affiliation(s)
- Eva Kontopodi
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Human Milk Bank, Amsterdam, the Netherlands; Food Quality and Design Group, Wageningen University & Research, the Netherlands.
| | - Kasper Hettinga
- Food Quality and Design Group, Wageningen University & Research, the Netherlands
| | - Bernd Stahl
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands; Danone Nutricia Research, Utrecht, the Netherlands
| | - Johannes B van Goudoever
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Human Milk Bank, Amsterdam, the Netherlands
| | - Ruurd M van Elburg
- Amsterdam UMC, University of Amsterdam, Vrije Universiteit, Emma Children's Hospital, Human Milk Bank, Amsterdam, the Netherlands
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Shi D, Shi H. Combining loop-mediated isothermal amplification and nanozyme-strip for ultrasensitive and rapid detection of viable Listeria monocytogenes cells and biofilms. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Morsi H, Golizeh M, Brosseau N, Janati AI, Emami E, Ndao M, Tran SD. Detection of Fusobacterium nucleatum subspecies in the saliva of pre-colorectal cancer patients, using tandem mass spectrometry. Arch Oral Biol 2021; 134:105337. [PMID: 34929558 DOI: 10.1016/j.archoralbio.2021.105337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/25/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rising evidence links Fusobacterium nucleatum (F. nucleatum) with its four subspecies; nucleatum, polymorphum, animalis, and vincentii, with the development of colorectal cancer (CRC) and its precursor colorectal adenoma (CRA). This study aims to optimize a technique for and explore the capability of matrix-assisted laser-desorption ionization-tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS) to detect F. nucleatum subspecies directly from the saliva samples of CRA patients and controls without preculturing. DESIGN Saliva samples were collected from four CRA patients and eight controls. Proteins were extracted and subjected to solid-phase extraction fractionation, enzymatically digested, and analyzed by MALDI-TOF/TOF MS. F. nucleatum subspecies strains were cultured and used as a positive control. RESULTS A proteomics approach was developed to identify F. nucleatum subspecies directly from saliva samples. With this approach, the bacterial culturing step, which could take up to seven days, was bypassed. Overall, 157 F. nucleatum subspecies proteins were detected in the saliva samples. F. nucleatum subsp. nucleatum was absent in the patients while detected in half of the controls. CONCLUSION This study presents a novel technique for detecting F. nucleatum subspecies from saliva specimens that could later be employed to better understand a potential role of those subspecies in CRC development.
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Sophian A, Purwaningsih R, Muindar M, Igirisa EPJ, Amirullah ML. Use of Direct PCR Technique Without DNA Extraction in Confirmation Test for Salmonella typhimurium Bacteria on Meatball Samples. Borneo J Pharm 2021. [DOI: 10.33084/bjop.v4i4.2187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of direct PCR technique without DNA extraction in the confirmation test for Salmonella typhimurium ATCC 14028 bacteria on meatball samples was carried out in the Food and Drug molecular biology testing laboratory Administration in Gorontalo. The basis of this research is to have an impact on economic value in carrying out the confirmation test for S. typhimurium ATCC 14028, where testing is carried out conventionally, namely DNA extraction, which requires a large amount of money. Hence, it is necessary to innovate to modify the testing phase so that it is more effective and efficient. The purpose of this study was to see whether the direct PCR technique without DNA extraction can be done for the confirmation test of S. typhimurium ATCC 14028 on meatball samples. This study's sample consisted of 20 types of meatball samples spiked with S. typhimurium ATCC 14028 cultures. The method used in this study was qPCR analysis using the SYBR Green method. Data analysis was carried out based on 2 main criteria: (1) Ct analysis and (2) Tm analysis. Real-time PCR analysis results obtained Ct values in the range 14.14 - 15.20 with an average of 14.82 and Tm values 85.20 - 86.30 with an average of 85.79. Based on these data, it can be concluded that using direct PCR can be used for testing confirmation of S. typhimurium ATCC 14028 on meatball samples.
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Affiliation(s)
- Alfi Sophian
- National Agency of Drug and Food Control of Republic of Indonesia
| | | | - Muindar Muindar
- National Agency of Drug and Food Control of Republic of Indonesia in Gorontalo
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Buszewski B, Maślak E, Złoch M, Railean-Plugaru V, Kłodzińska E, Pomastowski P. A new approach to identifying pathogens, with particular regard to viruses, based on capillary electrophoresis and other analytical techniques. Trends Analyt Chem 2021; 139:116250. [PMID: 34776563 PMCID: PMC8573725 DOI: 10.1016/j.trac.2021.116250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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] [Indexed: 12/26/2022]
Abstract
Fast determination, identification and characterization of pathogens is a significant challenge in many fields, from industry to medicine. Standard approaches (e.g., culture media and biochemical tests) are known to be very time-consuming and labor-intensive. Conversely, screening techniques demand a quick and low-cost grouping of microbial isolates, and current analysis call for broad reports of pathogens, involving the application of molecular, microscopy, and electromigration techniques, DNA fingerprinting and also MALDI-TOF methods. The present COVID-19 pandemic is a crisis that affects rich and poor countries alike. Detection of SARS-CoV-2 in patient samples is a critical tool for monitoring disease spread, guiding therapeutic decisions and devising social distancing protocols. The goal of this review is to present an innovative methodology based on preparative separation of pathogens by electromigration techniques in combination with simultaneous analysis of the proteome, lipidome, and genome using laser desorption/ionization analysis.
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Affiliation(s)
- Bogusław Buszewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland.,Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland.,Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Viorica Railean-Plugaru
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
| | - Ewa Kłodzińska
- Institute of Sport - National Research Institute, Department of Analytical Chemistry and Instrumental Analysis, 01-982, Warsaw, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 87-100, Torun, Poland
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25
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Norouz Dizaji A, Ali Z, Ghorbanpoor H, Ozturk Y, Akcakoca I, Avci H, Dogan Guzel F. Electrochemical-based ''antibiotsensor'' for the whole-cell detection of the vancomycin-susceptible bacteria. Talanta 2021; 234:122695. [PMID: 34364491 DOI: 10.1016/j.talanta.2021.122695] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/04/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022]
Abstract
In this study, we aim to develop an antibiotic-based biosensor platform 'Antibiotsensor' for the specific detection of gram-positive bacteria using vancomycin modified Screen Printed Gold Electrodes (SPGEs). Through this pathway, vancomycin molecules were first functionalized with thiol groups and characterized with quadrupole time of flight (q-TOF) mass spectroscopy analysis. Immobilization of thiolated vancomycin molecules (HS-Van) onto SPGEs was carried out based on self-assembled monolayer (SAM) phenomenon. Electrochemical impedance spectroscopy (EIS) was employed to test the detection and showed a considerable change in impedance value upon the binding of HS-Van molecules onto the electrode surface. Atomic Force Microscopy analysis indicated that SPGE was successfully modified upon the treatment with HS-Van molecules based on the shift in surface roughness from 173 ± 2 nm to 301 ± 3 nm. Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy proved the EIS and AFM results as well by showing characteristic peaks of immobilized HS-Van molecule. As a proof-of-concept, EIS-based susceptibility testing was performed using Escherichia coli, Staphylococcus aureus and Mycobacterium smegmatis bacteria to prove the specificity of obtained SPGE-Van. EIS data showed that the charge transfer resistance (Rct) values changed from 1.08, 1.18 to 26.5, respectively, indicating that vancomycin susceptible S. aureus was successfully attached onto SPGE-Van surface strongly, while vancomycin resistance E. coli and M. smegmatis did not show any significant attachment properties. In addition, different concentration (108-10 CFU/mL) of S. aureus was performed to investigate sensitivity of proposed sensor platform. Limit of detection and limit of quantitation was calculated as 101.58 and 104.81 CFU/mL, respectively. Scanning electron microscopy (SEM) analysis also confirmed that only S. aureus bacteria was attached to the surface in a dense monolayer distribution. We believe that the proposed approach is selective and sensitive towards the whole-cell detection of vancomycin-susceptible bacteria and can be modified for different purposes in the future.
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Affiliation(s)
- Araz Norouz Dizaji
- Department of Biomedical Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Zahraa Ali
- Department of Material Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Hamed Ghorbanpoor
- Department of Biomedical Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey; Department of Biomedical Engineering, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Yasin Ozturk
- Department of Material Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Iremnur Akcakoca
- Department of Material Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Huseyin Avci
- Department of Metallurgical and Materials Engineering & Cellular Therapy and Stem Cell Research Center, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Fatma Dogan Guzel
- Department of Biomedical Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey.
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26
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Gupta Y, Ghrera AS. Recent advances in gold nanoparticle-based lateral flow immunoassay for the detection of bacterial infection. Arch Microbiol 2021; 203:3767-3784. [PMID: 34086107 DOI: 10.1007/s00203-021-02357-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 01/11/2021] [Revised: 04/24/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022]
Abstract
Diagnosis of bacterial infections (BI) is becoming an increasingly difficult task in clinical practice due to their high prevalence and frequency, as well as the growth of antibiotic resistance worldwide. World Health Organization (WHO) reported antibiotic resistance is a major public health problem. BI becomes difficult or impossible to treat when the bacteria acquire immunity against antibiotics. Thus, there is a need for a quick and accurate technique to detect infection. Lateral flow immunoassay (LFIA) is an ideal technique for point-of-care testing of a disease or pathological changes inside the human body. In recent years, several LFIA based strips are being used for the detection of BI by targeting specific analytes which may range from the causative bacterium, whole-cell, DNA, or biomarker. Numerous nanoparticles like lipid-based nanoparticles, polymeric nanoparticles, and inorganic nanoparticles such as quantum dots, magnetic, ceramic, and metallic nanoparticles (copper, silver gold, iron) are widely being used in the advanced treatment of BI. Out of these gold nanoparticle (AuNPs), is being used for detection BI more effectively than other nanoparticles due to their surface functionalization, extraordinary chemical stability, biorecognition, and signal amplification properties and help to improve in conjugation with capture antibodies, and act as a color marker with unique optical properties on LFIA strips. Herein, a review that provides an overview of the principle of LFIA, how LFIA based strip is developed, and how it is helpful to detect a specific biomarker for bedside detection of the BI.
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Affiliation(s)
- Yachana Gupta
- Applied Science Department, The NorthCap University, Gurugram, India
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27
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Lu X, Chow JJM, Koo SH, Jiang B, Tan TY, Yang D, Ai Y. Sheathless and high-throughput elasto-inertial bacterial sorting for enhancing molecular diagnosis of bloodstream infection. Lab Chip 2021; 21:2163-2177. [PMID: 33899072 DOI: 10.1039/d1lc00085c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Purification of bacteria from human blood samples is essential for rapid identification of pathogens by molecular methods, enabling faster and more accurate diagnosis of bloodstream infection than conventional gold standard blood culture methods. The inertial microfluidic method has been broadly studied to isolate biological cells of interest in various biomedical applications due to its label-free and high-throughput advantages. However, because of the bacteria's tininess, which ranges from 0.5 μm to 3 μm, they are challenging to be effectively focused and sorted out in existing inertial microfluidic devices that work well with biological cells larger than 10 μm. Efforts have been made to sort bacterial cells by utilizing extremely small channel dimensions or employing a sheath flow, which thus results in limitations on the throughput and ease of operation. To overcome this challenge, we develop a method that integrates a non-Newtonian fluid with a novel channel design to allow bacteria to be successfully sorted from larger blood cells in a channel dimension of 120 μm × 20 μm without the use of sheath flows. The throughput of this device with four parallel channels is above 400 μL per minute. The real-time polymerase chain reaction (qPCR) analysis indicates that our inertial sorting approach has a nearly 3-fold improvement in pathogen recovery compared with the commonly used lysis-centrifugation method at pathogen abundances as low as 102 cfu mL-1. With the rapid and simple purification and enrichment of bacterial pathogens, the present inertial sorting method exhibits an ability to enhance the fast and accurate molecular diagnosis of bloodstream bacterial infection.
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Affiliation(s)
- Xiaoguang Lu
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore 487372, Singapore.
| | - Joycelyn Jia Ming Chow
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore 487372, Singapore.
| | - Seok Hwee Koo
- Clinical Trials & Research Unit, Changi General Hospital, Singapore 529889, Singapore
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, Singapore 529889, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, Singapore 529889, Singapore
| | - Dahou Yang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore 487372, Singapore.
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore 487372, Singapore.
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Mafiana MO, Kang XH, Leng Y, He LF, Li SW. Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria. Environ Sci Pollut Res Int 2021; 28:31447-31461. [PMID: 33604834 DOI: 10.1007/s11356-021-12955-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 10/20/2020] [Accepted: 02/10/2021] [Indexed: 05/25/2023]
Abstract
Soil microbial community structure is altered by petroleum contamination in response to compound toxicity and degradation. Understanding the relation between petroleum contamination and soil microbial community structure is crucial to determine the amenability of contaminated soils to bacterial- and fungal-aided remediation. To understand how petroleum contamination and soil physicochemical properties jointly shaped the microbial structure of soils from different oilfields, high-throughput sequencing of 16S and ITS amplicons were used to evaluate the shifts of microbial communities in the petroleum-contaminated soils in Ughelli East (UE), Utorogu (UT), and Ughelli West (UW) oilfields located in Delta State, Nigeria. The results showed 1515 bacteria and 919 fungal average OTU number, and community richness and diversity, trending as AL > UT > UW > UE and AL > UW > UT > UE for bacteria, and AL > UW > UT > UE and UW > UT > AL > UE for fungi, respectively. The bacterial taxa KCM-B-112, unclassified Saccharibacteria, unclassified Rhizobiales, Desulfurellaceae, and Acidobacteriaceae and fungal Trichocomaceae, unclassified Ascomycota, unclassified Sporidiobolales, and unclassified Fungi were found to be the dominant families in petroleum-contaminated soils. Redundancy analysis (RDA) and Spearman's correlation analysis revealed that total carbon (TC), electric conductivity (EC), pH, and moisture content (MO) were the major drivers of bacterial and fungal communities, respectively. Gas chromatography-mass spectrophotometer (GC-MS) analysis exhibited that the differences in C7-C10, C11-C16, and C12-C29 compounds in the crude oil composition and soil MO content jointly constituted the microbial community variance among the contaminated soils. This study revealed the bacterial and fungal communities responsible for the biodegradation of petroleum contamination from these oilfields, which could serve as biomarkers to monitor oil spill site restoration within these areas. Further studies on these contaminated sites could offer useful insights into other contributing factors such as heavy metals.
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Affiliation(s)
- Macdonald Ogorm Mafiana
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, 730070, Lanzhou, People's Republic of China.
| | - Xiao-Hu Kang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, 730070, Lanzhou, People's Republic of China
| | - Yan Leng
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, 730070, Lanzhou, People's Republic of China
| | - Li-Fang He
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, 730070, Lanzhou, People's Republic of China
| | - Shi-Weng Li
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, 730070, Lanzhou, People's Republic of China.
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29
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S P Galhano B, G Ferrari R, Panzenhagen P, S de Jesus AC, A Conte-Junior C. Antimicrobial Resistance Gene Detection Methods for Bacteria in Animal-Based Foods: A Brief Review of Highlights and Advantages. Microorganisms 2021; 9:923. [PMID: 33925810 DOI: 10.3390/microorganisms9050923] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial resistance is a major public health problem and is mainly due to the indiscriminate use of antimicrobials in human and veterinary medicine. The consumption of animal-based foods can contribute to the transfer of these genes between animal and human bacteria. Resistant and multi-resistant bacteria such as Salmonella spp. and Campylobacter spp. have been detected both in animal-based foods and in production environments such as farms, industries and slaughterhouses. This review aims to compile the techniques for detecting antimicrobial resistance using traditional and molecular methods, highlighting their advantages and disadvantages as well as the effectiveness and confidence of their results.
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31
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Abdel-Rhman SH, Rizk DE. Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates. Infect Drug Resist 2021; 14:1019-1035. [PMID: 33762830 PMCID: PMC7982794 DOI: 10.2147/idr.s298838] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/20/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Pseudomonas aeruginosa is one of the important causes of nosocomial infections. Analyzing the diversity of these isolates is important to control the diseases caused by them. Studies of molecular epidemiology depend on the application of typing methods. Purpose This study aims to assess the performance of PCR- based typing techniques (RAPD, ribotyping, tDNA, and ERIC) in determining the genetic diversity of 44 P. aeruginosa urinary isolates. Methods Performance parameters were analyzed for each of the tested methods. The banding pattern was assessed by calculating polymorphism, genotypic gene diversity and the effective multiplex ratio. Moreover, strain diversity, typeability, and discriminatory power were used to measure the efficiency of typing methods. The congruence among typing methods was calculated by Rand’s and Wallace coefficients. Results P-640 among RAPD primers and Ribo-2 among ribotyping primers were more informative as they gave high strain diversity, the highest number of clusters, and highest discriminatory power (ISD=70.45%, 29 clusters at 70% cutoff, DI=0.97 and ISD=75%, 25 clusters at 70% cutoff DI=0.969, respectively). Comparison of typing methods showed that RAPD-PCR gave the highest mean percent polymorphism per assay (76.85%) followed by ERIC-PCR. ERIC-PCR outperformed in most marker parameters; highest mean number of alleles, number of monomorphic bands per assay unit, mean genotypic gene diversity, effective multiplex ratio, and assay efficiency index. Calculated congruence revealed that individual methods demonstrate moderate to poor predictive power. Interestingly, this power increased by combining data obtained from another method. Conclusion RAPD primer (P-640) had more discrimination power followed by ribo-2 and ERIC. The performance and predictive power of typing methods can be improved by combining data obtained from different methods as ERIC+OPA-02 and ERIC+P-640 combinations gave complete typeability and discrimination of isolates. ERIC, ERIC+OPA-02, and ERIC+P-640 combinations can provide finer discrimination and classification of P. aeruginosa strains than the other tested methods.
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Affiliation(s)
- Shaymaa H Abdel-Rhman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Pharmaceutics and Pharmaceutical Biotechnology, Faculty of Pharmacy, Taibah University, AlMadinah Al Munawwarah, Saudi Arabia
| | - Dina E Rizk
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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32
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Sivaraman G, Muneeb K, Sudha S, Shome B, Holmes M, Cole J. Fish-borne methicillin resistant Staphylococcus haemolyticus carrying atypical staphylococcal cassette chromosome mec (SCCmec) elements. Gene Reports 2021. [DOI: 10.1016/j.genrep.2020.100982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Arreguin-Campos R, Jiménez-Monroy KL, Diliën H, Cleij TJ, van Grinsven B, Eersels K. Imprinted Polymers as Synthetic Receptors in Sensors for Food Safety. Biosensors (Basel) 2021; 11:46. [PMID: 33670184 PMCID: PMC7916965 DOI: 10.3390/bios11020046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 01/08/2023]
Abstract
Foodborne illnesses represent high costs worldwide in terms of medical care and productivity. To ensure safety along the food chain, technologies that help to monitor and improve food preservation have emerged in a multidisciplinary context. These technologies focus on the detection and/or removal of either biological (e.g., bacteria, virus, etc.) or chemical (e.g., drugs and pesticides) safety hazards. Imprinted polymers are synthetic receptors able of recognizing both chemical and biological contaminants. While numerous reviews have focused on the use of these robust materials in extraction and separation applications, little bibliography summarizes the research that has been performed on their coupling to sensing platforms for food safety. The aim of this work is therefore to fill this gap and highlight the multidisciplinary aspects involved in the application of imprinting technology in the whole value chain ranging from IP preparation to integrated sensor systems for the specific recognition and quantification of chemical and microbiological contaminants in food samples.
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Affiliation(s)
| | | | | | | | | | - Kasper Eersels
- Sensor Engineering Department, Faculty of Science and Engineering, Maastricht University, P.O. Box 616,6200 MD Maastricht, The Netherlands; (R.A.-C.); (K.L.J.-M.); (H.D.); (T.J.C.); (B.v.G.)
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Confield LR, Black GP, Wilson BC, Lowe DJ, Theakstone AG, Baker MJ. Vibrational spectroscopic analysis of blood for diagnosis of infections and sepsis: a review of requirements for a rapid diagnostic test. Anal Methods 2021; 13:157-168. [PMID: 33284291 DOI: 10.1039/d0ay01991g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Infections and sepsis represent a growing global burden. There is a widespread clinical need for a rapid, high-throughput and sensitive technique for the diagnosis of infections and detection of invading pathogens and the presence of sepsis. Current diagnostic methods primarily consist of laboratory-based haematology, biochemistry and microbiology that are time consuming, labour- and resource-intensive, and prone to both false positive and false negative results. Current methods are insufficient for the increasing demands on healthcare systems, causing delays in diagnosis and initiation of treatment, due to the intrinsic time delay in sample preparation, measurement, and analysis. Vibrational spectroscopic techniques can overcome these limitations by providing a rapid, label-free and low-cost method for blood analysis, with limited sample preparation required, potentially revolutionising clinical diagnostics by producing actionable results that enable early diagnosis, leading to improved patient outcomes. This review will discuss the challenges associated with the diagnosis of infections and sepsis, primarily within the UK healthcare system. We will consider the clinical potential of spectroscopic point-of-care technologies to enable blood analysis in the primary-care setting.
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Affiliation(s)
- L R Confield
- CDT Medical Devices, Department of Biomedical Engineering, Wolfson Centre, 106 Rottenrow, G4 0NW, UK
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35
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Vishwakarma A, Lal R, Ramya M. Aptamer-based approaches for the detection of waterborne pathogens. Int Microbiol 2021; 24:125-140. [PMID: 33404933 DOI: 10.1007/s10123-020-00154-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 06/12/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.
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Affiliation(s)
- Archana Vishwakarma
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Roshni Lal
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Mohandass Ramya
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India.
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36
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Igwaran A, Okoh AI. Molecular determination of genetic diversity among Campylobacter jejuni and Campylobacter coli isolated from milk, water, and meat samples using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Infect Ecol Epidemiol 2020; 10:1830701. [PMID: 33133420 PMCID: PMC7580821 DOI: 10.1080/20008686.2020.1830701] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Consumption of contaminated meat, milk, and water are among the major routes of human campylobacteriosis. This study aimed to determined the genetic diversity of C. coli and C. jejuni isolated from meat, milk, and water samples collected from different locations. From the 376 samples (meat = 248, cow milk = 72, and water = 56) collected, a total of 1238 presumptive Campylobacter isolates were recovered and the presence of the genus Campylobacter were detected in 402 isolates, and from which, 85 and 67 isolates were identified asC. jejuni and C. coli respectively. Of which, 71 isolates identified as C. coli (n = 35) and C. jejuni (n = 36) were randomly selected from meat, milk, and water samples and were genotyped using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). The digital images of the ERIC-PCR genotype were analyzed by GelJ v.2.0 software. The diversity and similarity of the isolates were assessed via an unweighted-pair group method using average linkages clustering algorithm. The results showed that the 36 C. jejuni strains separated into 29 ERIC-genotypes and 4 clusters while the 35 C. coli were delineated into 29 ERIC-genotypes and 6 clusters. The study revealed the genetic diversity among C. coli and C. jejuni strains recovered from different matrices characterized by Gelj.
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Affiliation(s)
- Aboi Igwaran
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa.,Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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37
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Redelinghuys MJ, Geldenhuys J, Jung H, Kock MM. Bacterial Vaginosis: Current Diagnostic Avenues and Future Opportunities. Front Cell Infect Microbiol 2020; 10:354. [PMID: 32850469 PMCID: PMC7431474 DOI: 10.3389/fcimb.2020.00354] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
A healthy female genital tract harbors a microbiome dominated by lactic acid and hydrogen peroxide producing bacteria, which provide protection against infections by maintaining a low pH. Changes in the bacterial compositions of the vaginal microbiome can lead to bacterial vaginosis (BV), which is often associated with vaginal inflammation. Bacterial vaginosis increases the risk of acquiring sexually transmitted infections (STIs) like human immunodeficiency virus (HIV) and affects women's reproductive health negatively. In pregnant women, BV can lead to chorioamnionitis and adverse pregnancy outcomes, including preterm premature rupture of the membranes and preterm birth. In order to manage BV effectively, good diagnostic procedures are required. Traditionally clinical and microscopic methods have been used to diagnose BV; however, these methods require skilled staff and time and suffer from reduced sensitivity and specificity. New diagnostics, including highly sensitive and specific point-of-care (POC) tests, treatment modalities and vaccines can be developed based on the identification of biomarkers from the growing pool of vaginal microbiome and vaginal metabolome data. In this review the current and future diagnostic avenues will be discussed.
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Affiliation(s)
- Mathys J. Redelinghuys
- School of Clinical Medicine, Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Janri Geldenhuys
- UP-Ampath Translational Genomics Initiative, Department of Biochemistry, Genetics and Microbiology, Faculty of Health Sciences and Faculty of Natural and Agricultural Sciences, Division of Genetics, University of Pretoria, Pretoria, South Africa
| | - Hyunsul Jung
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Marleen M. Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
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Jeong OM, Kang MS, Blackall PJ, Jeon BW, Kim JH, Jeong J, Lee HJ, Kim DW, Kwon YK, Kim JH. Genotypic divergence of Avibacterium paragallinarum isolates with different growth requirements for nicotinamide adenine dinucleotide. Avian Pathol 2019; 49:153-160. [PMID: 31709803 DOI: 10.1080/03079457.2019.1692128] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In 2017, for the first time in Asia, we reported the isolation of variants of Avibacterium paragallinarum with atypical NAD dependency. The present study was conducted to characterize the genotypes of 24 isolates of Av. paragallinarum in Korea, including the four variants reported previously. Most of the typical isolates (19/20) showed a unique ERIC-PCR pattern with no ERIC-PCR patterns in common between the typical isolates and the variants. Furthermore, the variants shared no ERIC-PCR patterns among themselves. All the typical NAD-dependent isolates belonged to the same phylogenetic group based on both 16S rRNA and hagA gene sequences. The four variants were placed in several groups distinct from the typical isolates. In the 16S rRNA phylogenetic analysis, two of the variants were not closely aligned to any other Av. paragallinarum, isolate although they were clearly members of the genus Avibacterium. The other variants were clustered together with NAD atypical isolates from geographically diverse global locations. Compared with the Modesto reference strain AY498870, all the variants lacked a TTTTT stretch at positions 182-186 in the 16S rRNA gene and the same deletion was shown in most of the reported variants. The typical isolates and variants shared 97.3-98.2% and 95.2-97.2% nucleotide sequence similarity, for 16S rRNA and hagA, respectively. In addition, the similarities among variants were within 98.3-100% and 96.5-98.4% for the two genes, respectively. Our results indicate that the Av. paragallinarum variants with altered NAD growth requirements were genetically different and highly divergent from the typical NAD-dependent isolates.RESEARCH HIGHLIGHTS NAD variant Korean Av. paragallinarum isolates show genetic diversity, whereas typical Korean Av. paragallinarum isolates do not.The Korean variants were not closely aligned to all other Av. paragallinarum in the 16S rRNA phylogeny.NAD atypical isolates from geographically diverse global locations clustered together.Almost all variants, including all Korean variants of Av. paragallinarum, lack a specific fragment of the 16S rRNA gene.
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Affiliation(s)
- Ok-Mi Jeong
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Min-Su Kang
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, the University of Queensland, St Lucia, Australia
| | - Byung-Woo Jeon
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Jin-Hyun Kim
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Jiyeon Jeong
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hye-Jin Lee
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong-Wan Kim
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Yong-Kuk Kwon
- Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Jae-Hong Kim
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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Huayhongthong S, Khuntayaporn P, Thirapanmethee K, Wanapaisan P, Chomnawang MT. Raman spectroscopic analysis of food-borne microorganisms. Lebensm Wiss Technol 2019; 114:108419. [DOI: 10.1016/j.lwt.2019.108419] [Citation(s) in RCA: 13] [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: 11/21/2022]
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Rajapaksha P, Elbourne A, Gangadoo S, Brown R, Cozzolino D, Chapman J. A review of methods for the detection of pathogenic microorganisms. Analyst 2019; 144:396-411. [PMID: 30468217 DOI: 10.1039/c8an01488d] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The testing and rapid detection of pathogenic organisms is a crucial protocol in the prevention and identification of crises related to health, safety and wellbeing. Pathogen detection has become one of the most challenging aspects in the food and water industries, because of the rapid spread of waterborne and foodborne diseases in the community and at significant costs. With the prospect of inevitable population growth, and an influx of tourism to certain water bodies testing will become a requirement to control and prevent possible outbreaks of potentially fatal illnesses. The legislation is already particularly rigorous in the food industry, where failure to detect pathogenic materials represents a catastrophic event, particularly for the elderly, very young or immune-compromised population types. In spite of the need and requirement for rapid analytical testing, conventional and standard bacterial detection assays may take up to seven days to yield a result. Given the advent of new technologies, biosensors, chemical knowledge and miniaturisation of instrumentation this timescale is not acceptable. This review presents an opportunity to fill a knowledge gap for an extremely important research area; discussing the main techniques, biology, chemistry, miniaturisation, sensing and the emerging state-of-the-art research and developments for detection of pathogens in food, water, blood and faecal samples.
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Affiliation(s)
- P Rajapaksha
- School of Science, RMIT University, La Trobe Street, Melbourne, 3000, Victoria, Australia.
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Moosavian M, Emam N. The first report of emerging mobilized colistin-resistance ( mcr) genes and ERIC-PCR typing in Escherichia coli and Klebsiella pneumoniae clinical isolates in southwest Iran. Infect Drug Resist 2019; 12:1001-1010. [PMID: 31118706 PMCID: PMC6500874 DOI: 10.2147/idr.s192597] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 11/03/2018] [Accepted: 02/20/2019] [Indexed: 01/11/2023] Open
Abstract
Background: The emergence of the plasmid-mediated mcr colistin-resistance gene in bacteria poses a potential threat for treatment of patients, especially when hospitalized. The aims of this study were to search for the presence of mcr-1 and mcr-2 genes among colistin-resistant Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) isolates from clinical specimens and to determine the fingerprint of strains by enterobacterial repetitive intergenic consensus sequences PCR (ERIC-PCR) method. Methods: In this study, 712 nonduplicate Enterobacteriaceae isolates from clinical specimens were examined. All of the isolates were subcultured on suitable media, and the isolated colonies were identified by standard biochemical tests. Antimicrobial susceptibility test on 7 antibiotics was performed by disk diffusion method, and minimal inhibitory concentration (MIC) of isolates to colistin was determined by the E-test method. These isolates were typed by ERIC-PCR method, and the presence of mcr-1 and mcr-2 genes was investigated by PCR method. Results: Out of 712 nonduplicate Enterobacteriaceae, 470 isolates, including 351 (74.7%) E. coli and 119 (25.3%) K. pneumoniae, were detected. The results of antibiogram tests showed that most of the isolates (81.3%) were resistant to ceftazidime; however, the most susceptibility among of E. coli and K. pneumoniae isolates was observed (81.5%) to colistin. The typing results by ERIC-PCR method showed 36 and 23 fingerprint patterns for colistin-resistant E. coli and K. pneumoniae strains, respectively. Among 64 (13.6%) colistin-phenotypically-resistant Enterobacteriaceae, 8 isolates (1.7%) had mcr-1 gene. These 8 isolates were attributed to E. coli and K. pneumoniae with 6 and 2 isolates, respectively. Whereas no isolates carrying the mcr-2 gene was found. These colistin-resistant isolates displayed colistin MIC values >2 μg/ml in the antibiotic concentration by E-test method. Conclusion: Spreading of Enterobacteriaceae strains harboring plasmid-mediated mcr could fail the colistin-included therapy regimen as the last line of treatment against multidrug-resistant bacterial infections.
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Affiliation(s)
- Mojtaba Moosavian
- Infectious and Tropical Diseases Research Center, Health Research Institue, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nasrin Emam
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Adzitey F, Assoah-Peprah P, Teye GA. Whole-genome sequencing of Escherichia coli isolated from contaminated meat samples collected from the Northern Region of Ghana reveals the presence of multiple antimicrobial resistance genes. J Glob Antimicrob Resist 2019; 18:179-182. [PMID: 30926467 DOI: 10.1016/j.jgar.2019.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES This study reports the draft genomes of 14 Escherichia coli isolated from contaminated meat samples collected from the Northern Region of Ghana in order to determine the presence of antimicrobial resistance genes (ARGs) and genetic relatedness of the isolates. METHODS The 14 E. coli isolates were of beef (n=3), mutton (n=2), chevon (n=3), local chicken (n=3) and guinea fowl (n=3) origin. Whole-genome sequencing (WGS) was performed using an Illumina MiSeq sequencer. Double-disk synergy test (DDST) was also used to confirm the production of extended-spectrum β-lactamase (ESBL). RESULTS WGS confirmed the identity of all of the E. coli isolates. All of the isolates contained at least one ARG and 57.1% (8/14) of them were multidrug-resistant (MDR). The mdf(A) gene was most common ARG, found in all 14 isolates. DDST confirmed the production of an ESBL in a MDR E. coli of guinea fowl origin. The sequence types (STs) varied among the E. coli isolates, with the exception of three isolates of ST155. Similarly, the serotypes of the E. coli isolates from meat sample were genetically diverse. Eleven different plasmid sequences were detected in ten of the isolates. CONCLUSION E. coli from contaminated meat sources in Ghana possessed multiple ARGs and were genetically diverse. To the best of our knowledge, this is the first work on WGS of E. coli isolated from various meat samples in the study area. The sequence data add to data base for epidemiological studies.
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Affiliation(s)
- Frederick Adzitey
- Department of Animal Science, Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana; Department of Veterinary Science, Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana.
| | - Prince Assoah-Peprah
- Department of Veterinary Science, Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana
| | - Gabriel Ayum Teye
- Department of Animal Science, Faculty of Agriculture, University for Development Studies, P.O. Box TL 1882, Tamale, Ghana
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Abstract
The opportunistic pathogen Proteus mirabilis engages in visually dramatic and dynamic social behaviors. Populations of P. mirabilis can rapidly occupy surfaces, such as high-percentage agar and latex, through a collective surface-based motility termed swarming. When in these surface-occupying swarm colonies, P. mirabilis can distinguish between clonal siblings (self) and foreign P. mirabilis strains (nonself). This ability can be assessed by at least two standard methods: boundary formation, aka a Dienes line, and territorial exclusion. Here we describe methods for quantitative analysis of swarm colony expansion, of boundary formation, and of territorial exclusion. These assays can be employed to assess several aspects of P. mirabilis sociality including collective swarm motility, competition, and self versus nonself recognition.
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Affiliation(s)
- Kristin Little
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Karine A Gibbs
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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Rocha R, Sousa JM, Cerqueira L, Vieira MJ, Almeida C, Azevedo NF. Development and application of Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Listeria monocytogenes. Food Microbiol 2018; 80:1-8. [PMID: 30704592 DOI: 10.1016/j.fm.2018.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 02/25/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023]
Abstract
Listeria monocytogenes is one of the most important foodborne pathogens due to the high hospitalization and mortality rates associated to an outbreak. Several new molecular methods that accelerate the identification of L. monocytogenes have been developed, however conventional culture-based methods still remain the gold standard. In this work we developed a novel Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) method for the specific detection of L. monocytogenes. The method was based on an already existing PNA probe, LmPNA1253, coupled with a novel blocker probe in a 1:2 ratio. The method was optimized for the detection of L. monocytogenes in food samples through an evaluation of several rich and selective enrichment broths. The best outcome was achieved using One Broth Listeria in a two-step enrichment of 24 h plus 18 h. For validation in food samples, ground beef, ground pork, milk, lettuce and cooked shrimp were artificially contaminated with two ranges of inoculum: a low level (0.2-2 CFU/25 g or mL) and a high level (2-10 CFU/25 g or mL). The PNA-FISH method performed well in all types of food matrices, presenting an overall accuracy of ≈99% and a detection limit of 0.5 CFU/25 g or mL of food sample.
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Affiliation(s)
- Rui Rocha
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal.
| | - José M Sousa
- BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal
| | - Laura Cerqueira
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal
| | - Maria J Vieira
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carina Almeida
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal; INIAV, IP- National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, 4485-655, Vairão, Vila do Conde, Portugal
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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Jones SL, Ricke SC, Keith Roper D, Gibson KE. Swabbing the surface: critical factors in environmental monitoring and a path towards standardization and improvement. Crit Rev Food Sci Nutr 2018; 60:225-243. [DOI: 10.1080/10408398.2018.1521369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sarah L. Jones
- Department of Food Science, Center for Food Safety, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas, USA
| | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas, USA
| | - D. Keith Roper
- Department of Chemical Engineering, College of Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Kristen E. Gibson
- Department of Food Science, Center for Food Safety, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas, USA
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Mishra A, Narang J, Pundir CS, Pilloton R, Khanuja M. Morphology-Preferable MoSe 2 Nanobrooms as a Sensing Platform for Highly Selective Apta-Capturing of Salmonella Bacteria. ACS Omega 2018; 3:13020-13027. [PMID: 30411026 PMCID: PMC6217589 DOI: 10.1021/acsomega.8b01074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
The present report employed nanobroom (NB)-shaped two-dimensional molybdenum diselenide (MoSe2) for the preparation of a sensing matrix for the detection of Salmonella paratyphi. An aptamer specific to salmonella was immobilized onto MoSe2NB-modified fluorine-doped tin oxide via glutaraldehyde cross-linking. Structural and morphological characterizations were performed using UV-vis spectroscopy, scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction techniques. Characterizations confirmed the nanobroom morphology and nanosize of the MoSe2 material. Electrochemical studies revealed a good linear detection range of 10-2-10-10 CFU/mL with low detection limit of 1 × 10-10 CFU/mL and with R 2 = 0.98. The developed preferable nanobroom-shaped sensing matrix can provide a promising platform for rapid and accurate detection of Salmonella in real samples due to its tremendous stability and sensitivity.
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Affiliation(s)
- Annu Mishra
- Amity
Institute of Nanotechnology, AMITY University, Noida 201303, UP, India
| | - Jagriti Narang
- Amity
Institute of Nanotechnology, AMITY University, Noida 201303, UP, India
| | | | - Roberto Pilloton
- CNR-IC,
Area della Ricerca di RM1, Via Salaria km 29.3, Monterotondo, Rome I-00015, Italy
| | - Manika Khanuja
- Centre
for Nanoscience and Nanotechnology, Jamia
Millia Islamia University, New
Delhi 110025, India
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Staji H, Birgani SF, Raeisian B. Comparative clustering and genotyping of Campylobacter jejuni strains isolated from broiler and turkey feces by using RAPD-PCR and ERIC-PCR analysis. ANN MICROBIOL 2018; 68:755-62. [DOI: 10.1007/s13213-018-1380-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Khamesipour F, Dida GO, Anyona DN, Razavi SM, Rakhshandehroo E. Tick-borne zoonoses in the Order Rickettsiales and Legionellales in Iran: A systematic review. PLoS Negl Trop Dis 2018; 12:e0006722. [PMID: 30204754 PMCID: PMC6181433 DOI: 10.1371/journal.pntd.0006722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 10/11/2018] [Accepted: 07/27/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Tick-borne zoonoses in the Order Rickettsiales and Legionellales cause infections that often manifest as undifferentiated fevers that are not easy to distinguish from other causes of acute febrile illnesses clinically. This is partly attributed to difficulty in laboratory confirmation since convalescent sera, specific diagnostic reagents, and the required expertise may not be readily available. As a result, a number of tick-borne zoonoses are underappreciated resulting in unnecessary morbidity, mortality and huge economic loses. In Iran, a significant proportion of human infectious diseases are tick-borne, with anecdotal evidence suggesting that tick-borne zoonoses are widespread but underreported in the country. Epidemiological review is therefore necessary to aid in the effective control and prevention of tick-borne zonooses in Iran. The aim of this review is to provide an in-depth and comprehensive overview of anaplasmosis, ehrlichiosis, spotted fever group rickettsioses and coxiellosis in Iran. METHODS Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, all relevant publications on tick-borne zoonoses in the Order Rickettsiales and Legionellales in Iran were searched using a number of search terms. The search was confined to authentic resources from repositories of popular data bases among them PubMed, Web of Science, Google Scholar, Science Direct, SpringerLink and SCOPUS. The search items included peer reviewed journals, books and book chapters published between 1996 and 2017. RESULTS A total of 1 205 scientific publications and reports were sourced, of which 63 met the search criteria and were reviewed. Of the 63 articles reviewed, 36 (57.1%) reported on coxiellosis, 15 (23.8%) on anaplasmosis, 11 (17.5%) on ehrlichiosis and 1(1.6%) on spotted fever group rickettsiae in a large scale study involving four countries, among them Iran. The existence of tick-borne pathogens in the Order Rickettsiales and Legionellales was confirmed by molecular, serological and microscopic techniques conducted on samples obtained from sheep, cattle, goats, camels, poultry, animal products (milk and eggs), dogs, ticks and even human subjects in different parts of the country; pointing to a countrywide distribution. DISCUSSION Based on the review, coxiellosis, anaplasmosis, ehrlichiosis, and SFG rickettsiae can be categorized as emerging tick-borne zoonotic diseases in Iran given the presence of their causiative agents (C. burnetii, A. phagocytophilum, A. marginale, A. bovis, A. ovis, A. central, E. canis, E. ewingii, E. chaffeensis and R. conorii) collectively reported in a variety of domestic animals, animal products, arthropods and human beings drawn from 22 provinces in Iran. CONCLUSION Given the asymptomatic nature of some of these zoonoses, there is a high likelihood of silent transmission to humans in many parts of the country, which should be considered a public health concern. Presently, information on the transmission intensity of tick-borne zoonoses caused by pathogens in the Order Rickettsiales and Legionellales to humans and its public health impact in Iran is scanty.
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Affiliation(s)
- Faham Khamesipour
- Cellular and Molecular Research Centre, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Gabriel O. Dida
- School of Public Health and Community Development, Maseno University, Maseno, Kenya
- Department of Community and Public Health, Technical University of Kenya, Nairobi, Kenya
| | - Douglas N. Anyona
- School of Environment and Earth Sciences, Maseno University, Maseno, Kenya
| | - S. Mostafa Razavi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ehsan Rakhshandehroo
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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Alegbeleye OO, Singleton I, Sant'Ana AS. Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review. Food Microbiol 2018; 73:177-208. [PMID: 29526204 PMCID: PMC7127387 DOI: 10.1016/j.fm.2018.01.003] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/31/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
Foodborne illness resulting from the consumption of contaminated fresh produce is a common phenomenon and has severe effects on human health together with severe economic and social impacts. The implications of foodborne diseases associated with fresh produce have urged research into the numerous ways and mechanisms through which pathogens may gain access to produce, thereby compromising microbiological safety. This review provides a background on the various sources and pathways through which pathogenic bacteria contaminate fresh produce; the survival and proliferation of pathogens on fresh produce while growing and potential methods to reduce microbial contamination before harvest. Some of the established bacterial contamination sources include contaminated manure, irrigation water, soil, livestock/ wildlife, and numerous factors influence the incidence, fate, transport, survival and proliferation of pathogens in the wide variety of sources where they are found. Once pathogenic bacteria have been introduced into the growing environment, they can colonize and persist on fresh produce using a variety of mechanisms. Overall, microbiological hazards are significant; therefore, ways to reduce sources of contamination and a deeper understanding of pathogen survival and growth on fresh produce in the field are required to reduce risk to human health and the associated economic consequences.
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Affiliation(s)
| | - Ian Singleton
- School of Applied Sciences, Sighthill Campus, Edinburgh Napier University, Edinburgh, UK
| | - Anderson S Sant'Ana
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil.
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Abstract
OBJECTIVES Listeria monocytogenes is a foodborne pathogenic bacteria causing the infection listeriosis, which possibly affects all people, particularly immunocompromised persons and pregnant women. This microorganism can be found in several processed foods, dairy products, raw milk, meat and fish products, seafoods, eggs, fruits, and vegetables. This review discusses about the epidemiological significance, incidence, contamination routes of L. monocytogenes in different products and current data about listeriosis in the Iran. MATERIALS AND METHODS For accessing to relevant articles and studies, a search was done in main databases and also, almost all Iranian published articles were studied in this field. RESULTS Outbreaks of listeriosis have been reported in many parts of the worldwide, however there is scanty data about the prevalence of listeriosis in Iran. Accordingly, as a result of high incidence of L. monocytogenes in women with bad obstetric history or history of abortions, diagnosis procedures for detection of L. monocytogenes and timely treatment was suggested. CONCLUSION In spite of low incidence of infection in the past, increased interest for lightly preserved and/or ready-to-eat (RTE) food products has recently led to increasing of L. monocytogenes prevalence which has become a public health concern. Subsequently, further researches about the prevalence of L. monocytogenes and also antibiotic susceptibility testing is needed to enable the detection of the contaminated foods, as well as ensures the effective treatment.
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Affiliation(s)
- Abed Zahedi Bialvaei
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Vajihe Sheikhalizadeh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Mojtahedi
- Department of Microbiology, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Gholamreza Irajian
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran,Corresponding author: Gholamreza Irajian. Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran. Tel: +98-21-66728112-3 (103); Fax: +98-21-66728121;
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