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Vohra M, Babariya M, Parmar JS, Kamath N, Warghane A, Zala D. Integration of phenotypic, qPCR and genome sequencing methodologies for the detection of antimicrobial resistance and virulence in clinical isolates of a tertiary hospital, India. 3 Biotech 2023; 13:368. [PMID: 37849769 PMCID: PMC10577111 DOI: 10.1007/s13205-023-03797-4] [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: 03/31/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) and virulence in clinical isolates is a significant public health concern. The rapid and accurate detection of these traits in clinical isolates is essential for effective infection control and treatment. We demonstrated the integration of multiple detection methodologies, including phenotypic testing, quantitative polymerase chain reaction (qPCR), and genome sequencing, to detect AMR and virulence in clinical isolates. One hundred sixty-two gram-negative bacterial clinical isolates were selected for this study from the Shri Vinoba Bhave Civil Hospital, Silvassa, a tertiary government hospital. Antimicrobial susceptibility was detected by determining the Minimum Inhibitory Concentration (MIC) using Vitek-2, whereas the combined disk (CD) method was used for phenotypic detection of carbapenemase activity. The highest sensitivity rates were obtained for antibiotics colistin 87.93%, amikacin 67.52%, tigecycline 63.39%, nitrofurantoin 60.87%, and gentamycin 56.08%. The most resistant antibiotics were ceftazidime (71.93%), ciprofloxacin (67.95%) and trimethoprim/sulfamethoxazole (65.56%). Approximately 46.91% (76) of all the isolates were MBL isolates. The qPCR results confirmed the presence of blaNDM-1 in 29.01% of the isolates. The blaNDM-1 harbouring isolates in descending order, were Acinetobacter, Enterobacter cloacae, and Klebsiella pneumoniae. Klebsiella and Acinetobacter isolates were extensively drug-resistant. Whole genome sequencing performed on one of the Klebsiella pneumoniae isolates revealed the presence of many virulence factors, which increased the pathogenicity of the clinical isolates. The results showed that antimicrobial resistance, including carbapenem resistance, blaNDM-1, and virulence factors, was highly prevalent among isolates from tertiary clinical hospitals. The integration of multiple detection methodologies can potentially improve the detection of AMR and virulence in clinical isolates, leading to better patient outcomes and a reduced spread of these essential traits.
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Affiliation(s)
- Mustafa Vohra
- Department of Microbiology, Shri Vinoba Bhave Civil Hospital, Silvassa, 396230 India
| | - Manjula Babariya
- Department of Microbiology, NAMO Medical Education and Research Institute, Silvassa, 396230 India
| | - Jitendrakumar S. Parmar
- Department of Pathology, NAMO Medical Education and Research Institute, Silvassa, 396230 India
| | - Narayan Kamath
- Department of Microbiology, NAMO Medical Education and Research Institute, Silvassa, 396230 India
| | - Ashish Warghane
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad, 382424 India
| | - Dolatsinh Zala
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad, 382424 India
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Cozzolino L, Nicastro KR, Seuront L, McQuaid CD, Zardi GI. The relative effects of interspecific and intraspecific diversity on microplastic trapping in coastal biogenic habitats. Sci Total Environ 2022; 848:157771. [PMID: 35926622 DOI: 10.1016/j.scitotenv.2022.157771] [Citation(s) in RCA: 6] [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: 05/25/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Our understanding of how anthropogenic stressors such as climate change and plastic pollution interact with biodiversity is being widened to include diversity below the species level, i.e., intraspecific variation. The emerging appreciation of the key ecological importance of intraspecific diversity and its potential loss in the Anthropocene, further highlights the need to assess the relative importance of intraspecific versus interspecific diversity. One such issue is whether a species responds as a homogenous whole to plastic pollution. Using manipulative field transplant experiments and laboratory-controlled hydrodynamic simulations, we assessed the relative effects of intraspecific and interspecific diversity on microplastic trapping in coastal biogenic habitats dominated by two key bioengineers, the brown intertidal macroalgae Fucus vesiculosus and F. guiryi. At the individual level, northern morphotypes of F. guiryi trapped more microplastics than southern individuals, and F. vesiculosus trapped more microplastics than F. guiryi. Canopy density varied among species, however, leading to reversed patterns of microplastic accumulation, with F. guiryi canopies accumulating more microplastics than those of F. vesiculosus, while no differences were observed between the canopies of F. guiryi morphotypes. We emphasize the importance of assessing the effects of intraspecific variation which, along with other crucial factors such as canopy density, flow velocity and polymer composition, modulates the extent of microplastic accumulation in coastal biogenic habitats. Our findings indicate that a realistic estimation of plastic accumulation in biogenic habitats requires an understanding of within- and between-species traits at both the individual and population levels.
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Affiliation(s)
- Lorenzo Cozzolino
- CCMAR-Centro de Ciencias do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal.
| | - Katy R Nicastro
- CCMAR-Centro de Ciencias do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000 Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown 6140, South Africa
| | - Laurent Seuront
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000 Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown 6140, South Africa; Department of Marine Resources and Energy, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Christopher D McQuaid
- Department of Zoology and Entomology, Rhodes University, Grahamstown 6140, South Africa
| | - Gerardo I Zardi
- Department of Zoology and Entomology, Rhodes University, Grahamstown 6140, South Africa; Normandie Université, UNICAEN, Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques, UMR 8067 BOREA (CNRS, MNHN, UPMC, UCBN, IRD-207), CS 14032, 14000 Caen, France
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Mariappan V, Ngoi ST, Lim YAL, Ngui R, Chua KH, Teh CSJ. Genotypic and phenotypic characterization of Escherichia coli isolated from indigenous individuals in Malaysia. Iran J Basic Med Sci 2022; 25:468-473. [PMID: 35656079 PMCID: PMC9150813 DOI: 10.22038/ijbms.2022.61612.13637] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/14/2022] [Indexed: 11/17/2022]
Abstract
Objectives The occurrence of asymptomatic verocytotoxin (VT)-producing Escherichia coli (VTEC) infections among humans in recent years is posing a high risk to public health. Thus, the role of asymptomatic human carriers as a source of dissemination should not be underestimated. This study aimed to elucidate the phenotypic and genotypic characteristics of E. coli in the stool samples collected from indigenous individuals in Malaysia. Materials and Methods E. coli strains (n=108) were isolated from stool samples obtained from 41 indigenous individuals. All strains were subjected to Repetitive Extragenic Palindromic-Polymerase Chain Reaction (REP-PCR) typing and confirmation of VTEC variants. Non-duplicate strains were selected based on REP-PCR profiles and further subjected to antimicrobial susceptibility test (AST). The genotypic and phenotypic characteristics of the strains were then correlated with the demographic data of the subjects. Results A total of 66 REP-PCR profiles grouped in 53 clusters (F=85%) were obtained. Four genetically distinct strains were confirmed as VTEC (eaeA-positive). The predominant resistance was against ampicillin (34.2%), followed by trimethoprim-sulfamethoxazole (32.9%), ampicillin-sulbactam (5.5%), and ciprofloxacin (1.4%). All isolates were sensitive to amoxicillin-clavulanate, cefuroxime, ceftriaxone, imipenem, and meropenem. Conclusion Genetically diverse E. coli and VTEC strains were found to colonize the intestines of the indigenous populations. This study is important for the prospective surveillance of E. coli among the indigenous individuals in Malaysia, especially in asymptomatic VTEC infection and antimicrobial resistance phenomenon.
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Affiliation(s)
- Vanitha Mariappan
- Centre of Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, 50300 Kuala Lumpur, Malaysia ,Corresponding authors: Vanitha Mariappan. Centre of Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, National University of Malaysia, 50300 Kuala Lumpur, Malaysia. ; Cindy Shuan Ju Teh. Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Soo Tein Ngoi
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia,Centre for Malaysian Indigenous Studies (CMIS), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Romano Ngui
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia,Corresponding authors: Vanitha Mariappan. Centre of Toxicology and Health Risk Studies (CORE), Faculty of Health Sciences, National University of Malaysia, 50300 Kuala Lumpur, Malaysia. ; Cindy Shuan Ju Teh. Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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Gupta NK, Ish P. Tuberculosis with discordant drug resistance patterns- A diagnostic dilemma. Indian J Tuberc 2022; 69:8-11. [PMID: 35074156 DOI: 10.1016/j.ijtb.2021.05.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/22/2021] [Indexed: 06/14/2023]
Abstract
Programmatic management of drug-resistant tuberculosis (PMDT) guidelines in India specify the use of cartridge based nucleic acid amplification test (CBNAAT) and Line probe assay (LPA) for early diagnosis of drug-resistant Tuberculosis. However, discrepancy among these genotypic tests (CBNAAT and LPA) or with the phenotypic DST in real practice poses a clinical dilemma. The usual solutions are to rely on methods with short turnaround times like CBNAAT and LPA to start an initial regimen. The culture and DST results, that are typically available after at least a few weeks, are used to modify the regimen if required. This practice is based on the fact that culture and DST based sensitivity patterns are considered the gold standard for diagnosing and drug resistance. DNA sequencing by pyrosequencing, Sanger sequencing and next generation sequencing (NGS) are being evaluated; their future availability may help in early clarifications in discordant drug resistance patterns. Such tests are costly and have limited availability, however, in view of immense benefit to detect TB Drug-resistant phenotypes, national guidelines plan to scale up their use in national and well-performing intermediate TB reference laboratories.
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Affiliation(s)
- Neeraj Kumar Gupta
- Department of Pulmonary, Critical Care and Sleep Medicine and Nodal Officer for DOTS, VMMC and Safdarjung Hospital, New Delhi, India
| | - Pranav Ish
- Department of Pulmonary, Critical Care and Sleep Medicine, VMMC and Safdarjung Hospital, New Delhi, India.
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Webale MK, Guyah B, Wanjala C, Nyanga PL, Webale SK, Abonyo C, Kitungulu N, Kiboi N, Bowen N. Phenotypic and Genotypic Antibiotic Resistant diarrheagenic Escherichia coli pathotypes isolated from Children with Diarrhea in Nairobi City, Kenya. Ethiop J Health Sci 2021; 30:881-890. [PMID: 33883832 PMCID: PMC8047252 DOI: 10.4314/ejhs.v30i6.5] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The marked genome plasticity of diarrheagenic Escherichia coli promotes emergence of pathotypes displaying unique phenotypic and genotypic resistance. This study examined phenotypic and genotypic antibiotic resistant diarrheagenic Escherichia coli pathotypes among children in Nairobi City, Kenya. Methods In a cross-sectional study, diarrheagenic Escherichia coli pathotypes were isolated from stool samples and their phenotypic and genotypic resistance against eight antimicrobial agents assayed. Results Diarrheagenic Escherichia coli was detected in 136(36.4%) children. Most of diarrheagenic Escherichia coli that were resistant to ampicillin, ceftriaxone, streptomycin, gentamycin, ciprofloxacin, chloramphenicol, erythromycin and tetracycline, harbored citm, bla CMY, aadA1, aac(3)-IV, qnr, catA, ere(A) and tet(A) corresponding resistant genes. Conclusion Antimicrobial-resistant genes are highly prevalent among phenotypic resistant ETEC pathotypes indicating a possibility of horizontal gene transfer in spreading antibiotic resistant genes among E. coli pathotypes.
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Affiliation(s)
| | | | - Christine Wanjala
- School of Public Health, Masinde Muliro University of Science and Technology, Kakamega, Kenya Unit, Ministry of Health, Nairobi city, Kenya
| | | | | | - Collins Abonyo
- School of Public Health, Masinde Muliro University of Science and Technology, Kakamega, Kenya Unit, Ministry of Health, Nairobi city, Kenya
| | - Nicholas Kitungulu
- School of Natural Sciences, Masinde Muliro University of Science and Technology, Kenya
| | - Nathan Kiboi
- School of Pure and Applied Sciences, Kenyatta University, Kenya
| | - Nancy Bowen
- National Public health Laboratories, Ministry of Health, Nairobi city, Kenya
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Alzahrani FM, Aldossary N, Hassan FM. Phenotypic and Genotypic Characterization of von Willebrand Factor Gene (Exon 18 and 20) in Saudi Healthy Individuals. Med Arch 2021; 74:337-341. [PMID: 33424085 PMCID: PMC7780826 DOI: 10.5455/medarh.2020.74.337-341] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Introduction: Von Willebrand disease (VWD) is an autosomal congenital bleeding syndrome that was described as being the most widespread genetic condition among men. In Saudi Arabia, the genotyping of the VWF gene is necessary to establish a diagnosis procedure for VWD. Aim: The current research, however, attempted to evaluate the phenotypic-genotypic association of the Von Willebrand factor (exon 18 and 20) gene in healthy subjects to establish effective molecular diagnostic strategies. Methods: This was a cross-sectional retrospective included 100 healthy people who have been chosen from King Fahad University Hospital. Whole blood samples were collected from all individuals, as well as the laboratory analysis was done using automatic analyzers for; platelet count, ABO blood group and coagulation parameters. DNA Sanger sequencing has been used to sequestrate the full exons 18 and 20. Results: In exon 18 of healthy people, three unusual sequence variations (1 missense and 2 synonymous; rs775479826, rs1286572448 and rs369828268) compared to other recorded VWF variations (3 missense and 1 synonymous; c.2365A > G, c.2385T > C, c.2344C > T and c.2340C > G). But in exon 20 only 1 synonymous novel (rs113240752) 1 registered VWF variations in missense (c.2555G > A) were identified. Conclusion: The present variants found on those participates could be a realistic approach to detect mutation in the VWF gene to illustrating the relationship of phenotypic and genetic abnormalities variables may lead to determining the functional effect in mutations specific to the Saudi people that can be used to develop a diagnostic tool for VWD in KSA.
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Affiliation(s)
- Faisal M Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University. KSA
| | - Nemat Aldossary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University. KSA
| | - Fathelrahman Mahdi Hassan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University. KSA
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Lubembe DM, Odongo DO, Salih DA, Sibeko-Matjila KP. Microsatellite and minisatellite genotyping of Theileria parva population from southern Africa reveals possible discriminatory allele profiles with parasites from eastern Africa. Ticks Tick Borne Dis 2020; 11:101539. [PMID: 32993948 DOI: 10.1016/j.ttbdis.2020.101539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/20/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
The control of Theileria parva, a protozoan parasite that threatens almost 50% of the cattle population in Africa, is still a challenge in many affected countries. Theileria parva field parasites from eastern Africa, and parasites comprising the current live T. parva vaccine widely deployed in the same region have been reported to be genotypically diverse. However, similar reports on T. parva parasites from southern Africa are limited, especially in Corridor disease designated areas. Establishing the extent of genetic exchange in T. parva populations is necessary for effective control of the parasite infection. Twelve polymorphic microsatellite and minisatellite loci were targeted for genotypic and population genetics analysis of T. parva parasites from South Africa, Mozambique, Kenya and Uganda using genomic DNA prepared from cattle and buffalo blood samples. The results revealed genotypic similarities among parasites from the two regions of Africa, with possible distinguishing allelic profiles on three loci (MS8, MS19 and MS33) for parasites associated with Corridor disease in South Africa, and East Coast fever in eastern Africa. Individual populations were in linkage equilibrium (VD<L), but when considered as one combined population, linkage disequilibrium (VD>L) was observed. Genetic divergence was observed to be more within (AMOVA = 74%) than between (AMOVA = 26%) populations. Principal coordinate analysis showed clustering that separated buffalo-derived from cattle-derived T. parva parasites, although parasites from cattle showed a close genetic relationship. The results also demonstrated geographic sub-structuring of T. parva parasites based on the disease syndromes caused in cattle in the two regions of Africa. These findings provide additional information on the genotypic diversity of T. parva parasites from South Africa, and reveal possible differences based on three loci (MS8, MS19 and MS33) and similarities between buffalo-derived T. parva parasites from southern and eastern Africa.
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Affiliation(s)
- Donald M Lubembe
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa.
| | - David O Odongo
- School of Biological Sciences, University of Nairobi, P.O. Box 30197, Nairobi, 00100, Kenya
| | - Diaeldin A Salih
- Central Veterinary Research Laboratory, P.O. Box 8067, Khartoum, Sudan
| | - Kgomotso P Sibeko-Matjila
- Vectors and Vector-borne Diseases Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
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Wang SN, Sun Y, Zhou HH, Lu G, Qi M, Liu WS, Zhao W. Prevalence and genotypic identification of Cryptosporidium spp. and Enterocytozoon bieneusi in captive Asiatic black bears (Ursus thibetanus) in Heilongjiang and Fujian provinces of China. BMC Vet Res 2020; 16:84. [PMID: 32151253 PMCID: PMC7063761 DOI: 10.1186/s12917-020-02292-9] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/19/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Cryptosporidium and Enterocytozoon bieneusi are two important pathogens with zoonotic potential that cause enteric infections in a wide range of hosts, including humans. Both are transmitted from animals to humans by direct contact or through contaminated equipment. Bears are frequently found in Chinese zoos as ornamental animals as well as farmed as commercial animals, and are therefore in close contact with zoo- or farm-keepers, but the prevalence and zoonotic potential of Cryptosporidium and E. bieneusi in bears is poorly understood. In this study, we aimed to provide data on the occurrence and genetic diversity of Cryptosporidium and E. bieneusi in Asiatic black bears from Heilongjiang and Fujian, China. From May 2015 to December 2017, 218 fresh fecal specimens were collected from captive Asiatic black bears in Heilongjiang (n = 36) and Fujian (n = 182), China. Cryptosporidium and E. bieneusi were examined by PCR amplification of the partial small subunit of ribosomal DNA (SSU rDNA) and the internal transcribed spacer (ITS) region of rDNA, respectively. C. andersoni-positive isolates were subtyped through PCR analysis of the four minisatellite/microsatellite (MS1, MS2, MS3 and MS16) loci. RESULTS The overall prevalence of Cryptosporidium and E. bieneusi were 2.4% (4/218) and 6.4% (14/218), respectively, with 2.8% (1/36) and 22.2% (8/36) in the Heilongjiang Province, and 1.6% (3/182) and 3.3% (6/182) in the Fujian Province. Sequence analysis confirmed the presence of Cryptosporidium species: C. andersoni (n = 3) and a genotype termed Cryptosporidium rat genotype IV (n = 1). All three identified C. andersoni belonged to the MLST subtype A4, A4, A4, A1. Two known E. bieneusi genotypes D (n = 4) and SC02 (n = 10) were identified, both of which belong to zoonotic Group 1. CONCLUSIONS This is the first report of C. andersoni and Cryptosporidium rat genotype IV in bears. The discovery of the zoonotic potential of E. bieneusi genotype D in bears highlights its significant zoonotic potential and potential threat to human health.
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Affiliation(s)
- Sheng-Nan Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
| | - Yun Sun
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China.,The Animal Husbandry and Veterinary Research Institute of HaiBei Tibetan Autonomous Prefecture, Xining, 810299, HaiBei Tibetan Autonomous Prefecture, China
| | - Huan-Huan Zhou
- Department of Pathogenic Biology, Hainan Medical University, Haikou, Hainan, 571199, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, 571199, China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Gang Lu
- Department of Pathogenic Biology, Hainan Medical University, Haikou, Hainan, 571199, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, 571199, China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Meng Qi
- College of Animal Science, Tarim University, Alar, Xinjiang, 843300, China
| | - Wei-Shi Liu
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China.
| | - Wei Zhao
- Department of Pathogenic Biology, Hainan Medical University, Haikou, Hainan, 571199, China. .,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan, 571199, China. .,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, 571199, China. .,Department of Parasitology, Wenzhou Medical University, Wenzhou, 325035, China.
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Ghaly MF, Shaheen AA, Bouhy AM, Bendary MM. Alternative therapy to manage otitis media caused by multidrug-resistant fungi. Arch Microbiol 2020; 202:1231-40. [PMID: 32108246 DOI: 10.1007/s00203-020-01832-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/29/2020] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
Abstract
During the last few decades, the increase in the incidence of multidrug-resistant (MDR) fungal infections has become an emerging threat to public health. Therefore, it is important to illuminate the usage of alternative therapy to treat MDR fungal infection. This study was carried out to elucidate the usage of plant extract and essential oil, either alone or with other antifungal drugs to treat otitis media caused by MDR fungi. Medicinal plant is a safe and cheap source when compared with chemical antifungal drugs. Twenty-one fungal isolates out of 104 ear swabs from patients suffering from otitis media were characterized using both phenotypic and genotypic methods. The antibiogram typing was used to determine the MDR isolates. The sensitivity of MDR fungal isolates was tested against several plant extracts and essential oils, either alone or with other antifungal drugs. Thyme oil and clove extracts proved to have synergistic effects suggesting their use in the treatment of fungal infections, especially otitis media caused by MDR fungi. The ultrastructure of MDR fungal isolates exhibited a complete destruction post exposure to the used materials when observed under the transmission microscope (TEM). Thyme oil and clove extract were found to be the most effective agents against MDR fungal isolates and they constitute a promising tool for the management of fungal infection causing the otitis media.
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Ernieenor FCL, Apanaskevich DA, Ernna G, Mariana A. Description and characterization of questing hard tick, Dermacentor steini (Acari: Ixodidae) in Malaysia based on phenotypic and genotypic traits. Exp Appl Acarol 2020; 80:137-149. [PMID: 31832837 DOI: 10.1007/s10493-019-00439-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/08/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Identifying certain species of Dermacentor ticks in Malaysia is challenging as there is no comprehensive work on their systematics and lack of specific taxonomic keys. In this study, we described and characterized D. steini ticks collected from a forest reserve in the vicinity of the Forest Research Institute of Malaysia using integrated phenotypic and genotypic traits. In total two males and three females of questing D. steini ticks were morphologically identified using specific illustrated taxonomic keys based on their special characters. Further confirmation and characterization of the tick species were then examined using PCR, followed by sequencing partial mitochondrial 16S rDNA gene (mt-rrs). Clustering analysis based on mt-rrs was carried out by constructing neighbor-joining tree topology to clarify the genetic variation of local D. steini. Based on external morphological characterizations, all ticks were successfully identified down to the species as adult D. steini. The molecular traits based on phylogenetic tree provide very strong support for the monophyletic clade of D. steini including high percentages of similarity (97-100%) with available sequences in GenBank. Furthermore, a low intraspecific variation (4%) among the species of D. steini was observed but it was genetically different from other Dermacentor species with high interspecific value (8-15%). These findings produced the first genotypic data of D. steini using 16S rDNA gene which confirmed the presence of this species in Malaysia. Moreover, this study supports the taxonomic status of local D. steini and adds to the knowledge of accurate identification of ticks.
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Affiliation(s)
- F C L Ernieenor
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Ministry of Health Malaysia, Jalan Pahang, 50588, Kuala Lumpur, Malaysia.
| | - D A Apanaskevich
- United States National Tick Collection, The James H. Oliver, Jr. Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA, 30460-8056, USA
| | - G Ernna
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Ministry of Health Malaysia, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
| | - A Mariana
- Acarology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Ministry of Health Malaysia, Jalan Pahang, 50588, Kuala Lumpur, Malaysia
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Abstract
With emerging antimicrobial resistance, rapid antimicrobial susceptibility testing (AST) is needed to provide early definitive therapeutic guidance to optimize patient outcome. Genotypic methods are fast, but can identify only a subset of known resistance elements. Phenotypic methods determine clinically predictive minimal inhibitory concentrations and include very sensitive optical and biophysical methods to detect changes in replication or physiology of pathogens in response to antibiotics. For the potential of rapid AST to be fully realized, results must be linked with robust decision support solutions that will implement therapeutic changes in real time.
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Affiliation(s)
- Kenneth P Smith
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Center for Life Science, 3 Blackfan Circle-CLS624, Boston, MA 02115, USA
| | - James E Kirby
- Clinical Microbiology, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue-YA309, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
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Bonyadian M, Barati S, Mahzounieh MR. Phenotypic and genotypic characterization of antibiotic-resistant in Escherichia coli isolates from patients with diarrhea. Iran J Microbiol 2019; 11:220-4. [PMID: 31523405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND AND OBJECTIVES Escherichia coli is a common enteric pathogen of human and livevestock. Antibiotic resistance is the main concern of public health. The aim of this study was to detect this bacterium in stool samples of diarrheal patients and identify the phenotypic and genotypic characterizations of antibiotic-resistant isolates such as dfrA1, sul1, citm, tetA, qnr, aac(3)-IV in Shahrekord. MATERIALS AND METHODS Two hundred fifty diarrheal stool samples from patients were collected. Microbiological and biochemical examinations were done to detect E. coli. Phenotypic and genotypic antibiotic resistance of the isolates were determined using dick diffusion method and polymerase chain reaction (PCR), respectively. RESULTS Among 114 E. coli isolates, the least resistance was for gentamicin (0%) and the most resistance was for trimethoprim (79.8%). The resistance to sulfamethoxazole, ciprofloxacin, ampicillin, and tetracycline were 71.05%, 10.5%, 52.63%, and 3.5% respectively. The results of PCR assay revealed that 10 isolates contain sul1, 49 isolates harbor citm, 8 isolates tetA, 36 isolates dfrA1, 11 isolates qnr genes but there was no isolate with aac(3)-IV gene. In comparison between phenotypic and genotypic of the isolates revealed that citm, tetA, dfrA1, qnr, sul1, aac(3)-IV genes covered 42.98%, 7.01%, 31.57%, 9.64%, 8.7%, 0% of the antibiotic resistance, respectively. CONCLUSION Our results revealed that all isolates harbor one or more antibiotic resistance genes and that the PCR is a fast practical and appropriate method to determine the presence of antibiotic resistance genes.
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Badiee P, Rezapour A, Abbasian A, Foroutan HR, Jafarian H. Prevalence of colonization and mitochondrial large subunit rRNA mutation of Pneumocystis jiroveci among Iranian children. Iran J Microbiol 2016; 8:326-330. [PMID: 28149493 PMCID: PMC5277602] [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] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Pneumocystis jiroveci is an important causative agent of Pneumocystis pneumonia. During childhood, exposure to Pneumocystis occurs and antibody was built in early childhood. The aim of this study was to describe the molecular epidemiology of P. jiroveci in children without any respiratory syndrome and survey the distribution of different mitochondrial large subunit, ribosomal ribonucleic acid (mtLSU- rRNA) genotypes. MATERIALS AND METHODS Mini-bronchoalveolar lavage (mini-BAL) fluids from pediatric patients with no history of lung disorders were obtained during a 14-month period. P. jiroveci colonization was confirmed by immunofluorescence staining, nested PCR and sequencing. Genotypic characterization at the mitochondrial large subunit rRNA gene was performed by direct sequencing. RESULTS Of 172 BAL specimens from patients, with mean age of 4.9 years, the prevalence of P. jiroveci colonization was 3.5% (6 samples). The results of sequencing revealed the two polymorphisms; 85/A; 248/C in 3 cases, and 85/T; 248/C in other cases. One sample also showed a mutation replacement at position 258 (T-to-C change), which was not reported previously. CONCLUSION Colonized person as an environmental reservoir might play an important role in the progression of infection in immunocompromised patients. Diagnosis of the reservoir and genotyping can be essential for the prevention of nosocomial infections.
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Affiliation(s)
- Parisa Badiee
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rezapour
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Abbasian
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Corresponding author: Amin Abbasian, M.Sc, Prof. Alborzi Clinical Microbiology Research Center, Nemazee Hospital, Zand Ave, Shiraz, Fars, Iran. 7193711351., Tel: +98 713-647-4292, Fax: +98 713-647-4303, E-mail:
| | - Hamid Reza Foroutan
- Department of Pediatric Surgery, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hadis Jafarian
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Azimi L, Talebi M, Owlia P, Pourshafie MR, Najafi M, Lari ER, Lari AR. Tracing of false negative results in phenotypic methods for identification of carbapenemase by Real-time PCR. Gene 2015; 576:166-70. [PMID: 26456106 DOI: 10.1016/j.gene.2015.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/19/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Carbapenemase production causes multi antibiotics resistant in Gram-negative bacteria. A simple rapid and accurate phenotypic test for detection of Gram-negative carbapenemase-producing bacteria is useful for the treatment of infections. The aim of this study was to track the negative results in carbapenemase phenotypic test by Real-time PCR. MATERIALS AND METHODS In this study, 161 imipenem resistant Gram-negative bacteria were surveyed. Modified Hodge Test (MHT), boronic acid (BA), EDTA and dipicolinic acid were used for detection of Klebsiella pneumoniae carbapenemase (KPC) and metallo-beta-lactamase (MBLs). Different phenotypic methods and PCR confirmation followed by Real-time PCR for determination of phenotypic false-negative results were used. RESULTS Our results indicated that 85, 51 and 112 strains were MHT, BA and dipicolinic acid positive, respectively. No synergistic effect was observed between imipenem and EDTA. Sixty-nine strains were confirmed as carbapenemase-producers according to the results of molecular tests. All of the isolates carried the gene and expressed carbapenemase. CONCLUSION Comparison between the results of phenotypic and genotypic methods showed that the phenotypic methods could be used as the primary screening and the PCR remains as the gold standard for detection of carbapenemase positive strains.
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Affiliation(s)
- Leila Azimi
- Pediatric Infectious Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center, Shahed University, Tehran, Iran
| | | | - Mohamad Najafi
- Department of Biochemistry, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Rastegar Lari
- Luxembourg University, Faculty of Science Technology and Communication, Belgium; Liege University, Faculty of Science and Environment, Belgium
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15
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Farahani A, Mohajeri P, Gholamine B, Rezaei M, Abbasi H. Comparison of different phenotypic and genotypic methods for the detection of methicillin-resistant Staphylococcus aureus. N Am J Med Sci 2014; 5:637-40. [PMID: 24404541 PMCID: PMC3877436 DOI: 10.4103/1947-2714.122305] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: Staphylococcus aureus is known as a powerful pathogen that causes various infections. Emergence of methicillin-resistant S. aureus (MSRA) is responsible for nosocomial and community-acquired infections worldwide. Aims: The present study aimed to evaluate the performance and ability of eight different phenotypic and genotypic methods for the detection of MSRA. Materials and Methods: A total of 186 S. aureus isolates were defined as methicillin-susceptible S. aureus (MSSA; 95) and MSRA (91) using polymerase chain reaction (PCR) as the gold standard. Susceptibility to methicillin was investigated using oxacillin, methicillin, cefotetan, cefoxitin, and cefmetazole disks, by oxacillin Adata Tab and strips. For all S. aureus isolates minimal inhibitory concentrations of oxacillin were determined using the broth microdilution method according to Clinical and Laboratory Standards Institute guidelines. Results: Among the diagnostic methods studied, broth microdilution and the cefoxitin disk had the highest specificity (98.9 and 94.7%), sensitivity (100 and 98.9%), and concordance with PCR results (98.9 and 93.6%). The cefotetan and cefmetazole disks had the lowest concordance with PCR results. Conclusion: Our results suggest that microdilution and cefoxitin disk methods have high sensitivities compared with other methods for detection of MSRA. The cefoxitin disk method may be preferred in clinical laboratories because it is easy to perform and does not require special equipment.
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Affiliation(s)
- Abbas Farahani
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parviz Mohajeri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Babak Gholamine
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mansour Rezaei
- Department of Biological Statistics, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hassan Abbasi
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Pholwat S, Stroup S, Gratz J, Trangan V, Foongladda S, Kumburu H, Juma SP, Kibiki G, Houpt E. Pyrazinamide susceptibility testing of Mycobacterium tuberculosis by high resolution melt analysis. Tuberculosis (Edinb) 2014; 94:20-5. [PMID: 24246607 PMCID: PMC3877170 DOI: 10.1016/j.tube.2013.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/19/2013] [Accepted: 10/24/2013] [Indexed: 11/17/2022]
Abstract
Pyrazinamide (PZA) plays the important role in shortening the tuberculosis treatment period and in treating MDR-TB. Phenotypic PZA susceptibility methods are limited because they require specialized acidified media, which increases costs and complexity. In this study we developed a genotypic high resolution melt (HRM) analysis technique to detect pncA mutations associated with PZA resistant Mycobacterium tuberculosis. Seven overlapping primer pairs were designed to cover the entire pncA gene and upstream regions. Each gene segment was individually amplified by real-time PCR followed by HRM analysis. The assay was evaluated on 98 clinical M. tuberculosis isolates (41 PZA susceptible by MGIT method, 55 PZA resistant, 2 undetermined). HRM was 94% concordant to full-length sequencing results, with most discrepancies attributable to mixed populations per HRM or transversions. Sequencing and HRM yielded 82% and 84% concordance, respectively, to phenotypic PZA susceptibilities by MGIT, with most discrepancies attributable to isolates with wild-type pncA but phenotypic PZA resistance. This HRM technique is a simple and high-throughput method for screening clinical M. tuberculosis samples for PZA resistance.
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Affiliation(s)
- Suporn Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Varittha Trangan
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suporn Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
| | - Saumu Pazia Juma
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
| | - Gibson Kibiki
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
| | - Eric Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
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