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Aiyegoro OA, Moyane JN, Adegoke AA, Jideani AIO, Reddy P, Okoh AI. Virulence Signatures, Integrons, and Antibiotic Resistance Genes in Bacterial Strains Recovered from Selected Commercial Dairy Products and Fresh Raw Meat. Curr Microbiol 2023; 80:254. [PMID: 37355481 DOI: 10.1007/s00284-023-03371-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023]
Abstract
Bacterial species responsible for food infections and intoxication are sometimes carried through the food production and processing. Very few published literatures exist on integrons among antibiotic-resistant staphylococcal strains from foods of animal origin in Gauteng Province, South Africa, hence this study. A total of 720 samples (360 meat and 360 dairies) from a community abattoir of a research farm in South Africa, using conventional bacteriological and molecular methods. Nine (9) bacterial strains, including Bacillus subtilis AYO-123, Acinetobacter baumannii AYO-241, Staphylococcus lentus AYO-352, among others were identified and submitted to GenBank. More bacterial strains were recovered from raw meat (90.5%) than dairy products (9.5%). Resistance was shown (0-100%) to Imipenem, Meropenem, Norfloxacin, Clindamycin, and 22 other antibiotics, without any carbapenem-resistant Acinetobacter baumannii and methicillin/vancomycin-resistant Staphylococcus species (MRSS/VRSS). Virulence genes for fibronectin-binding protein A (FnbA) were predominant (56.24%) followed by the circulating nucleic acids (cna) gene (43.75%). Others were staphylococcal enterotoxin A (sea, 41%), staphylococcal enterotoxin B (seb, 23.5%). Co-presence of sea and seb genes occurred in 11.76% of the isolates, but no coa genes was amplified. Antibiotic resistance genes (ARGs), tetK (70.58%), linA (29.4%), and ermA (11.76%) were detected, but none of the mecA and vat genes was amplified. Class 2 integron (50%) was more predominantly detected than integron 1 (25%), but no Class 3 integron was detected. Bacteria with both the detected virulence and antibiotic resistance genes are of potential risks to human health.
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Affiliation(s)
- Olayinka A Aiyegoro
- Collaborating Partner, Department of Microbiology, Faculty of Science, University of Uyo, Uyo, Nigeria
- Research Unit for Environmental Sciences and Management, North West University, Potchefstroom, 2520, North West, South Africa
| | - Jeremia N Moyane
- School of Agriculture, Department of Food Science and Technology, University of Venda, Thohoyandou, 0950, South Africa
| | - Anthony A Adegoke
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo, Nigeria.
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology (DUT), Durban, 4001, KwaZulu-Natal, South Africa.
| | - Afam I O Jideani
- School of Agriculture, Department of Food Science and Technology, University of Venda, Thohoyandou, 0950, South Africa
- Postharvest-Handling Group, ISEKI-Food Association, Vienna, Austria
| | - Poovendhree Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology (DUT), Durban, 4001, KwaZulu-Natal, South Africa
| | - Anthony I Okoh
- Department of Environmental Health Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- SAMRC Microbial Water Quality Monitoring Centre, University of For Hare, Alice, South Africa
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Liu H, Liu B, Zheng F, Chen X, Ye L, He Y. Distribution of pathogenic bacteria in lower respiratory tract infection in lung cancer patients after chemotherapy and analysis of integron resistance genes in respiratory tract isolates of uninfected patients. J Thorac Dis 2020; 12:4216-4223. [PMID: 32944333 PMCID: PMC7475539 DOI: 10.21037/jtd-20-928] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background We studied the distribution of pathogenic bacteria in lower respiratory tract infection in lung cancer patients after chemotherapy and analyzed the integron resistance genes in respiratory tract isolates of uninfected patients. Methods Retrospective analysis was used to select sputum samples from 400 lung cancer patients after chemotherapy admitted in Fuyang People’s Hospital from July 2017 to July 2019. Culture, isolation and identification of strains were conducted in accordance with the national clinical examination operating procedures. Results A total of 134 strains were identified. In 120 patients with pulmonary infection, 114 strains were cultured. Twenty strains of klebsiella pneumoniae were cultured in 280 patients without pulmonary infection. Among the 134 strains, the detection rate of gram-negative bacteria was 79.10%. The first four strains were Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Haemophilus influenzae. The gram-positive bacteria detection rate was 4.47%, mainly Staphylococcus aureus and Streptococcus. The fungus detection rate was 16.42%. The drug sensitivity results showed that the resistance rate of gram-negative bacillus to penicillin and cephalosporin was higher, and were more sensitive to carbapenem, piperacillin tazobactam and cefoperazone sulbactam. Gram-positive cocci were resistant to penicillin, macrolide and clindamycin, and sensitive to linezolid, vancomycin and rifampicin. All strains of fungal culture were candida albicans, which were sensitive to common antifungal drugs. Among the 20 strains of klebsiella pneumoniae cultured in sputum specimens of non-infected patients with lung cancer undergoing chemotherapy, 2 strains were integron-positive strains, and all of them were class I integrons. Conclusions Lung cancer patients after chemotherapy have a high resistance to commonly used antimicrobial drugs, so it is necessary to detect the resistance of pathogenic microorganisms in clinical practice. The strains carried by patients with lung cancer without pulmonary infection during chemotherapy can isolate type I integrons, suggesting that the spread of drug resistance at gene level should be closely detected.
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Affiliation(s)
- Haiyan Liu
- Department of Respiratory and Critical Care Medicine, Fuyang People's Hospital, Fuyang, China
| | - Bin Liu
- Department of Respiratory and Critical Care Medicine, Fuyang People's Hospital, Fuyang, China
| | - Fade Zheng
- Department of Respiratory and Critical Care Medicine, Fuyang People's Hospital, Fuyang, China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Lingyun Ye
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
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Aggarwal A, Bhalla M, Fatima KH. Detection of New Delhi metallo-beta-lactamase enzyme gene bla NDM-1 associated with the Int-1 gene in Gram-negative bacteria collected from the effluent treatment plant of a tuberculosis care hospital in Delhi, India. Access Microbiol 2020; 2:acmi000125. [PMID: 32974589 PMCID: PMC7494198 DOI: 10.1099/acmi.0.000125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Background Organisms possessing the blaNDM-1 gene (responsible for carbapenem resistance) with a class-1 integron can acquire many other antibiotic resistance genes from the community sewage pool and become multidrug-resistant superbugs. In this regard, hospital sewage, which contains a large quantity of residual antibiotics, metals and disinfectants, is being recognized as a significant cause of antimicrobial resistance (AMR) origination and spread across the major centres of the world and is thus routinely investigated as a marker for tracing the origin of drug resistance. Therefore, in this study, an attempt has been made to identify and characterize the carbapenem-resistant microbes associated with integron genes amongst the organisms isolated from the effluent treatment plant (ETP) installed in a tertiary respiratory care hospital in Delhi, India. Methods One hundred and thirty-eight organisms belonging to Escherichia, Klebsiella, Pseudomonas and Acinetobacter spp. were collected from the incoming and outgoing sewage lines of the ETP. Carbapenem sensitivity and characterization was performed by the imipenem and imipenem-EDTA disc diffusion method. Later DNA extraction and PCR steps were performed for the Int-1 and blaNDM-1 genes. Results Of the 138 organisms, 86 (62.3 %) were imipenem-resistant (P<0.05). One hundred and twenty-four (89.9 %) organisms had one or both of the genes. Overall, the blaNDM-1 gene (genotypic resistance) was present in 71 % (98/138) of organisms. 53.6 % (74/138) organisms were double gene-positive (blaNDM-1 + Int-1), of which 40 were producing the metallo-beta-lactamase enzyme, making up almost 28.9 % (40/138) of the collected organisms. Conclusion The current study strengthens the hypothesis that Carbapenem resistant organisms are in a high-circulation burden through the human gut and hospital ETPs are providing an environment for resistance origination and amplification.
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Affiliation(s)
- Amit Aggarwal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Delhi, India
| | - Manpreet Bhalla
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Delhi, India
| | - Khan Hena Fatima
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Delhi, India
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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Stearns JC, Davidson CJ, McKeon S, Whelan FJ, Fontes ME, Schryvers AB, Bowdish DME, Kellner JD, Surette MG. Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME JOURNAL 2015; 9:1246-59. [PMID: 25575312 DOI: 10.1038/ismej.2014.250] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 01/24/2023]
Abstract
The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1-4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.
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Affiliation(s)
| | - Carla J Davidson
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Suzanne McKeon
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Fiona J Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Michelle E Fontes
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anthony B Schryvers
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dawn M E Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - James D Kellner
- 1] Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada [2] Department of Paediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Michael G Surette
- 1] Department of Medicine, McMaster University, Hamilton, Ontario, Canada [2] Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada [3] Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME JOURNAL 2014; 9:1269-79. [PMID: 25500508 PMCID: PMC4438328 DOI: 10.1038/ismej.2014.226] [Citation(s) in RCA: 807] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Royal Cornwall Hospital, Truro, UK
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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Yahaghi E, Imani Fooladi AA, Amin M, Mirnejad R, Nezamzade R, Amani J. Detection of Class I Integrons in Staphyloacoccus aurous Isolated From Clinical Samples. IRANIAN RED CRESCENT MEDICAL JOURNAL 2014; 16:e16234. [PMID: 25763211 PMCID: PMC4329933 DOI: 10.5812/ircmj.16234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/12/2014] [Accepted: 09/16/2014] [Indexed: 11/21/2022]
Abstract
Background: Staphylococcus aurous is a major pathogen, causing variety of diseases and death in Iran and in the world. Despite the use of a spectrum of new antibiotics, this organism has caused severe infections in burns as well as in different parts of the body, due to acquired drug resistance. Widespread inappropriate use of antibiotics in treating bacterial infections has led to the selection and circulation of resistant strains and the growing risk of transferring resistant genes to sensitive bacteria. One of the causes of antibiotic resistance in S. aurous strains is the gain of resistance genes including integrase and qac/sul1. Objectives: The purpose of this study was to investigate the presence of class 1 integron in S. aurous strains isolated from clinical samples for the first time in Iran. Materials and Methods: This descriptive study was performed on 200 strains of S. aurous isolated from patients admitted to Baqiyatallah Hospital in Tehran in 2013. These strains were confirmed using biochemical and serological tests and the presence of class 1 integron was determined by polymerase chain reaction (PCR). Results: Among the 200 samples, 1% of the strains (two isolates) contained the class 1 integron gene. The results of this study showed that the highest frequency of the obtained samples belonged to males and the isolates occurred mostly in individuals aged 51-60 years old. The highest number of strains was found in wound samples. The strains were most frequently isolated from the emergency ward and the intensive care unit (ICU). Conclusions: Findings of this study showed that integron can have a limited frequency in S. aurous isolated from clinical sample in Tehran.
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Affiliation(s)
- Emad Yahaghi
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Damghan, IR Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Abbas Ali Imani Fooladi, Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran. Tel: +98-9122269267, E-mail:
| | - Mohsen Amin
- Department of Drug and Food Control, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Reza Mirnejad
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Reza Nezamzade
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Damghan, IR Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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Sarria-Guzmán Y, López-Ramírez MP, Chávez-Romero Y, Ruiz-Romero E, Dendooven L, Bello-López JM. Identification of antibiotic resistance cassettes in class 1 integrons in Aeromonas spp. strains isolated from fresh fish (Cyprinus carpio L.). Curr Microbiol 2013; 68:581-6. [PMID: 24370627 DOI: 10.1007/s00284-013-0511-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/08/2013] [Indexed: 01/15/2023]
Abstract
Forty-six Aeromonas spp. strains were isolated from fresh fish and investigated for their antimicrobial susceptibility, detection of Class 1 integrons by PCR, and arrangement of gene cassettes. Selected isolates were further characterized by enterobacterial repetitive intergenic consensus-PCR. Twenty isolates were found to carry Class 1 integrons. Amplification of the variable regions of the integrons revealed diverse bands ranging in size from 150 to 1,958 pb. Sequence analysis of the variable regions revealed the presence of several gene cassettes, such as adenylyl transferases (aadA2 and aadA5), dihydrofolate reductases (dfrA17 and dfrA1), chloramphenicol acetyl transferase (catB3), β-lactamase (oxa2), lincosamide nucleotidil transferase (linF), aminoglycoside-modifying enzyme (apha15), and oxacillinase (bla OXA-10). Two open reading frames with an unknown function were identified as orfC and orfD. The aadA2 cassette was the most common integron found in this study. Interestingly, five integrons were detected in the plasmids that might be involved in the transfer of resistance genes to other bacteria. This is a first report of cassette encoding for lincosamides (linF) resistance in Aeromonas spp. Implications on the incidence of integrons in isolates of Aeromonas spp. from fresh fish for human consumption, and its possible consequences to human health are discussed.
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