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Sykes EME, Mateo-Estrada V, Engelberg R, Muzaleva A, Zhanel G, Dettman J, Chapados J, Gerdis S, Akineden Ö, Khan IUH, Castillo-Ramírez S, Kumar A. Phylogenomic and phenotypic analyses highlight the diversity of antibiotic resistance and virulence in both human and non-human Acinetobacter baumannii. mSphere 2024; 9:e0074123. [PMID: 38440986 PMCID: PMC10964423 DOI: 10.1128/msphere.00741-23] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative, opportunistic pathogen that causes infections in the immunocompromised. With a high incidence of muti-drug resistance, carbapenem-resistant A. baumannii is designated as a priority 1 pathogen by the WHO. The current literature has expertly characterized clinical isolates of A. baumannii. As the challenge of these infections has recently been classified as a One Health issue, we set out to explore the diversity of isolates from human and non-clinical sources, such as agricultural surface water, urban streams, various effluents from wastewater treatment plants, and food (tank milk); and, importantly, these isolates came from a wide geographic distribution. Phylogenomic analysis considering almost 200 isolates showed that our diverse set is well-differentiated from the main international clones of A. baumannii. We discovered novel sequence types in both hospital and non-clinical settings and five strains that overexpress the resistance-nodulation-division efflux pump adeIJK without changes in susceptibility reflected by this overexpression. Furthermore, we detected a bla ADC-79 in a non-human isolate despite its sensitivity to all antibiotics. There was no significant differentiation between the virulence profiles of clinical and non-clinical isolates in the Galleria mellonella insect model of virulence, suggesting that virulence is neither dependent on geographic origin nor isolation source. The detection of antibiotic resistance and virulence genes in non-human strains suggests that these isolates may act as a genetic reservoir for clinical strains. This endorses the notion that in order to combat multi-drug-resistant infection caused by A. baumannii, a One Health approach is required, and a deeper understanding of non-clinical strains must be achieved.IMPORTANCEThe global crisis of antibiotic resistance is a silent one. More and more bacteria are becoming resistant to all antibiotics available for treatment, leaving no options remaining. This includes Acinetobacter baumannii. This Gram-negative, opportunistic pathogen shows a high frequency of multi-drug resistance, and many strains are resistant to the last-resort drugs carbapenem and colistin. Research has focused on strains of clinical origin, but there is a knowledge gap regarding virulence traits, particularly how A. baumannii became the notorious pathogen of today. Antibiotic resistance and virulence genes have been detected in strains from animals and environmental locations such as grass and soil. As such, A. baumannii is a One Health concern, which includes the health of humans, animals, and the environment. Thus, in order to truly combat the antibiotic resistance crisis, we need to understand the antibiotic resistance and virulence gene reservoirs of this pathogen under the One Health continuum.
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Affiliation(s)
- Ellen M. E. Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Raelene Engelberg
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anna Muzaleva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Julie Chapados
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ömer Akineden
- Dairy Sciences, Institute of Veterinary Food Science, Justus-Liebig, University of Giessen, Giessen, Germany
| | - Izhar U. H. Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Sheikh AA, Schneiderman D, Sykes EME, Kumar A, Chen W, Lapen DR, Khan IUH. Three novel multiplex PCR assays for rapid detection of virulence, antimicrobial resistance, and toxin genes in Acinetobacter calcoaceticus-baumannii complex species. Lett Appl Microbiol 2024; 77:ovae027. [PMID: 38460955 DOI: 10.1093/lambio/ovae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/11/2024]
Abstract
The Acinetobacter calcoaceticus-baumannii (ACB) complex is an often-overlooked group of nosocomial pathogens with a significant environmental presence. Rapid molecular screening methods for virulence, antimicrobial resistance, and toxin (VAT) genes are required to investigate the potential pathogenicity of environmental isolates. This study aimed to develop and apply novel ACB complex-specific multiplex PCR (mPCR) primers and protocols for the rapid detection of eight VAT genes. We optimized three single-tube mPCR assays using reference DNA from ACB complex and other Acinetobacter species. These assays were then applied to detect VAT genes in cultured ACB complex isolates recovered from clinical and environmental sources. Widespread detection of VAT genes in environmental isolates confirmed the validity, functionality, and applicability of these novel assays. Overall, the three newly developed ACB complex species-specific mPCR assays are rapid and simple tools that can be adopted in diagnostic and clinical lab settings. The detection of VAT genes in environmental isolates suggests that environmental niches could serve as a reservoir for potentially pathogenic ACB complex and warrants further investigation. The newly developed mPCR assays are specific, sensitive, and efficient, making them well-suited for high-throughput screening in epidemiological studies and evaluating the potential pathogenicity of ACB complex recovered from various sources.
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Affiliation(s)
- Alexander A Sheikh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
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Almashhadany DA, Hassan AA, Rashid RF, Abdulmawjood A, Khan IUH. Assessment and Assay Comparison for Detection of Antimicrobial Residues in Freshwater Aquaculture Fish in Erbil Governorate, Iraq. Antibiotics (Basel) 2024; 13:225. [PMID: 38534660 DOI: 10.3390/antibiotics13030225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The excessive and uncontrolled application of antibiotics in the fish farming industry, coupled with a lack of health monitoring and medication practices, is a driving force behind the escalating development of antimicrobial resistance. The present study assessed and compared qualitative field diffusion (QFD) and disk diffusion (DD) assays for the detection of antimicrobial residues (ARs) in diverse freshwater aquaculture fish. A total of 380 freshwater aquaculture fish (160 fresh and 180 frozen) samples were systematically collected between January and June 2021 from various retail stores located in Erbil Governorate, Iraq. Based on QFDA results, overall, ARs were detected (52; 15.3%) at a relatively lower frequency with comparatively higher frequency (21; 31.1%) in fresh than (31; 17.2%) frozen fish samples. On the other hand, DDA also revealed a comparable (45; 13.2%) prevalence rate of ARs. However, a low detection was observed more in fresh (17; 10.6%) than frozen (28; 15.6%) fish samples. Moreover, no statistically significant disparity (χ2 = 0.069; p = 0.79) between two assays and types of fish was recorded. In conclusion, the results of the present study showed that detecting a considerable frequency of ARs in these fish samples raises concerns about potential threats to public health. This underscores the necessity for understanding antibiotic application in aquaculture and its potential connection to antibiotic resistance in bacterial pathogens. Such comprehension is pivotal for formulating and implementing effective control and farm management strategies to address this pressing issue.
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Affiliation(s)
- Dhary Alewy Almashhadany
- Department of Medical Laboratory Science, College of Science, Knowledge University, Erbil 44001, Iraq
| | - Abdulwahed Ahmed Hassan
- Metedi Medical Technology Distributions, Rathenaustraße 2, 35394 Giessen, Germany
- Department of Veterinary Public Health (DVPH), College of Veterinary Medicine, University of Mosul, Mosul 41002, Iraq
| | - Rzgar Farooq Rashid
- Department of Medical Laboratory Science, College of Science, Knowledge University, Erbil 44001, Iraq
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
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Khan IUH, Chen W, Cloutier M, Lapen DR, Craiovan E, Wilkes G. Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water. BMC Microbiol 2024; 24:17. [PMID: 38191309 PMCID: PMC10773081 DOI: 10.1186/s12866-023-03119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites. RESULTS All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic. CONCLUSIONS The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.
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Affiliation(s)
- Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
| | - Wen Chen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Natural Resources Canada, Ottawa, ON, Canada
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Shi Y, Khan IUH, Radford D, Guo G, Sunohara M, Craiovan E, Lapen DR, Pham P, Chen W. Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function. BMC Microbiol 2023; 23:62. [PMID: 36882680 PMCID: PMC9990217 DOI: 10.1186/s12866-023-02755-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 10/06/2022] [Accepted: 01/03/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND The freshwater microbiome regulates aquatic ecological functionality, nutrient cycling, pathogenicity, and has the capacity to dissipate and regulate pollutants. Agricultural drainage ditches are ubiquitous in regions where field drainage is necessary for crop productivity, and as such, are first-line receptors of agricultural drainage and runoff. How bacterial communities in these systems respond to environmental and anthropogenic stressors are not well understood. In this study, we carried out a three year study in an agriculturally dominated river basin in eastern Ontario, Canada to explore the spatial and temporal dynamics of the core and conditionally rare taxa (CRT) of the instream bacterial communities using a 16S rRNA gene amplicon sequencing approach. Water samples were collected from nine stream and drainage ditch sites that represented the influence of a range of upstream land uses. RESULTS The cross-site core and CRT accounted for 5.6% of the total number of amplicon sequence variants (ASVs), yet represented, on average, over 60% of the heterogeneity of the overall bacterial community; hence, well reflected the spatial and temporal microbial dynamics in the water courses. The contribution of core microbiome to the overall community heterogeneity represented the community stability across all sampling sites. CRT was primarily composed of functional taxa involved in nitrogen (N) cycling and was linked to nutrient loading, water levels, and flow, particularly in the smaller agricultural drainage ditches. Both the core and the CRT were sensitive responders to changes in hydrological conditions. CONCLUSIONS We demonstrate that core and CRT can be considered as holistic tools to explore the temporal and spatial variations of the aquatic microbial community and can be used as sensitive indicators of the health and function of agriculturally dominated water courses. This approach also reduces computational complexity in relation to analyzing the entire microbial community for such purposes.
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Affiliation(s)
- Yichao Shi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Devon Radford
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Galen Guo
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Mark Sunohara
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Phillip Pham
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada.,Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON, K1N 9A7, Canada
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada. .,Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, ON, K1N 9A7, Canada.
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Hassan AA, Rahawy M, Alkattan LM, Khan IUH, Abdulmawjood A, Bülte M. First report of paratuberculosis (Johne's disease) in livestock farms of river buffaloes (Bubalus Bubalis) in Nineveh, Iraq. Vet Ital 2022; 58. [PMID: 36586121 DOI: 10.12834/vetit.1866.9913.1] [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] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/17/2020] [Indexed: 01/01/2023]
Abstract
The present study was designed to investigate Mycobacterium avium subsp. paratuberculosis (MAP) in dairy buffalo herds from six different geographical areas in Nineveh, Iraq. A total of 87 individual faecal samples from river buffaloes, representing 12 dairy herds, were investigated
for detection of MAP using cultural, Ziehl‑Neelsen and MAP‑specific PCR‑based methods. Overall, MAP was detected at a higher frequency at herd‑level (4/12; 33%) compared to the total individual faecal samples (14/87; 16%) with a cell density ranging from 101 to 103 CFU g‑1. A significantly (p < 0.05) higher frequency (9/17; 53%) of MAP was observed in faecal samples collected from clinically diseased as compared to healthy (5/70; 7%) buffaloes selected for the study. However, no statistically significant difference (p ≥ 0.05) was observed in the frequency of MAP occurrence between clinical (9; 64%) and apparently healthy (5; 36%) cases. This report, which is the first MAP study based on data from Iraqi dairy buffalo herds suggests that MAP transmission is a significant health risk for grazing livestock. In conclusion, this study would help farm owners and regulatory authorities to realise the importance of developing and applying best farm management practices in order to prevent transmission of MAP to healthy animals and the environment. In addition, effective diagnostic tests should be taken into account when carrying out the screening tests.
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Affiliation(s)
| | - Mohammed Rahawy
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, Mosul University, Mosul, Iraq
| | - Layth Mahmoud Alkattan
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, Mosul University, Mosul, Iraq
| | - Izhar U H Khan
- Ottawa Research and Development Center (ORDC), Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Ontario, Canada
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Michael Bülte
- Institute of Veterinary Food Science, Justus-Liebig-University Giessen, Frankfurter Street 92, 35392 Giessen, Germany
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Khan IUH, Murdock A, Mahmud M, Cloutier M, Benoit T, Bashar S, Patidar R, Mi R, Daneshfar B, Farenhorst A, Kumar A. Quantitative Assessment of First Nations Drinking Water Distribution Systems for Detection and Prevalence of Thermophilic Campylobacter Species. Int J Environ Res Public Health 2022; 19:10466. [PMID: 36078183 PMCID: PMC9518054 DOI: 10.3390/ijerph191710466] [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] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Water is considered a major route for transmitting human-associated pathogens. Although microbial water quality indicators are used to test for the presence of waterborne pathogens in drinking water, the two are poorly correlated. The current study investigates the prevalence of thermophilic DNA markers specific for Campylobacter spp. (C. jejuni and C. coli) in source water and throughout the water distribution systems of two First Nations communities in Manitoba, Canada. A total of 220 water samples were collected from various points of the drinking water distribution system (DWDS) between 2016 and 2018. Target Campylobacter spp. were always (100%) detected in a home with a fiberglass (CF) cistern, as well as the community standpipe (SP). The target bacteria were also frequently detected in treated water at the Water Treatment Plant (WTP) (78%), homes with polyethylene (CP) (60%) and concrete (CC) (58%) cisterns, homes with piped (P) water (43%) and water truck (T) samples (20%), with a maximum concentration of 1.9 × 103 cells 100 mL-1 (C. jejuni) and 5.6 × 105 cells 100 mL-1 (C. coli). Similarly, target bacteria were detected in 68% of the source water samples with a maximum concentration of 4.9 × 103 cells 100 mL-1 (C. jejuni) and 8.4 × 105 cells 100 mL-1 (C. coli). Neither target Campylobacter spp. was significantly associated with free and total chlorine concentrations in water. The study results indicate that there is an immediate need to monitor Campylobacter spp. in small communities of Canada and, particularly, to improve the DWDS in First Nations communities to minimize the risk of Campylobacter infection from drinking water sources. Further research is warranted in improving/developing processes and technologies to eliminate microbial contaminants from water.
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Affiliation(s)
- Izhar U. H. Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Anita Murdock
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Maria Mahmud
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Thomas Benoit
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Sabrin Bashar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Rakesh Patidar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ruidong Mi
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Bahram Daneshfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Annemieke Farenhorst
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Chuan J, Belov A, Cloutier M, Li X, Khan IUH, Chen W. Comparative genomics analysis and virulence-related factors in novel Aliarcobacter faecis and Aliarcobacter lanthieri species identified as potential opportunistic pathogens. BMC Genomics 2022; 23:471. [PMID: 35761183 PMCID: PMC9235176 DOI: 10.1186/s12864-022-08663-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/19/2022] [Indexed: 12/30/2022] Open
Abstract
Abstract
Background
Emerging pathogenic bacteria are an increasing threat to public health. Two recently described species of the genus Aliarcobacter, A. faecis and A. lanthieri, isolated from human or livestock feces, are closely related to Aliarcobacter zoonotic pathogens (A. cryaerophilus, A. skirrowii, and A. butzleri). In this study, comparative genomics analysis was carried out to examine the virulence-related, including virulence, antibiotic, and toxin (VAT) factors in the reference strains of A. faecis and A. lanthieri that may enable them to become potentially opportunistic zoonotic pathogens.
Results
Our results showed that the genomes of the reference strains of both species have flagella genes (flaA, flaB, flgG, flhA, flhB, fliI, fliP, motA and cheY1) as motility and export apparatus, as well as genes encoding the Twin-arginine translocation (Tat) (tatA, tatB and tatC), type II (pulE and pulF) and III (fliF, fliN and ylqH) secretory pathways, allowing them to secrete proteins into the periplasm and host cells. Invasion and immune evasion genes (ciaB, iamA, mviN, pldA, irgA and fur2) are found in both species, while adherence genes (cadF and cj1349) are only found in A. lanthieri. Acid (clpB), heat (clpA and clpB), osmotic (mviN), and low-iron (irgA and fur2) stress resistance genes were observed in both species, although urease genes were not found in them. In addition, arcB, gyrA and gyrB were found in both species, mutations of which may mediate the resistance to quaternary ammonium compounds (QACs). Furthermore, 11 VAT genes including six virulence (cadF, ciaB, irgA, mviN, pldA, and tlyA), two antibiotic resistance [tet(O) and tet(W)] and three cytolethal distending toxin (cdtA, cdtB, and cdtC) genes were validated with the PCR assays. A. lanthieri tested positive for all 11 VAT genes. By contrast, A. faecis showed positive for ten genes except for cdtB because no PCR assay for this gene was available for this species.
Conclusions
The identification of the virulence, antibiotic-resistance, and toxin genes in the genomes of A. faecis and A. lanthieri reference strains through comparative genomics analysis and PCR assays highlighted the potential zoonotic pathogenicity of these two species. However, it is necessary to extend this study to include more clinical and environmental strains to explore inter-species and strain-level genetic variations in virulence-related genes and assess their potential to be opportunistic pathogens for animals and humans.
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Alsharafani MAM, Abdullah T, Jabur ZA, Hassan AA, Alhendi AS, Abdulmawjood A, Khan IUH. Assessing synergistic effect of Jerusalem Artichoke juice and antioxidant compounds on enhanced viability and persistence of Bifidobacterium species, palatability, and shelf life. Food Sci Nutr 2022; 10:1994-2008. [PMID: 35702306 PMCID: PMC9179157 DOI: 10.1002/fsn3.2815] [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: 07/21/2021] [Revised: 09/29/2021] [Accepted: 02/18/2022] [Indexed: 11/07/2022] Open
Abstract
Commercial vegetable and fruit juices with probiotics are new functional type of beverages; however, limitations including persistence and impact of probiotic bacteria on palatability and shelf life may prevent their industrial development. This study evaluated the effect of antioxidant compounds (ascorbic acid, astaxanthin, and ginseng) on viability and persistence of Bifidobacterium spp. in Jerusalem Artichoke (JA) juice; and determine the impact of these antioxidants on the sensory (color, texture, flavor, acidity) properties, free reducing sugar (inulin and fructose), and shelf life in the fortified JA juice. Overall, the JA juice fortified with ascorbic acid showed a significant impact on the rate of persistence of two targeted bifidobacterial strains from 1 to 28 days at 5°C. Both strains produced slight acidity in ascorbic acid fortified JA juice as compared to other tested samples. Similarly, the JA juice fortified with ascorbic acid showed a significantly high increase in the total number of bifidobacterial cells of both species, enhanced palatability, and shelf life as compared to astaxanthin and ginseng extract. The quadratic model indicated a strong association between ascorbic acid, ginseng extract, and astaxanthin with a bifidobacterial cell concentration in the fortified JA juices. The Box–Behnken design was considered a feasible analysis for describing fortified JA juice and the rate of viability and persistence of bifidobacteria during 28 days of storage at 5°C in all trials. In conclusion, JA juice fortified with ascorbic acid showed a significant impact on improving the cell viability and persistence of probiotic bacteria, enhanced palatability, and shelf life as compared to other compounds tested.
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Affiliation(s)
- Mustafa A M Alsharafani
- Ministry of Science and Technology, Directorate of Environment and Water Research Food Pollution Center Baghdad Iraq
| | - Taghreed Abdullah
- Ministry of Science and Technology, Directorate of Environment and Water Research Food Pollution Center Baghdad Iraq
| | - Zahraa A Jabur
- Ministry of Science and Technology, Directorate of Environment and Water Research Food Pollution Center Baghdad Iraq
| | - Abdulwahed Ahmed Hassan
- Department of Veterinary Public Health (DVPH) College of Veterinary Medicine University Mosul Mosul Iraq.,Agriculture and Agri-Food Canada Ottawa Research and Development Centre Ottawa Ontario Canada
| | - Abeer S Alhendi
- Department of Quality Control Grain Board of Iraq Altaji, Baghdad Iraq
| | - Amir Abdulmawjood
- Agriculture and Agri-Food Canada Ottawa Research and Development Centre Ottawa Ontario Canada.,Institute of Food Quality and Food Safety University of Veterinary Medicine Hannover Hannover Germany
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada Ottawa Research and Development Centre Ottawa Ontario Canada
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10
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Khoran FP, Candlan EP, Hassan AA, Isihak FA, Abdulmawjood A, Khan IUH. Pheno- and genotypic characterization and identification of novel subtypes of Peste des Petits Ruminants virus in domestic and captive wild goats in Northern Iraq. BMC Microbiol 2021; 21:334. [PMID: 34876012 PMCID: PMC8650381 DOI: 10.1186/s12866-021-02372-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
Background Peste des Petits Ruminants (PPR) is an acute or peracute contagious transboundary viral disease that mainly affects caprine and ovine and causes significant economic impact in developing countries. After two PPR virus outbreaks in 2011 and 2014, an investigation, from August 2015 to September 2016, was carried out in Northern Iraq when an increased morbidity and mortality rates were reported in the domestic and captive wild goats. In the present study, ten domestic goat farms and seven captive wild goat herds located in seven geographical areas of Northern Iraq were clinically, pathologically, serologically and genotypically characterized to determine the prevalence and potential cause of PPR virus outbreak. Results The outbreak occurred with rate of morbidity (26.1%) and mortality (11.1%) in domestic goat farms as compared to captive wild goat herds where relatively high mortality (42.9%) and low morbidity (10.9%) rates were recorded. Based on the clinical symptoms (mucopurulent nasal discharges, ulceration and erosion of oral mucosa, profuse watery diarrhea) and necropsy (hemorrhage and congestion on mucous membranes of the colon and rectum with zebra stripes lesions) results, overall, the serological test findings revealed a high frequency (47.9%) of positive samples for anti-PPRV nucleoprotein antibodies. Furthermore, the nucleoprotein (N) gene was detected in 63.2 and 89.1% of samples using conventional and reverse transcription real-time quantitative PCR assays. A phylogenetic analysis of N gene amino acid sequences clustered with the reference strain revealed lineage IV similar to the strains isolated in 2011 and 2014, respectively. However, two sub-types of lineage IV (I and II), significantly distinct from the previous strains, were also observed. Conclusion The phylogenetic analysis suggests that movements of goats are possible cause and one of the important factors responsible for the spread of virus across the region. The study results would help in improving farm management practices by establishing a PPR virus eradication program using regular monitoring and vaccination program to control and mitigate the risk of re-emergence of PPR virus infection in domestic and captive wild goats in Iraq. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02372-2. 1. Assessment and detection of source of re-emergence of Peste des Petits Ruminants virus in goats. 2. High rate of mortality than morbidity in domestic and captive wild goat herds. 3. Identification of novel sub-types (I&II) of lineage IV. 4. Regular monitoring and strategies for improving on-site control and trade regulations enables mitigating risk of outbreaks.
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Affiliation(s)
- Faisal Polis Khoran
- Directorate of Central Veterinary Laboratory (DCVL), Erbil, Kurdistan Region, Iraq
| | - Elham Potros Candlan
- Directorate of Central Veterinary Laboratory (DCVL), Erbil, Kurdistan Region, Iraq
| | - Abdulwahed Ahmed Hassan
- Department of Veterinary Public Health (DVPH), College of Veterinary Medicine, University of Mosul, Mosul, Iraq.,Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Fanar A Isihak
- Department of Veterinary Microbiology, College of Veterinary Medicine, University of Mosul, Mosul, Iraq
| | - Amir Abdulmawjood
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada.,Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559, Hannover, Germany
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada.
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11
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Khan IUH, Becker A, Cloutier M, Plötz M, Lapen DR, Wilkes G, Topp E, Abdulmawjood A. Loop-mediated isothermal amplification: Development, validation and application of simple and rapid assays for quantitative detection of species of Arcobacteraceae family- and species-specific Aliarcobacter faecis and Aliarcobacter lanthieri. J Appl Microbiol 2020; 131:288-299. [PMID: 33174331 PMCID: PMC8359143 DOI: 10.1111/jam.14926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/29/2022]
Abstract
Aim The family Arcobacteraceae formerly genus Arcobacter has recently been reclassified into six genera. Among nine species of the genus Aliarcobacter, Aliarcobacter faecis and Aliarcobacter lanthieri have been identified as emerging pathogens potentially cause health risks to humans and animals. This study was designed to develop/optimize, validate and apply Arcobacteraceae family‐ and two species‐specific (A. faecis and A. lanthieri) loop‐mediated isothermal amplification (LAMP) assays to rapidly detect and quantify total number of cells in various environmental niches. Methods and Results Three sets of LAMP primers were designed from conserved and variable regions of 16S rRNA (family‐specific) and gyrB (species‐specific) genes. Optimized Arcobacteraceae family‐specific LAMP assay correctly amplified and detected 24 species, whereas species‐specific LAMP assays detected A. faecis and A. lanthieri reference strains as well as 91 pure and mixed culture isolates recovered from aquatic and faecal sources. The specificity of LAMP amplification of A. faecis and A. lanthieri was further confirmed by restriction fragment length polymorphism analysis. Assay sensitivities were tested using variable DNA concentrations extracted from simulated target species cells in an autoclaved agricultural water sample by achieving a minimum detection limit of 10 cells mL−1 (10 fg). Direct DNA‐based quantitative detection, from agricultural surface water, identified A. faecis (17%) and A. lanthieri (1%) at a low frequency compared to family‐level (93%) with the concentration ranging from 2·1 × 101 to 2·2 × 105 cells 100 mL−1. Conclusions Overall, these three DNA‐based rapid and cost‐effective novel LAMP assays are sensitive and can be completed in less than 40 min. They have potential for on‐site quantitative detection of species of family Arcobacteraceae, A. faecis and A. lanthieri in food, environmental and clinical matrices. Significance and Impact of the Study The newly developed LAMP assays are specific, sensitive, accurate with higher reproducibility that have potential to facilitate in a less equipped lab setting and can help in early quantitative detection and rate of prevalence in environmental niches. The assays can be adopted in the diagnostic labs and epidemiological studies.
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Affiliation(s)
- I U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - A Becker
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
| | - M Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Plötz
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
| | - D R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - G Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.,Natural Resources Canada, Ottawa, ON, Canada
| | - E Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - A Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
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12
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Benoit T, Cloutier M, Schop R, Lowerison MW, Khan IUH. Comparative assessment of growth media and incubation conditions for enhanced recovery and isolation of Acinetobacter baumannii from aquatic matrices. J Microbiol Methods 2020; 176:106023. [PMID: 32795636 DOI: 10.1016/j.mimet.2020.106023] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022]
Abstract
Acinetobacter baumannii causes serious multidrug resistant nosocomial infections around the world. This comprehensive comparative study was designed to assess the effect of temperature (30, 37 and 42 °C), incubation (aerobic and microaerobic) condition and selective [CHROMagar Acinetobacter (CHR) and Leeds Acinetobacter Medium (LAM)] and non-selective [Modified Karmali Agar (MKA)] growth media on the enhanced recovery of A. baumannii from a variety of water (agricultural, recreational, raw drinking intake source, pre-chlorinated and post-chlorinated wastewater effluent) samples spiked with a known number of A. baumannii cells. After spiking each water type with a known number of cells in 10 mL volume, the sample was passed through a membrane filter (pore size 0.45 μm) and filters were placed on different selective media plates and subjected to incubate at various incubation conditions. The results reported in this study show that for all water types tested (except post-chlorinated wastewater effluent), LAM was the most effective selective growth medium in combination with variable temperature and incubation conditions for yielding high recovery rates of A. baumannii cells. Overall, A. baumannii showed that it has a high adaptive capacity to grow on selective and non-selective growth media at different temperature and incubation conditions. The data described in this study suggest that no single incubation condition and growth media would efficiently recover A. baumannii from all environmental water types tested. This data also indicate that selective growth media and incubation condition can significantly affect the recovery of A. baumannii. Differences in recovery of A. baumannii observed in this study which appeared to be dependent on the temperature and environmental characteristics of incubation as well as the sample type, suggest the need for caution when comparing recovery using different protocols.
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Affiliation(s)
- Thomas Benoit
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Rhonda Schop
- Ontario Ministry of the Environment, Conservation and Parks, Etobioke, ON, Canada
| | | | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
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13
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Miltenburg MG, Cloutier M, Craiovan E, Lapen DR, Wilkes G, Topp E, Khan IUH. Real-time quantitative PCR assay development and application for assessment of agricultural surface water and various fecal matter for prevalence of Aliarcobacter faecis and Aliarcobacter lanthieri. BMC Microbiol 2020; 20:164. [PMID: 32546238 PMCID: PMC7298852 DOI: 10.1186/s12866-020-01826-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Aliarcobacter faecis and Aliarcobacter lanthieri are recently identified as emerging human and animal pathogens. In this paper, we demonstrate the development and optimization of two direct DNA-based quantitative real-time PCR assays using species-specific oligonucleotide primer pairs derived from rpoB and gyrA genes for A. faecis and A. lanthieri, respectively. Initially, the specificity of primers and amplicon size of each target reference strain was verified and confirmed by melt curve analysis. Standard curves were developed with a minimum quantification limit of 100 cells mL- 1 or g- 1 obtained using known quantities of spiked A. faecis and A. lanthieri reference strains in autoclaved agricultural surface water and dairy cow manure samples. RESULTS Each species-specific qPCR assay was validated and applied to determine the rate of prevalence and quantify the total number of cells of each target species in natural surface waters of an agriculturally-dominant and non-agricultural reference watershed. In addition, the prevalence and densities were determined for human and various animal (e.g., dogs, cats, dairy cow, and poultry) fecal samples. Overall, the prevalence of A. faecis for surface water and feces was 21 and 28%, respectively. The maximum A. faecis concentration for water and feces was 2.3 × 107 cells 100 mL- 1 and 1.2 × 107 cells g- 1, respectively. A. lanthieri was detected at a lower frequency (2%) with a maximum concentration in surface water of 4.2 × 105 cells 100 mL- 1; fecal samples had a prevalence and maximum density of 10% and 2.0 × 106 cells g- 1, respectively. CONCLUSIONS The results indicate that the occurrence of these species in agricultural surface water is potentially due to fecal contamination of water from livestock, human, or wildlife as both species were detected in fecal samples. The new real-time qPCR assays can facilitate rapid and accurate detection in < 3 h to quantify total numbers of A. faecis and A. lanthieri cells present in various complex environmental samples.
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Affiliation(s)
- Mary G Miltenburg
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada.,Canadian Food Inspection Agency (CFIA), Ottawa, ON, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada.,Natural Resources Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada.
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14
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Hassan AA, Khan IUH, Ganz S, Wehrend A, Failing K, Eisenberg T, Abdulmawjood A, Bülte M. Assessing efficacy of N-Acetyl-l-Cysteine-Sodium Hydroxide on bacterial viability and enhanced recovery of Mycobacterium avium subsp. paratuberculosis from bovine colostrum. J Microbiol Methods 2020; 175:105968. [PMID: 32479871 DOI: 10.1016/j.mimet.2020.105968] [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: 05/06/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
Abstract
The standard procedure for the improved cultural recovery of viable Mycobacterium spp. from diverse samples mainly depends on reducing the viability of background microbiota using different chemical compounds. This study was designed to i) evaluate the efficacy and comparison between N-Acetyl-l-Cysteine-Sodium hydroxide (NALC-2% NaOH) and hexadecylpyridinium chloride (0.75% HPC) treatment and exposure time on reducing the viability of undesirable microorganisms with minimal impact on colostrum consistency; and ii) assess the impact of NALC-2% NaOH on improved and enhanced recovery of Mycobacterium avium subsp. paratuberculosis (MAP) in spiked postpartum colostrum samples and consistency of colostrum. A total of 40 samples, each treated with NALC-2% NaOH for 15 min or 0.75% HPC for 5 h, were investigated for total mesophilic aerobic bacteria (MAB) and enterobacteria (EB) (CFU mL-1). The results showed that treatment of colostrum samples with NALC-2% NaOH completely eliminated EB and significantly reduced MAB (3.6 log10 CFU mL-1). Conversely, samples treated with 0.75% HPC produced a complex mixture following interaction with the colostrum protein and showed non-significant and variable results. In addition, the spiked colostrum treated with NALC-2% NaOH for 15 min revealed recovery of viable MAP cells with a minimum limit of detection of 1.36 log10 CFU 10 mL-1 where no change in the consistency of colostrum was observed. In conclusion, 15-min NALC-2% NaOH treatment of colostrum may significantly reduce the viability of undesirable microorganisms and help to enhance the efficient recovery of MAP without impacting the consistency of high quality postpartum colostrum. This rapid procedure is suitable for efficient recovery and early detection of MAP as well as preventing its transmission to neonates and young calves in MAP infected herds.
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Affiliation(s)
- Abdulwahed Ahmed Hassan
- Institute of Veterinary Food Science, Justus-Liebig-University Gießen, Frankfurter Street 92, D-35392 Gießen, Germany; Department of Veterinary Public Health (DVPH), College of Veterinary Medicine, Mosul University, Mosul, Iraq.
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Sebastian Ganz
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-University Gießen, Frankfurter Str. 106, D-35392 Gießen, Germany
| | - Axel Wehrend
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-University Gießen, Frankfurter Str. 106, D-35392 Gießen, Germany
| | - Klaus Failing
- Biomathematik und Datenverarbeitung, Justus-Liebig-University Gießen, Frankfurter Str. 95, D-35392 Gießen, Germany
| | - Tobias Eisenberg
- Landesbetrieb Hessisches Landeslabor, Schubertstr. 60, 35392 Gießen, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - Michael Bülte
- Institute of Veterinary Food Science, Justus-Liebig-University Gießen, Frankfurter Street 92, D-35392 Gießen, Germany
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15
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Hassan AA, Ganz S, Schneider F, Wehrend A, Khan IUH, Failing K, Bülte M, Abdulmawjood A. Quantitative assessment of German Holstein dairy cattle colostrum and impact of thermal treatment on quality of colostrum viscosity and immunoglobulins. BMC Res Notes 2020; 13:191. [PMID: 32228687 PMCID: PMC7106573 DOI: 10.1186/s13104-020-05019-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/13/2020] [Accepted: 03/13/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This study aimed to determine the color, fat, viscosity, IgG concentration, %Brix and refractive index of fresh postpartum colostrum of German Holstein dairy cattle and assess the impact of different thermal treatments on the visual and dynamic viscosity, in association to IgG concentration, of colostrum that can be used for pasteurization process. RESULTS Of the total 40 fresh postpartum colostrum, the color of colostrum (ranging from white-pale yellow to yellow and dark-yellowish), fat (1.4-8.2 100 g-1), IgG (4-116 mg mL-1), %Brix (8.5-35.4%), refractive index (1.3454-1.3905 nD), visual (ranging from watery to liquid and thick) and dynamic (4.9-219 cp) viscosity, were recorded. Statistical analysis between visual and dynamic viscosity of fresh colostrum showed significant correlation coefficients (rs = 634). Moreover, a significant correlation between viscosity and three IgG concentrations was also observed. Heat-treated colostrum showed dynamic viscosity ranged from 25 to 3066 cP, where dynamic viscosity of colostrum before- and after heat-treatment showed no significant correlation. Treated colostrum at 60 °C/60 min and 63.5 °C/30 min containing IgG concentration ≤ 80 mg mL-1 and ≤ 68 mg mL-1 showed no significant change in the viscosity and can successfully be applied for pasteurization of first postpartum colostrum.
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Affiliation(s)
- Abdulwahed Ahmed Hassan
- Institute of Veterinary Food Science, Justus-Liebig-University Gießen, Frankfurter Street 92, 35392, Giessen, Germany. .,Department of Veterinary Public Health (DVPH), College of Veterinary Medicine, Mosul University, Mosul, Iraq.
| | - Sebastian Ganz
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-University Gießen, Frankfurter Str. 106, 35392, Giessen, Germany
| | - Florian Schneider
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-University Gießen, Frankfurter Str. 106, 35392, Giessen, Germany
| | - Axel Wehrend
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-University Gießen, Frankfurter Str. 106, 35392, Giessen, Germany
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6, Canada
| | - Klaus Failing
- Biomathematik und Datenverarbeitung, Justus-Liebig-University Gießen, Frankfurter Str. 95, 35392, Giessen, Germany
| | - Michael Bülte
- Institute of Veterinary Food Science, Justus-Liebig-University Gießen, Frankfurter Street 92, 35392, Giessen, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany
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Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D, Newton G, Séguin A, Beaudette L, Bilkhu S, Bush A, Chen W, Comte J, Condie J, Crevecoeur S, El-Kayssi N, Emilson EJS, Fancy DL, Kandalaft I, Khan IUH, King I, Kreutzweiser D, Lapen D, Lawrence J, Lowe C, Lung O, Martineau C, Meier M, Ogden N, Paré D, Phillips L, Porter TM, Sachs J, Staley Z, Steeves R, Venier L, Veres T, Watson C, Watson S, Macklin J. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. Sci Total Environ 2020; 710:135906. [PMID: 31926407 DOI: 10.1016/j.scitotenv.2019.135906] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 07/05/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.
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Affiliation(s)
- Thomas A Edge
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.
| | | | - Nellie Gagné
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Charles Greer
- National Research Council Canada, Montreal, Quebec, Canada
| | - David Konkin
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Glen Newton
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | | | - Lee Beaudette
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Satpal Bilkhu
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Alexander Bush
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Wen Chen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jérôme Comte
- Environment and Climate Change Canada, Burlington, Ontario, Canada; Institut National de la Recherche Scientifique, Québec, Québec, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | | | | | - Erik J S Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Donna-Lee Fancy
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Iyad Kandalaft
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ian King
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - David Kreutzweiser
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - David Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John Lawrence
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Lowe
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | | | - Matthew Meier
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nicholas Ogden
- Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada
| | - David Paré
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Lori Phillips
- Agriculture and Agri-Food Canada, Harrow, Ontario, Canada
| | - Teresita M Porter
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada; Biodiversity Institute of Ontario, University of Guelph, Ontario, Canada
| | - Joel Sachs
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Zachery Staley
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Royce Steeves
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Lisa Venier
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Teodor Veres
- National Research Council Canada, Ottawa, Ontario, Canada
| | - Cynthia Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Susan Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - James Macklin
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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Zambri M, Cloutier M, Adam Z, Lapen DR, Wilkes G, Sunohara M, Topp E, Talbot G, Khan IUH. Novel virulence, antibiotic resistance and toxin gene-specific PCR-based assays for rapid pathogenicity assessment of Arcobacter faecis and Arcobacter lanthieri. BMC Microbiol 2019; 19:11. [PMID: 30634926 PMCID: PMC6330389 DOI: 10.1186/s12866-018-1357-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 05/25/2018] [Accepted: 11/28/2018] [Indexed: 11/30/2022] Open
Abstract
Background Arcobacter faecis and A. lanthieri are two newly classified species of genus Arcobacter. The prevalence and distribution of virulence, antibiotic resistance and toxin (VAT) genes in these species are required to assess their potential pathogenic health impacts to humans and animals. This study (i) developed species- and gene-specific primer pairs for the detection of six virulence, two antibiotic resistance, and three toxin genes in two target species; (ii) optimized eight single-tube multiplex and three monoplex PCR protocols using the newly developed species- and gene-specific primers; and (iii) conducted specificity and sensitivity evaluations as well as validation of eleven mono- and multiplex PCR assays by testing A. faecis (n= 29) and A. lanthieri (n= 10) strains isolated from various fecal and agricultural water sources to determine the prevalence and distribution of VAT genes and assess the degree of pathogenicity within the two species. Results Detection of all ten and eleven target VAT genes, and expression of cytolethal distending toxin (cdtA, cdtB and cdtC) genes in A. faecis and A. lanthieri reference strains with high frequency in field isolates suggest that they are potentially pathogenic strains. These findings indicate that these two species can pose a health risk to humans and animals. Conclusions The study results show that the developed mono- and multiplex PCR (mPCR) assays are simple, rapid, reliable and sensitive for the simultaneous assessment of the potential pathogenicity and antibiotic resistance profiling of tet(O) and tet(W) genes in these two newly discovered species. Also, these assays can be useful in diagnostic and analytical laboratories to determine the pathotypes and assessment of the virulence and toxin factors associated to human and animal infections. Electronic supplementary material The online version of this article (10.1186/s12866-018-1357-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew Zambri
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada.,Department of Biology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Zaky Adam
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada.,School of Information Technology and Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Mark Sunohara
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Guylaine Talbot
- Sherbrooke Research and Development Centre (SRDC), Agriculture and Agri-Food Canada, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada.
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Chen W, Wilkes G, Khan IUH, Pintar KDM, Thomas JL, Lévesque CA, Chapados JT, Topp E, Lapen DR. Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach. Front Microbiol 2018; 9:2301. [PMID: 30425684 PMCID: PMC6218688 DOI: 10.3389/fmicb.2018.02301] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/10/2018] [Indexed: 12/30/2022] Open
Abstract
This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Graham Wilkes
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | | | - Janis L Thomas
- Ontario Ministry of the Environment and Climate Change, Environmental Monitoring and Reporting Branch, Toronto, ON, Canada
| | - C André Lévesque
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Julie T Chapados
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, London, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Center, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Liu L, Cloutier M, Craiovan E, Edwards M, Frey SK, Gottschall N, Lapen DR, Sunohara M, Topp E, Khan IUH. Quantitative real-time PCR-based assessment of tile drainage management influences on bacterial pathogens in tile drainage and groundwater. Sci Total Environ 2018; 624:1586-1597. [PMID: 29929267 DOI: 10.1016/j.scitotenv.2017.10.200] [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] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 06/08/2023]
Abstract
This study compared the impact of controlled tile drainage (CD) and freely draining (FD) systems on the prevalence and quantitative real-time PCR-based enumeration of four major pathogens including Arcobacter butzleri, Campylobacter jejuni, Campylobacter coli, and Helicobacter pylori in tile- and groundwater following a fall liquid swine manure (LSM) application on clay loam field plots. Although the prevalence of all target pathogens were detected in CD and FD systems, the loads of A. butzleri, C. jejuni, and C. coli were significantly lower in CD tile-water (p<0.05), in relation to FD tile-water. However, concentrations of A. butzleri were significantly greater in CD than FD tile-water (p<0.05). In shallow groundwater (1.2m depth), concentrations of A. butzleri, C. coli, and H. pylori showed no significant difference between CD and FD plots, while C. jejuni concentrations were significantly higher in FD plots (p<0.05). No impact of CD on the H. pylori was observed since quantitative detection in tile- and groundwater was scarce. Although speculative, H. pylori occurrence may have been related to the application of municipal biosolids four years prior to the LSM experiment. Overall, CD can be used to help minimize off-field export of pathogens into surface waters following manure applications to land, thereby reducing waterborne pathogen exposure risks to humans.
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Affiliation(s)
- Linda Liu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - Michel Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - Emilia Craiovan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - Mark Edwards
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - Steven K Frey
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6; Aquanty Inc., 564 Weber Street North, Waterloo, Ontario, Canada, N2L 5C6
| | - Natalie Gottschall
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - Mark Sunohara
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada, N5V 4T3
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada, K1A 0C6.
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Khan IUH, Cloutier M, Libby M, Lapen DR, Wilkes G, Topp E. Enhanced Single-tube Multiplex PCR Assay for Detection and Identification of Six Arcobacter Species. J Appl Microbiol 2017; 123:1522-1532. [PMID: 28960631 DOI: 10.1111/jam.13597] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 11/30/2022]
Abstract
AIM A single-tube multiplex PCR (mPCR) assay was developed for rapid, sensitive and simultaneous detection and identification of six Arcobacter species including two new species, A. lanthieri and A. faecis, along with A. butzleri, A. cibarius, A. cryaerophilus and A. skirrowii on the basis of differences in the lengths of their PCR products. Previously designed monoplex, mPCR and RFLP assays do not detect or differentiate A. faecis and A. lanthieri from other closely related known Arcobacter spp. METHODS AND RESULTS Primer pairs for each target species (except A. skirrowii) and mPCR protocol were newly designed and optimized using variable regions of housekeeping including cpn60, gyrA, gyrB and rpoB genes. The accuracy and specificity of the mPCR assay was assessed using DNA templates from six targets and 11 other Arcobacter spp. as well as 50 other bacterial reference species and strains. Tests on the DNA templates of target Arcobacter spp. were appropriately identified, whereas all 61 other DNA templates from other bacterial species and strains were not amplified. Sensitivity and specificity of the mPCR assay was 10 pg μl-1 of DNA concentration per target species. The optimized assay was further evaluated, validated and compared with other mPCR assays by testing Arcobacter cultures isolated from various faecal and water sources. CONCLUSIONS Study results confirm that the newly developed mPCR assay is rapid, accurate, reliable, simple, and valuable for the simultaneous detection and routine diagnosis of six human- and animal-associated Arcobacter spp. SIGNIFICANCE AND IMPACT OF THE STUDY The new mPCR assay is useful not only for pure but also mixed cultures. Moreover, it has the ability to rapidly detect six species which enhances the value of this technology for aetiological and epidemiological studies.
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Affiliation(s)
- I U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Libby
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - D R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - G Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - E Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
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Fernando DM, Khan IUH, Patidar R, Lapen DR, Talbot G, Topp E, Kumar A. Isolation and Characterization of Acinetobacter baumannii Recovered from Campylobacter Selective Medium. Front Microbiol 2016; 7:1871. [PMID: 27917170 PMCID: PMC5114274 DOI: 10.3389/fmicb.2016.01871] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 09/06/2016] [Accepted: 11/07/2016] [Indexed: 11/29/2022] Open
Abstract
Acinetobacter baumannii, a Gram-negative opportunistic pathogen, is known to cause multidrug resistant infections. This organism has primarily been isolated from clinical environments and its environmental reservoirs remain largely unknown. In the present study, we recovered seven isolates of A. baumannii growing under conditions selective for Campylobacter spp. (microaerophilic at 42°C and in the presence of antibiotics) from dairy cattle manure storage tank or surface water impacted by livestock effluents. Antibiotic susceptibility tests revealed that all of these isolates were less susceptible to at least two different clinically relevant antibiotics, compared to the type strain A. baumannii ATCC17978. Expression of resistance-nodulation-division efflux pumps, an important mechanism of intrinsic resistance in these organisms, was analyzed, and adeB was found to be overexpressed in one and adeJ was overexpressed in three isolates. Comparison of these isolates using genomic DNA Macro-Restriction Fragment Pattern Analysis (MRFPA) revealed relatively low relatedness among themselves or with some of the clinical isolates from previous studies. This study suggests that A. baumannii isolates are capable of growing under selective conditions for Campylobacter spp. and that this organism can be present in manure and water.
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Affiliation(s)
- Dinesh M Fernando
- Department of Microbiology, University of Manitoba , Winnipeg, MB, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, ON, Canada
| | - Rakesh Patidar
- Department of Microbiology, University of Manitoba , Winnipeg, MB, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, ON, Canada
| | - Guylaine Talbot
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada , Sherbrooke, QC, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada , London, ON, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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Laprade N, Cloutier M, Lapen DR, Topp E, Wilkes G, Villemur R, Khan IUH. Detection of virulence, antibiotic resistance and toxin (VAT) genes in Campylobacter species using newly developed multiplex PCR assays. J Microbiol Methods 2016; 124:41-7. [PMID: 27012738 DOI: 10.1016/j.mimet.2016.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/03/2016] [Accepted: 03/16/2016] [Indexed: 11/17/2022]
Abstract
Campylobacter species are one of the leading causes of bacterial gastroenteritis in humans worldwide. This twofold study was sought to: i) develop and optimize four single-tube multiplex PCR (mPCR) assays for the detection of six virulence (ciaB, dnaJ, flaA, flaB, pldA and racR), three toxin (cdtA, cdtB and cdtC) and one antibiotic resistance tet(O) genes in thermophilic Campylobacter spp. and ii) apply and evaluate the developed mPCR assays by testing 470 previously identified C. jejuni, C. coli and C. lari isolates from agricultural water. In each mPCR assay, a combination of two or three sets of primer pairs for virulence, antibiotic resistance and toxin (VAT) genes was used and optimized. Assay 1 was developed for the detection of dnaJ, racR and cdtC genes with expected amplification sizes of 720, 584 and 182bp. Assay 2 generated PCR amplicons for tet(O) and cdtA genes of 559 and 370bp. Assay 3 amplified cdtB ciaB, and pldA genes with PCR amplicon sizes of 620, 527 and 385bp. Assay 4 was optimized for flaA and flaB genes that generated PCR amplicons of 855 and 260bp. The primer pairs and optimized PCR protocols did not show interference and/or cross-amplification with each other and generated the expected size of amplification products for each target VAT gene for the C. jejuni ATCC 33291 reference strain. Overall, all ten target VAT genes were detected at a variable frequency in tested isolates of thermophilic Campylobacter spp. where cdtC, flaB, ciaB, cdtB, cdtA and pldA were commonly detected compared to the flaA, racR, dnaJ and tet(O) genes which were detected with less frequency. The developed mPCR assays are simple, rapid, reliable and sensitive tools for simultaneously assessing potential pathogenicity and antibiotic resistance profiling in thermophilic Campylobacter spp. The mPCR assays will be useful in diagnostic and analytical settings for routine screening of VAT characteristics of Campylobacter spp. as well as being applicable in epidemiological studies by providing information that could be related to the risk of human infection.
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Affiliation(s)
- Natacha Laprade
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Richard Villemur
- INRS-Institute Armand-Frappier Research Centre, Laval, QC, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
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Whiteduck-Léveillée J, Cloutier M, Topp E, Lapen DR, Talbot G, Villemur R, Khan IUH. Development and evaluation of multiplex PCR assays for rapid detection of virulence-associated genes in Arcobacter species. J Microbiol Methods 2016; 121:59-65. [PMID: 26769558 DOI: 10.1016/j.mimet.2015.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/17/2015] [Accepted: 12/31/2015] [Indexed: 02/06/2023]
Abstract
As the pathogenicity of Arcobacter species might be associated with various virulence factors, this study was aimed to develop and optimize three single-tube multiplex PCR (mPCR) assays that can efficiently detect multiple virulence-associated genes (VAGs) in Arcobacter spp. including the Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii, respectively. The recognized target virulence factors used in the study were fibronectin binding protein (cj1349), filamentous hemagglutinin (hecA), hemolysin activation protein (hecB), hemolysin (tlyA), integral membrane protein virulence factor (mviN), invasin (ciaB), outer membrane protein (irgA) and phospholipase (pldA). Identical results were obtained between singleplex PCR and mPCR assays and no cross- and/or non-specific amplification products were obtained when tested against other closely related bacterial species. The sensitivities of these three mPCR assays were ranging from 1ngμL(-1) to 100ngμL(-1) DNA. The developed assays with combinations of duplex or triplex PCR primer pairs of VAGs were further evaluated and validated by applying them to isolates of the A. butzleri, A. cryaerophilus and A. skirrowii recovered from fecal samples of human and animal origins. The findings revealed that the distribution of the ciaB (90%), mviN (70%), tlyA (50%) and pldA (45%) genes among these target species was significantly higher than the hecA (16%), hecB (10%) and each of irgA and cj1349 (6%) genes, respectively. The newly developed mPCR assays can be used as rapid technique and useful markers for the detection, prevalence and profiling of VAGs in the Arcobacter spp. Moreover, these assays can easily be performed with a high throughput to give a presumptive identification of the causal pathogen in epidemiological investigation of human infections.
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Affiliation(s)
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Guylaine Talbot
- Sherbrooke Research and Development Centre (SRDC), Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Richard Villemur
- INRS-Institute Armand-Frappier Research Centre, Laval, QC, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
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Whiteduck-Léveillée K, Whiteduck-Léveillée J, Cloutier M, Tambong JT, Xu R, Topp E, Arts MT, Chao J, Adam Z, Lévesque CA, Lapen DR, Villemur R, Khan IUH. Identification, characterization and description of Arcobacter faecis sp. nov., isolated from a human waste septic tank. Syst Appl Microbiol 2015; 39:93-9. [PMID: 26723853 DOI: 10.1016/j.syapm.2015.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 07/06/2015] [Revised: 10/29/2015] [Accepted: 12/03/2015] [Indexed: 02/04/2023]
Abstract
A study on the taxonomic classification of Arcobacter species was performed on the cultures isolated from various fecal sources where an Arcobacter strain AF1078(T) from human waste septic tank near Ottawa, Ontario, Canada was characterized using a polyphasic approach. Genetic investigations including 16S rRNA, atpA, cpn60, gyrA, gyrB and rpoB gene sequences of strain AF1078(T) are unique in comparison with other arcobacters. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain is most closely related to Arcobacter lanthieri and Arcobacter cibarius. Analyses of atpA, cpn60, gyrA, gyrB and rpoB gene sequences suggested that strain AF1078(T) formed a phylogenetic lineage independent of other species in the genus. Whole-genome sequence, DNA-DNA hybridization, fatty acid profile and phenotypic analysis further supported the conclusion that strain AF1078(T) represents a novel Arcobacter species, for which the name Arcobacter faecis sp. nov. is proposed, with type strain AF1078(T) (=LMG 28519(T); CCUG 66484(T)).
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Affiliation(s)
| | | | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - James T Tambong
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
| | - Michael T Arts
- Ryerson University, Department of Chemistry and Biology, Toronto, ON, Canada
| | - Jerry Chao
- Ontario Ministry of the Environment, Toronto, ON, Canada
| | - Zaky Adam
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - C André Lévesque
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Richard Villemur
- INRS-Institute Armand-Frappier Research Centre, Laval, QC, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
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Frey SK, Topp E, Khan IUH, Ball BR, Edwards M, Gottschall N, Sunohara M, Lapen DR. Quantitative Campylobacter spp., antibiotic resistance genes, and veterinary antibiotics in surface and ground water following manure application: Influence of tile drainage control. Sci Total Environ 2015; 532:138-153. [PMID: 26065824 DOI: 10.1016/j.scitotenv.2015.03.114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 10/31/2014] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 06/04/2023]
Abstract
This work investigated chlortetracycline, tylosin, and tetracycline (plus transformation products), and DNA-based quantitative Campylobacter spp. and Campylobacter tetracycline antibiotic resistant genes (tet(O)) in tile drainage, groundwater, and soil before and following a liquid swine manure (LSM) application on clay loam plots under controlled (CD) and free (FD) tile drainage. Chlortetracycline/tetracycline was strongly bound to manure solids while tylosin dominated in the liquid portion of manure. The chlortetracycline transformation product isochlortetracycline was the most persistent analyte in water. Rhodamine WT (RWT) tracer was mixed with manure and monitored in tile and groundwater. RWT and veterinary antibiotic (VA) concentrations were strongly correlated in water which supported the use of RWT as a surrogate tracer. While CD reduced tile discharge and eliminated application-induced VA movement (via tile) to surface water, total VA mass loading to surface water was not affected by CD. At both CD and FD test plots, the biggest 'flush' of VA mass and highest VA concentrations occurred in response to precipitation received 2d after application, which strongly influenced the flow abatement capacity of CD on account of highly elevated water levels in field initiating overflow drainage for CD systems (when water level <0.3m below surface). VA concentrations in tile and groundwater became very low within 10d following application. Both Campylobacter spp. and Campylobacter tet(O) genes were present in groundwater and soil prior to application, and increased thereafter. Unlike the VA compounds, Campylobacter spp. and Campylobacter tet(O) gene loadings in tile drainage were reduced by CD, in relation to FD.
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Affiliation(s)
- Steven K Frey
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, 960 Carling Drive, Ottawa, ON K1A 0C6, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Center, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, 960 Carling Drive, Ottawa, ON K1A 0C6, Canada
| | - Bonnie R Ball
- Ontario Ministry of Agriculture, Food, and Rural Affairs, 581 Huron St, Stratford, Ontario N5A 5T8, Canada
| | - Mark Edwards
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, 960 Carling Drive, Ottawa, ON K1A 0C6, Canada
| | - Natalie Gottschall
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, 960 Carling Drive, Ottawa, ON K1A 0C6, Canada
| | - Mark Sunohara
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, 960 Carling Drive, Ottawa, ON K1A 0C6, Canada
| | - David R Lapen
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Center, 960 Carling Drive, Ottawa, ON K1A 0C6, Canada.
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Jokinen CC, Koot J, Cole L, Desruisseau A, Edge TA, Khan IUH, Koning W, Lapen DR, Pintar KDM, Reid-Smith R, Thomas JL, Topp E, Wang LY, Wilkes G, Ziebell K, van Bochove E, Gannon VPJ. The distribution of Salmonella enterica serovars and subtypes in surface water from five agricultural regions across Canada. Water Res 2015; 76:120-131. [PMID: 25799976 DOI: 10.1016/j.watres.2015.02.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 06/28/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
Serovar prevalence of the zoonotic pathogen, Salmonella enterica, was compared among 1624 surface water samples collected previously from five different Canadian agricultural watersheds over multiple years. Phagetyping, pulsed field gel electrophoresis (PFGE), and antimicrobial resistance subtyping assays were performed on serovars Enteritidis, Typhimurium, and Heidelberg. Serovars and subtypes from surface water were compared with those from animal feces, human sewage, and serovars reported to cause salmonellosis in Canadians. Sixty-five different serovars were identified in surface water; only 32% of these were isolated from multiple watersheds. Eleven of the 13 serovars most commonly reported to cause salmonellosis in Canadians were identified in surface water; isolates of these serovars constituted >40% of the total isolates. Common phagetypes and PFGE subtypes of serovars associated with illness in humans such as S. Enteritidis and S. Typhimurium were also isolated from surface water and animal feces. Antimicrobial resistance was generally low, but was highest among S. Typhimurium. Monitoring of these rivers helps to identify vulnerable areas of a watershed and, despite a relatively low prevalence of S. enterica overall, serovars observed in surface water are an indication of the levels of specific S. enterica serovars present in humans and animals.
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Affiliation(s)
- C C Jokinen
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Lethbridge, Alberta, Canada; Alberta Agriculture and Rural Development, Irrigation and Farm Water Division, Lethbridge, Alberta, Canada.
| | - J Koot
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Lethbridge, Alberta, Canada; University of Victoria, Victoria, BC, Canada.
| | - L Cole
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada.
| | - A Desruisseau
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada.
| | - T A Edge
- Environment Canada, Burlington, Ontario, Canada.
| | - I U H Khan
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada.
| | - W Koning
- Alberta Environment and Sustainable Resource Development, Calgary, Alberta, Canada.
| | - D R Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada.
| | - K D M Pintar
- FoodNet Canada, Centre for Foodborne Environmental and Zoonotic Infectious Diseases, Ottawa, Ontario, Canada.
| | - R Reid-Smith
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada.
| | - J L Thomas
- Ontario Ministry of the Environment and Climate Change, Toronto, Ontario, Canada.
| | - E Topp
- Agriculture and Agri-Food Canada, London, Ontario, Canada.
| | - L Y Wang
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Lethbridge, Alberta, Canada.
| | - G Wilkes
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada.
| | - K Ziebell
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada.
| | - E van Bochove
- Agriculture and Agri-Food Canada, Quebec, QC, Canada.
| | - V P J Gannon
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Lethbridge, Alberta, Canada.
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Whiteduck-Léveillée K, Whiteduck-Léveillée J, Cloutier M, Tambong JT, Xu R, Topp E, Arts MT, Chao J, Adam Z, André Lévesque C, Lapen DR, Villemur R, Talbot G, Khan IUH. Arcobacter lanthieri sp. nov., isolated from pig and dairy cattle manure. Int J Syst Evol Microbiol 2015; 65:2709-2716. [PMID: 25977280 DOI: 10.1099/ijs.0.000318] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A study was undertaken to determine the prevalence and diversity of species of the genus Arcobacter in pig and dairy cattle manure, which led to the identification of strains AF1440T, AF1430 and AF1581. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains confirmed that they belonged to the genus Arcobacter and were different from all known species of the genus. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. Their unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of the strains from other species of the genus Arcobacter. The isolates were found to be oxidase, catalase and esterase positive and urease negative; they grew well at 30 °C under microaerophilic conditions and produced nitrite and acetoin. Based on their common origin and various physiological properties, it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov. The type strain is AF1440T ( = LMG 28516T = CCUG 66485T); strains AF1430 ( = LMG 28515 = CCUG 66486) and AF1581 ( = LMG 28517 = CCUG 66487) are reference strains.
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Affiliation(s)
- Kerri Whiteduck-Léveillée
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Jenni Whiteduck-Léveillée
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michel Cloutier
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - James T Tambong
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Renlin Xu
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Edward Topp
- Southern Crop Protection and Food Research Centre (SCPFRC), Agriculture and Agri-Food Canada, London, ON, Canada
| | - Michael T Arts
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Jerry Chao
- Ontario Ministry of the Environment, Toronto, ON, Canada
| | - Zaky Adam
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - C André Lévesque
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - David R Lapen
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Richard Villemur
- INRS-Institute Armand-Frappier Research Centre, Laval, QC, Canada
| | - Guylaine Talbot
- Dairy and Swine Research Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Izhar U H Khan
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Samarajeewa AD, Hammad A, Masson L, Khan IUH, Scroggins R, Beaudette LA. Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia. J Microbiol Methods 2014; 108:103-11. [PMID: 25479430 DOI: 10.1016/j.mimet.2014.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 06/26/2014] [Revised: 11/24/2014] [Accepted: 11/24/2014] [Indexed: 10/24/2022]
Abstract
Characterization of commercial microbial consortia products for human and environmental health risk assessment is a major challenge for regulatory agencies. As a means to develop an approach to assess the potential environmental risk of these products, research was conducted to compare four genomics methods for characterizing bacterial communities; (i) Denaturing Gradient Gel Electrophoresis (DGGE), (ii) Clonal-Restriction Fragment Length Polymorphism (C/RFLP), (iii) partial 16S rDNA amplification, cloning followed by Sanger sequencing (PRACS) and (iv) Next-Generation Sequencing (NGS) based on Ion Torrent technology. A commercially available microbial consortium, marketed as a remediation agent for degrading petroleum hydrocarbon contamination in soil and water, was assessed. The bacterial composition of the commercial microbial product was characterized using the above four methods. PCR amplification of 16S rDNA was performed targeting the variable region V6 for DGGE, C/RFLP and PRACS and V5 for Ion Torrent sequencing. Ion Torrent technology was shown to be a promising tool for initial screening by detecting the majority of bacteria in the consortium that were also detected by DGGE, C/RFLP and PRACS. Additionally, Ion Torrent sequencing detected some of the bacteria that were claimed to be in the product, while three other methods failed to detect these specific bacteria. However, the relative proportions of the microbial composition detected by Ion Torrent were found to be different from DGGE, C/RFLP and PRACS, which gave comparable results across these three methods. The discrepancy of the Ion Torrent results may be due to the short read length generated by this technique and the targeting of different variable regions on the 16S rRNA gene used in this study. Arcobacter spp. a potential pathogenic bacteria was detected in the product by all methods, which was further confirmed using genus and species-specific PCR, RFLP and DNA-based sequence analyses. However, the viability of Arcobacter spp. was not confirmed. This study suggests that a combination of two or more methods may be required to ascertain the microbial constituents of a commercial microbial consortium reliably and for the presence of potentially human pathogenic contaminants.
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Affiliation(s)
- A D Samarajeewa
- Biological Assessment and Standardization Section, Environment Canada, 335 River Road, Ottawa, Ontario, Canada K1V 1C7.
| | - A Hammad
- Biological Assessment and Standardization Section, Environment Canada, 335 River Road, Ottawa, Ontario, Canada K1V 1C7
| | - L Masson
- National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Quebec, Canada H4P 2R2
| | - I U H Khan
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, Canada K1A 0C6
| | - R Scroggins
- Biological Assessment and Standardization Section, Environment Canada, 335 River Road, Ottawa, Ontario, Canada K1V 1C7
| | - L A Beaudette
- Biological Assessment and Standardization Section, Environment Canada, 335 River Road, Ottawa, Ontario, Canada K1V 1C7
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Khan IUH, Gannon V, Jokinen CC, Kent R, Koning W, Lapen DR, Medeiros D, Miller J, Neumann NF, Phillips R, Schreier H, Topp E, van Bochove E, Wilkes G, Edge TA. A national investigation of the prevalence and diversity of thermophilic Campylobacter species in agricultural watersheds in Canada. Water Res 2014; 61:243-252. [PMID: 24930011 DOI: 10.1016/j.watres.2014.05.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 01/06/2014] [Revised: 05/06/2014] [Accepted: 05/19/2014] [Indexed: 06/03/2023]
Abstract
The occurrence and diversity of thermophilic Campylobacter species (C. jejuni, coli, and lari) were studied in water samples from four river basins located across Canada. These basins located in Quebec (Bras d'Henri), Alberta (Oldman), Ontario (South Nation), and British Columbia (Sumas) represented some of the most intensive farming areas in Canada for hog, beef cattle, dairy cattle, and poultry, respectively. This study analyzed 769 water samples collected from 23 monitoring sites with agricultural influence, and four reference sites with limited or no agricultural influence. Water samples were collected bi-weekly over two years and analyzed for Campylobacter using a semi-quantitative minimum probable number (MPN) enrichment protocol. Putative isolates were confirmed by genus- and species-specific multiplex polymerase chain reaction (PCR) assays. A total of 377 (49%) water samples were positive for campylobacters with 355 samples having a cell density ranging from 4 to 4000 MPN L(-1). Campylobacters were more common at agricultural than reference sites in each river basin, although this difference was not significant in the Oldman and South Nation (p > 0.05). Campylobacter was significantly more common in the Bras d'Henri and Sumas (63%) compared to the South Nation (45%) and Oldman (33%) River basins (p < 0.05). C. jejuni, C. coli and C. lari were detected in each river basin, and these species occurred in 45% (n = 168), 34% (n = 128) and 19% (n = 73), of all Campylobacter positive samples, respectively. The remaining Campylobacter positive water samples without these three species (n = 67; 18%) were identified as other Campylobacter species. C. jejuni was the predominant species occurring in the Sumas, Oldman and South Nation River basins. However, in the Bras d'Henri River basin with intensive hog production, C. coli was the predominant species. This study found campylobacters to be common in some agricultural systems with intensive livestock farming activities, and different river basins could have strikingly different profiles of either C. jejuni or C. coli as the predominant waterborne thermophilic Campylobacter species.
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Affiliation(s)
- Izhar U H Khan
- Watershed Hydrology and Ecology Research Division (WHERD), Canada Centre for Inland Waters (CCIW), Environment Canada, 867 Lakeshore Road, Burlington L7R 4A6, Ontario, Canada; Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, K1A 0C6 Ontario, Canada.
| | - Vic Gannon
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Lethbridge, Alberta, Canada
| | - Cassandra C Jokinen
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Lethbridge, Alberta, Canada; Alberta Agriculture and Rural Development, Farm Irrigation Water Division, Lethbridge, Alberta, Canada
| | - Rob Kent
- National Water Quality Monitoring, Water Science and Technology, Environment Canada, Gatineau, Ontario, Canada
| | | | - David R Lapen
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, K1A 0C6 Ontario, Canada
| | - Diane Medeiros
- Water, and Air Quality Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Jim Miller
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | | | - Rob Phillips
- National Water Quality Monitoring, Water Science and Technology, Environment Canada, Gatineau, Ontario, Canada
| | - Hans Schreier
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Edward Topp
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Eric van Bochove
- Soils and Crop Research and Development Centre, Agriculture and Agri-Food Canada Québec, Québec, Canada
| | - Graham Wilkes
- Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, K1A 0C6 Ontario, Canada
| | - Thomas A Edge
- Watershed Hydrology and Ecology Research Division (WHERD), Canada Centre for Inland Waters (CCIW), Environment Canada, 867 Lakeshore Road, Burlington L7R 4A6, Ontario, Canada
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Adam Z, Tambong JT, Lewis CT, Lévesque CA, Chen W, Bromfield ESP, Khan IUH, Xu R. Draft Genome Sequence of Pantoea ananatis Strain LMG 2665T, a Bacterial Pathogen of Pineapple Fruitlets. Genome Announc 2014; 2:e00489-14. [PMID: 24855311 PMCID: PMC4031347 DOI: 10.1128/genomea.00489-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Pantoea ananatis LMG 2665(T), the bacterial causal agent of pineapple fruitlet rot.
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Affiliation(s)
- Zaky Adam
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - James T Tambong
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Christopher T Lewis
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - C André Lévesque
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Wen Chen
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Eden S P Bromfield
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Izhar U H Khan
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Renlin Xu
- Eastern Cereal and Oilseed Research Center (ECORC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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Ryu H, Elk M, Khan IUH, Harwood VJ, Molina M, Edge TA, Domingo JS. Comparison of two poultry litter qPCR assays targeting the 16S rRNA gene of Brevibacterium sp. Water Res 2014; 48:613-621. [PMID: 24169514 DOI: 10.1016/j.watres.2013.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 05/23/2013] [Revised: 09/18/2013] [Accepted: 10/06/2013] [Indexed: 06/02/2023]
Abstract
Chicken feces commonly contain human pathogens and are also important sources of fecal pollution in environmental waters. Consequently, methods that can detect chicken fecal pollution are needed in public health and environmental monitoring studies. In this study, we compared a previously developed SYBR green qPCR assay (LA35) to a novel TaqMan qPCR assay (CL) for the environmental detection of poultry-associated fecal pollution. We tested both assays against chicken litter (n = 40), chicken fecal samples (n = 186), non-chicken fecal sources (n = 484), and environmental water samples (n = 323). Most chicken litter samples (i.e., ≥ 98%) were positive for both assays with relatively high signal intensities, whereas only 23% and 12% of poultry fecal samples (n = 186) were positive with the LA35 and the CL assays, respectively. Data using fecal samples from non-target animal species showed that the assays are highly host-associated (≥ 95%). Bayesian statistical models showed that the two assays are associated with relatively low probability of false-positive and false-negative signals in water samples. The CL marker had a lower prevalence than the LA35 assay when tested against environmental water samples (i.e., 21% vs. 31% positive signals). However, by combining the results from the two assays the detection levels increased to 41%, suggesting that using multiple assays can improve the detection of chicken-fecal pollution in environmental waters.
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Affiliation(s)
- Hodon Ryu
- National Risk Management Research Laboratory, Cincinnati, OH, USA
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Edge TA, El-Shaarawi A, Gannon V, Jokinen C, Kent R, Khan IUH, Koning W, Lapen D, Miller J, Neumann N, Phillips R, Robertson W, Schreier H, Scott A, Shtepani I, Topp E, Wilkes G, van Bochove E. Investigation of an Escherichia coli environmental benchmark for waterborne pathogens in agricultural watersheds in Canada. J Environ Qual 2012; 41:21-30. [PMID: 22218170 DOI: 10.2134/jeq2010.0253] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Canada's National Agri-Environmental Standards Initiative sought to develop an environmental benchmark for low-level waterborne pathogen occurrence in agricultural watersheds. A field study collected 902 water samples from 27 sites in four intensive agricultural watersheds across Canada from 2005 to 2007. Four of the sites were selected as reference sites away from livestock and human fecal pollution sources in each watershed. Water samples were analyzed for Campylobacter spp., Salmonella spp., Escherichia coli O157:H7, Cryptosporidium spp., Giardia spp., and the water quality indicator E. coli. The annual mean number of pathogen species was higher at agricultural sites (1.54 ± 0.07 species per water sample) than at reference sites (0.75 ± 0.14 species per water sample). The annual mean concentration of E. coli was also higher at agricultural sites (491 ± 96 colony-forming units [cfu] 100 mL(-1)) than at reference sites (53 ± 18 cfu 100 mL(-1)). The feasibility of adopting existing E. coli water quality guideline values as an environmental benchmark was assessed, but waterborne pathogens were detected at agricultural sites in 80% of water samples with low E. coli concentrations (<100 cfu 100 mL(-1)). Instead, an approach was developed based on using the natural background occurrence of pathogens at reference sites in agricultural watersheds to derive provisional environmental benchmarks for pathogens at agricultural sites. The environmental benchmarks that were derived were found to represent E. coli values lower than geometric mean values typically found in recreational water quality guidelines. Additional research is needed to investigate environmental benchmarks for waterborne pathogens within the context of the "One World, One Health" perspective for protecting human, domestic animal, and wildlife health.
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Affiliation(s)
- T A Edge
- Water Science & Technology, National Water Research Institute, Environment Canada, Burlington, ON L7R 4A6, Canada.
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Selvaraju SB, Khan IUH, Yadav JS. Susceptibility of Mycobacterium immunogenum and Pseudomonas fluorescens to formaldehyde and non-formaldehyde biocides in semi-synthetic metalworking fluids. Int J Mol Sci 2011; 12:725-41. [PMID: 21340010 PMCID: PMC3039976 DOI: 10.3390/ijms12010725] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium immunogenum, a newly identified member of the Mycobacterium chelonae_M. abscessus complex is considered a potential etiological agent for hypersensitivity pneumonitis (HP) in machine workers exposed to contaminated metalworking fluid (MWF). This study investigated the biocidal efficacy of the frequently applied commercial formaldehyde-releasing (HCHO) biocides Grotan and Bioban CS 1135 and non-HCHO type biocides Kathon 886 MW (isothiazolone) and Preventol CMK 40 (phenolic) toward this emerging mycobacterial species (M. immunogenum) in HP-linked MWFs, alone and in presence of a representative of the Gram-negative bacterial contaminants, Pseudomonas fluorescens, using two semi-synthetic MWF matrices (designated Fluid A and Fluid B). Relative biocide susceptibility analysis indicated M immunogenum to be comparatively more resistant (2-1600 fold) than P. fluorescens to the tested biocides under the varied test conditions. In terms of minimum inhibitory concentration, Kathon was the most effective biocide against M. immunogenum. Fluid factors had a major effect on the biocide susceptibility. Fluid A formulation provided greater protective advantage to the test organisms than Fluid B. Fluid dialysis (Fluid A) led to an increased biocidal efficacy of Grotan, Kathon and Preventol against M. immunogenum further implying the role of native fluid components. Used fluid matrix, in general, increased the resistance of the two test organisms against the biocides, with certain exceptions. M. immunogenum resistance increased in presence of the co-contaminant P. fluorescens. Collectively, the results show a multifactorial nature of the biocide susceptibility of MWF-colonizing mycobacteria and highlight the importance of more rigorous efficacy testing and validation of biocides prior to and during their application in metalworking fluid operations.
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Affiliation(s)
| | | | - Jagjit S. Yadav
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267, USA
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Yadav JS, Khan IUH, Fakhari F, Soellner MB. DNA-Based Methodologies for Rapid Detection, Quantification, and Species- or Strain-Level Identification of Respiratory Pathogens (Mycobacteria and Pseudomonads) in Metalworking Fluids. ACTA ACUST UNITED AC 2010; 18:966-75. [PMID: 14555451 DOI: 10.1080/10473220390237700] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Mycobacteria and pseudomonads occurring in modern metalworking fluids (MWF) have been implicated in occupational health hazards as causal agents for hypersensitivity pneumonitis (HP) and other respiratory illnesses in machine workers exposed to these fluids and their aerosols. Unlike the conventional cultural and biochemical methods, which are often slow and ambiguous and detect only culturable cells, DNA-based methods offer a time-saving alternative for reliable detection and identification of both culturable and nonculturable bacteria in MWF and for selective quantification of individual genera of pathogens of interest in these fluids. This is the first report on DNA-based direct detection of mycobacteria and pseudomonads in MWF without culturing. Genus-specific PCR approach was successfully applied for screening of field MWF samples originating from different industrial users for detection of mycobacteria or pseudomonads including both culturable and nonculturable cells. PCR in combination with amplicon DNA sequencing led to the identification of Mycobacterium chelonae, Pseudomonas nitroreducens, and an undefined Pseudomonas species from these fluids. Genome fingerprinting by pulsed-field gel electrophoresis (PFGE) on Mycobacterium isolates further showed that the isolates represented three strains of M. chelonae although the possibility of one of the strains being clonal with M. immunogenum cannot be excluded. In parallel efforts, a quantitative competitive PCR method developed based on the Pseudomonas-specific PCR was applied to quantify total P. fluorescens cells in contaminated metalworking fluid and MWF aerosol without culturing. The DNA-based protocols developed in this study will allow rapid screening of field MWF samples for the presence of both culturable and nonculturable cells and thus facilitate effective fluid management and timely exposure assessment.
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Affiliation(s)
- Jagjit S Yadav
- Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
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Khan IUH, Gannon V, Loughborough A, Jokinen C, Kent R, Koning W, Lapen DR, Medeiros D, Miller J, Neumann N, Phillips R, Robertson W, Schreier H, Topp E, van Bochove E, Edge TA. A methods comparison for the isolation and detection of thermophilic Campylobacter in agricultural watersheds. J Microbiol Methods 2009; 79:307-13. [PMID: 19818368 DOI: 10.1016/j.mimet.2009.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 09/25/2009] [Accepted: 09/26/2009] [Indexed: 11/29/2022]
Abstract
Campylobacter species contribute to an enormous burden of enteric illnesses around the world. This study compared two different methods for detecting Campylobacter species in surface water samples from agricultural watersheds across Canada. One method was based on membrane filtration (MF) of 500 ml water samples followed by selective microaerophilic enrichment at 42 degrees C in Bolton broth, isolation of Campylobacter on CCDA, and subsequent identification confirmation by a PCR assay. The second method was based on centrifugation (CF) of 1000 ml water samples, followed by selective microaerophilic enrichment at 42 degrees C in Bolton broth, isolation of Campylobacter on Modified Karmali Agar, and subsequent identification confirmation by a different PCR assay. Overall comparison of the CF and MF methods indicated that both methods found Camylobacterjejuni to be the most commonly detected Campylobacter species in 699 water samples from four agricultural watersheds across Canada, and that C. jejuni frequency of occurrence was similar by both methods. However, the CF method detected significantly higher frequencies of Campylobactercoli (17%) and other Campylobacter species (13%) than the MF method (11% and 3%, respectively). It was frequently found that one method would detect Campylobacter in a water sample when the other method would not for a simultaneously collected, duplicate water sample. This study indicates that methods can have significantly different recovery efficiencies for Campylobacter species, and that caution is needed when comparing studies that report on the frequency of occurrence of waterborne Campylobacter at the genus level when different detection methods are used.
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Affiliation(s)
- Izhar U H Khan
- Aquatic Ecosystem Protection Research Division, Water Science & Technology Directorate, National Water Research Institute (NWRI), Environment Canada, Burlington, Ontario, Canada L7R 4A6
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Khan IUH, Loughborough A, Edge TA. DNA-based real-time detection and quantification of aeromonads from fresh water beaches on Lake Ontario. J Water Health 2009; 7:312-323. [PMID: 19240357 DOI: 10.2166/wh.2009.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The present study was designed to develop a novel, rapid, direct DNA-based protocol to enumerate aeromonads in recreational waters. An Aeromonas genus-specific real-time quantitative polymerase chain reaction (Q-PCR) protocol was developed and optimized using newly designed genus-specific oligonucleotide primers derived from the gyrase B subunit (GyrB) gene. A standard curve was developed based on the PCR protocol with a minimum quantification limit of 10 cell equivalents ml(-1) achieved using an autoclaved water sample from recreational water spiked with known quantities of an Aeromonas ATCC strain. The Q-PCR protocol was validated and applied to detect and quantify the total number of aeromonads in water samples collected from two fresh water beaches on Lake Ontario. The Q-PCR protocol revealed significantly higher numbers of aeromonads in all water samples than a culture-based assay at both beaches. Foreshore sand was found to serve as a reservoir of high concentrations of Aeromonas similar to this phenomenon noted for enteric bacteria like Eschershia coli. The new real-time Q-PCR protocol facilitated the rapid quantification of total numbers of Aeromonas cells present in recreational water samples in <3 hours without culturing.
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Affiliation(s)
- Izhar U H Khan
- National Water Research Institute, Water Science and Technology Directorate, Environment Canada, Burlington, ON L7R 4A6, Canada
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Selvaraju SB, Khan IUH, Yadav JS. Differential biocide susceptibility of the multiple genotypes of Mycobacterium immunogenum. J Ind Microbiol Biotechnol 2007; 35:197-203. [PMID: 18196302 DOI: 10.1007/s10295-007-0286-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 11/29/2007] [Indexed: 11/25/2022]
Abstract
The non-tuberculous mycobacterium Mycobacterium immunogenum colonizes industrial metalworking fluids (MWFs) presumably due to its relative resistance to the currently practiced biocides and has been implicated in occupational respiratory hazards, particularly hypersensitivity pneumonitis. With an aim to understand its inherent biocide susceptibility profile and survival potential in MWF, five different genotypes of this organism, including a reference genotype (700506) and four novel test genotypes (MJY-3, MJY-4, MJY-10 and MJY-12) isolated in our recent study from diverse MWF operations were evaluated. For this, two commercial biocide formulations, Grotan (Hexahydro-1,3,5-tris(2-hydroxyethyl)-s-triazine) and Kathon (5-chloro-2-methyl-4-isothiazolin-3-one) currently practiced for the control of microorganisms, including mycobacteria, in MWF operations were tested. Effect of the fluid matrix on the biocide susceptibility was investigated for the synthetic (S) and semi-synthetic (SS) MWF matrices. In general, the minimum inhibitory concentration values were higher for the HCHO-releasing biocide Grotan than the isothiazolone biocide Kathon. All genotypes (except the reference genotype) showed lower susceptibility in SS as compared to S fluid matrix for Grotan. However, in case of Kathon, a greater susceptibility was observed in SS fluid for majority of the test genotypes (MJY-3, 4 and 10). The test genotypes were more resistant than the reference genotype to either biocide in both fluid types. Furthermore, the individual genotypes showed differential biocidal susceptibility, with MJY-10 being the most resistant. These observations emphasize the importance of using the resistant genotypes of M. immunogenum as the test strains for formulation or development and evaluation of existing and novel biocides, for industrial applications.
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Affiliation(s)
- Suresh B Selvaraju
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, 45267-0056, USA
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Khan IUH, Gannon V, Kent R, Koning W, Lapen DR, Miller J, Neumann N, Phillips R, Robertson W, Topp E, van Bochove E, Edge TA. Development of a rapid quantitative PCR assay for direct detection and quantification of culturable and non-culturable Escherichia coli from agriculture watersheds. J Microbiol Methods 2007; 69:480-8. [PMID: 17433480 DOI: 10.1016/j.mimet.2007.02.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 02/19/2007] [Accepted: 02/26/2007] [Indexed: 11/19/2022]
Abstract
A real-time quantitative polymerase chain reaction (Q-PCR) assay was developed for detecting and quantifying Escherichia coli in water samples from agricultural watersheds. The assay included optimization of DNA extraction and purification from water samples, and Q-PCR amplification conditions using newly designed species-specific oligonucleotide primers derived from conserved flanking regions of the 16S rRNA gene, the internal transcribed spacer region (ITS) and the 23S rRNA gene. The assay was optimized using a pure culture of E. coli with known quantities spiked into autoclaved agricultural water samples. The optimized assay was capable of a minimum quantification limit of 10 cells/ml of E. coli in the spiked agricultural water samples. A total of 121 surface water samples from three agricultural watersheds across Canada were analyzed, and results were compared with conventional culture-based enumerations of E. coli. The Q-PCR assay revealed significantly higher numbers of E. coli in water samples than the culture-based assay in each agricultural watershed. The new Q-PCR assay can facilitate the quantification of E. coli in a single water sample in < 3 h, including melt curve analysis, across a range of agricultural water quality conditions.
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Affiliation(s)
- Izhar U H Khan
- National Water Research Institute, Aquatic Ecosystem Protection Research Division, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, Canada
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Khan IUH, Selvaraju SB, Yadav JS. Occurrence and characterization of multiple novel genotypes of Mycobacterium immunogenum and Mycobacterium chelonae in metalworking fluids. FEMS Microbiol Ecol 2006; 54:329-38. [PMID: 16332331 DOI: 10.1016/j.femsec.2005.04.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Revised: 04/17/2005] [Accepted: 04/20/2005] [Indexed: 01/13/2023] Open
Abstract
Rapidly growing mycobacteria colonize metalworking fluids, leading to contamination of occupational environments and exposure-related respiratory illnesses in machine workers. Lately, it has been emphasized that these fluids are colonizable by a single genotype of a rapidly growing mycobacterium species, Mycobacterium immunogenum. Here, we report on the genotypic diversity of mycobacteria in these fluids, including isolation and characterization of multiple novel genotypes of two distinct species, Mycobacterium chelonae and M. immunogenum. Using agar culturing and Mycobacterium-specific PCR, 13 mycobacterial isolates were recovered from 100 geographically diverse in-use metalworking fluid samples. Based on restriction fragment length polymorphism of PCR products, DNA sequencing (hsp65 gene segment), and phylogenetic analysis of 16S-23S rDNA internal transcribed spacer (ITS) sequences, six isolates were identified as M. immunogenum and seven as M. chelonae; an additional isolate from metalworking fluid diluent water was identified as M. diernhoferi. Genomic DNA macro-restriction fragment pattern analysis, using pulsed-field gel electrophoresis with XbaI and SpeI restriction digestions, showed intraspecies variation among the isolates of M. immunogenum and M. chelonae. Visual and computer-assisted dendrogram analysis of the XbaI macro-restriction patterns revealed three novel genotypes of M. immunogenum and two of M. chelonae, whereas SpeI macro-restriction patterns revealed only two genotypes for each isolate. None of the identified genotypes matched the reportedly dominant one of M. immunogenum from metalworking fluids. Both mycobacterial species are prevalent in metalworking fluids and there is a considerable strain-level genetic diversity within them.
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Affiliation(s)
- Izhar U H Khan
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267-0056, USA
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Khan IUH, Selvaraju SB, Yadav JS. Method for rapid identification and differentiation of the species of the Mycobacterium chelonae complex based on 16S-23S rRNA gene internal transcribed spacer PCR-restriction analysis. J Clin Microbiol 2005; 43:4466-72. [PMID: 16145093 PMCID: PMC1234067 DOI: 10.1128/jcm.43.9.4466-4472.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the Mycobacterium chelonae complex (MCC), including M. immunogenum, M. chelonae, and M. abscessus, have been associated with nosocomial infections and occupational hypersensitivity pneumonitis due to metalworking fluid (MWF) exposures. In order to minimize these health hazards, an effective and rapid assay for detection of MCC species and differentiation of MCC species from other species of rapidly growing mycobacteria (RGM) and from one another is warranted. Here we report such a method, based on the variable 16S-23S rRNA gene internal transcribed spacer (ITS) region. Mycobacterium genus-specific primers derived from highly conserved sequences in the ITS region and the flanking 16S rRNA gene were used. Specificity of the primers was verified using the MCC member species, 11 non-MCC RGM species, 3 slow-growing mycobacterial (SGM) species (two strains each), and 19 field isolates, including 18 MCC isolates (from in-use MWF) and one non-MCC isolate (from reverse osmosis water). The ITS amplicon size of M. immunogenum varied from those of M. chelonae and M. abscessus. Sequencing of the approximately 250-bp-long ITS amplicons of the three MCC member species showed differences in 24 to 34 bases, thereby yielding variable deduced restriction maps. ITS PCR-restriction analysis using the in silico-selected restriction enzyme MaeII or HphI differentiated the three MCC members from one another and from other RGM and SGM species without sequencing. The enzyme MaeII discriminated all three member species; however, HphI could only differentiate M. immunogenum from M. chelonae and M. abscessus. Use of an optimized rapid DNA template preparation step based on direct cell lysis in the PCR tube added to the simplicity and adaptability of the developed assay.
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Affiliation(s)
- Izhar U H Khan
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati Medical Center, OH 45267-0056, USA
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Selvaraju SB, Khan IUH, Yadav JS. Biocidal activity of formaldehyde and nonformaldehyde biocides toward Mycobacterium immunogenum and Pseudomonas fluorescens in pure and mixed suspensions in synthetic metalworking fluid and saline. Appl Environ Microbiol 2005; 71:542-6. [PMID: 15640232 PMCID: PMC544221 DOI: 10.1128/aem.71.1.542-546.2005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbicidal activity of four different biocides was studied in synthetic metalworking fluid (MWF) against Mycobacterium immunogenum, a suspected causative agent for hypersensitivity pneumonitis, and Pseudomonas fluorescens, a representative for the predominant gram-negative bacterial contaminants of MWF. The results indicated that M. immunogenum is more resistant than P. fluorescens to the tested formaldehyde-releasing biocides (Grotan and Bioban), isothiazolone (Kathon), and phenolic biocide (Preventol). Kathon was effective against mycobacteria at lower concentrations than the other three test biocides in MWF. In general, there was a marked increase in biocidal resistance of both the test organisms when present in MWF matrix compared to saline. Increased resistance of the two test organisms to biocides was observed when they were in a mixed suspension (1:1 ratio). The results indicate the protective effect of the MWF matrix against the action of commonly used biocides on the MWF-colonizing microbial species of occupational health significance, including mycobacteria.
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Affiliation(s)
- Suresh B Selvaraju
- Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267-0056, USA
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Selvaraju SB, Khan IUH, Yadav JS. A new method for species identification and differentiation of Mycobacterium chelonae complex based on amplified hsp65 restriction analysis (AHSPRA). Mol Cell Probes 2004; 19:93-9. [PMID: 15680210 DOI: 10.1016/j.mcp.2004.09.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 09/30/2004] [Indexed: 11/26/2022]
Abstract
Members of the Mycobacterium chelonae complex (MCC), namely M. chelonae, Mycobacterium abscessus and Mycobacterium immunogenum, have been implicated in nosocomial infections and occupational respiratory illnesses like hypersensitivity pneumonitis (HP) associated with contaminated metalworking fluid (MWF) exposures. Close relationship among these member species makes their differentiation cumbersome using the existing methods. Here we report a simple and rapid method for unambiguous identification and differentiation of the three-member species of the MCC group with PCR-restriction analysis targeting a 667-bp segment of a variable region of the 65-kDa-heat shock protein (hsp65) gene. This assay, described as Amplified hsp65 Restriction Analysis (AHSPRA), can discriminate all the three individual species using a one-step restriction digestion using either BbvI or Eco0109I. The enzyme NarI can differentiate M. immunogenum from the other two MCC species (M. chelonae and M. abscessus). The developed method was validated using several non-MCC reference species of other rapidly growing mycobacteria (RGM) and MCC field isolates from MWF samples. Direct cell-lysis was used instead of the conventional DNA template preparation, which improved the rapidity, simplicity and adaptability of the developed method. The results suggest that the developed method can unambiguously differentiate species of the M. chelonae complex from other RGM species and from one another.
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Affiliation(s)
- Suresh B Selvaraju
- Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267-0056, USA
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Khan IUH, Yadav JS. Real-time PCR assays for genus-specific detection and quantification of culturable and non-culturable mycobacteria and pseudomonads in metalworking fluids. Mol Cell Probes 2004; 18:67-73. [PMID: 15036372 DOI: 10.1016/j.mcp.2003.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2003] [Accepted: 09/12/2003] [Indexed: 11/23/2022]
Abstract
Genus-specific real-time PCR assays were developed and optimized for the direct culture-independent detection and quantification of Mycobacteria and Pseudomonads in contaminated metalworking fluids (MWF) and the results were compared with conventional culturing using selective media. It included optimization of the direct DNA isolation from the fluid matrix and the amplification conditions using genus-specific primers. Mycobacterium-specific primers based on 65-kDa heat shock protein (hsp) gene, and Pseudomonas-specific primers based on 16S rRNA gene were used. A standard curve was developed each for the two model bacterial species Mycobacterium immunogenum and Pseudomonas fluorescens, representing two important genera frequently isolated from MWF. A minimum quantification limit of 10 cells/ml was achieved although as low as 1 cell/ml yielded a detectable amplicon signal. Of the twenty MWF field samples contaminated with mixed microflora, only two samples yielded putative colonies of Mycobacteria and Pseudomonads by culturing method, while seven samples responded to the genus-specific real-time PCR detection and quantification for each genus. In contrast to the low culturable counts, the real-time PCR based cell counts ranged from 1.3 x 10(2) to 5.5 x 10(5)cells/ml and 5.2 x 10(2) to 7.0 x 10(5)cells/ml for Mycobacteria and Pseudomonads, respectively, indicating a significant non-culturable fraction in the fluids, for the two genera. This is the first application of real-time PCR protocol to MWF samples for detection and quantification of total (culturable and non-culturable) Mycobacteria and Pseudomonads without culturing.
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Affiliation(s)
- Izhar U H Khan
- Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, OH 45267-0056, USA
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Khan IUH, Yadav JS. Development of a single-tube, cell lysis-based, genus-specific PCR method for rapid identification of mycobacteria: optimization of cell lysis, PCR primers and conditions, and restriction pattern analysis. J Clin Microbiol 2004; 42:453-7. [PMID: 14715804 PMCID: PMC321669 DOI: 10.1128/jcm.42.1.453-457.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A single-tube PCR method was developed for efficient identification of nontuberculous mycobacteria (NTM) and their environmental isolates in about 3 h without conventional DNA isolation. The following three steps were optimized or developed: (i). a simple, 6-min direct cell lysis protocol as a PCR prestep for generation of DNA-template, (ii). an improved Mycobacterium-specific PCR amplification protocol with a broader species specificity using newly designed primers targeting a 228-bp region of the 65-kDa heat shock protein (hsp) gene and optimal PCR amplification conditions, and (iii). a genus-specific restriction analysis of the PCR product for conclusive identification of the unknown NTM isolates.
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Affiliation(s)
- Izhar U H Khan
- Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, Ohio 45267-0056, USA
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