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Kilgore PB, Sha J, Hendrix EK, Neil BH, Lawrence WS, Peel JE, Hittle L, Woolston J, Sulakvelidze A, Schwartz JA, Chopra AK. A bacteriophage cocktail targeting Yersinia pestis provides strong post-exposure protection in a rat pneumonic plague model. Microbiol Spectr 2024:e0094224. [PMID: 39292000 DOI: 10.1128/spectrum.00942-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/04/2024] [Indexed: 09/19/2024] Open
Abstract
Yersinia pestis, one of the deadliest bacterial pathogens ever known, is responsible for three plague pandemics and several epidemics, with over 200 million deaths during recorded history. Due to high genomic plasticity, Y. pestis is amenable to genetic mutations as well as genetic engineering that can lead to the emergence or intentional development of pan-drug-resistant strains. Indeed, antibiotic-resistant strains (e.g., strains carrying multidrug-resistant or MDR plasmids) have been isolated in various countries and endemic areas. Thus, there is an urgent need to develop novel, safe, and effective treatment approaches for managing Y. pestis infections. This includes infections by antigenically distinct strains for which vaccines (none FDA approved yet) may not be effective and those that cannot be managed by currently available antibiotics. Lytic bacteriophages provide one such alternative approach. In this study, we examined post-exposure efficacy of a bacteriophage cocktail, YPP-401, to combat pneumonic plague caused by Y. pestis CO92. YPP-401 is a four-phage preparation effective against a panel of at least 68 genetically diverse Y. pestis strains. Using a pneumonic plague aerosol challenge model in gender-balanced Brown Norway rats, YPP-401 demonstrated ~88% protection when delivered 18 h post-exposure for each of two administration routes (i.e., intraperitoneal and intranasal) in a dose-dependent manner. Our studies provide proof-of-concept that YPP-401 could be an innovative, safe, and effective approach for managing Y. pestis infections, including those caused by naturally occurring or intentionally developed multidrug-resistant strains.IMPORTANCECurrently, there are no FDA-approved plague vaccines. Since antibiotic-resistant strains of Y. pestis have emerged or are being intentionally developed to be used as a biothreat agent, new treatment modalities are direly needed. Phage therapy provides a viable option against potentially antibiotic-resistant strains. Additionally, phages are nontoxic and have been approved by the FDA for use in the food industry. Our study provides the first evidence of the protective effect of a cocktail of four phages against pneumonic plague, the most severe form of disease. When treatment was initiated 18 h post infection by either the intranasal or intraperitoneal route in Brown Norway rats, up to 87.5% protection was observed. The phage cocktail had a minimal impact on a representative human microbiome panel, unlike antibiotics. This study provides strong proof-of-concept data for the further development of phage-based therapy to treat plague.
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Affiliation(s)
- Paul B Kilgore
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jian Sha
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections & Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily K Hendrix
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Blake H Neil
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - William S Lawrence
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections & Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jennifer E Peel
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections & Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
| | | | | | | | | | - Ashok K Chopra
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections & Immunity, and the Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
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2
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Kilgore PB, Sha J, Hendrix EK, Neil BH, Lawrence WS, Peel JE, Hittle L, Woolston J, Sulakvelidze A, Schwartz JA, Chopra AK. A Bacteriophage Cocktail Targeting Yersinia pestis Provides Strong Post-Exposure Protection in a Rat Pneumonic Plague Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576055. [PMID: 38293171 PMCID: PMC10827167 DOI: 10.1101/2024.01.17.576055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Yersinia pestis , one of the deadliest bacterial pathogens ever known, is responsible for three plague pandemics and several epidemics, with over 200 million deaths during recorded history. Due to high genomic plasticity, Y. pestis is amenable to genetic mutations as well as genetic engineering that can lead to the emergence or intentional development of pan-drug resistant strains. The dissemination of such Y. pestis strains could be catastrophic, with public health consequences far more daunting than those caused by the recent COVID-19 pandemic. Thus, there is an urgent need to develop novel, safe, and effective treatment approaches for managing Y. pestis infections. This includes infections by antigenically distinct strains for which vaccines, none FDA approved yet, may not be effective, and those that cannot be controlled by approved antibiotics. Lytic bacteriophages provide one such alternative approach. In this study, we examined post-exposure efficacy of a bacteriophage cocktail, YPP-401, to combat pneumonic plague caused by Y. pestis CO92. YPP-401 is a four-phage preparation with a 100% lytic activity against a panel of 68 genetically diverse Y. pestis strains. Using a pneumonic plague aerosol challenge model in gender-balanced Brown Norway rats, YPP-401 demonstrated ∼88% protection when delivered 18 hours post-exposure for each of two administration routes (i.e., intraperitoneal and intranasal) in a dose-dependent manner. Our studies suggest that YPP-401 could provide an innovative, safe, and effective approach for managing Y. pestis infections, including those caused by naturally occurring or intentionally developed strains that cannot be managed by vaccines in development and antibiotics.
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3
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Lisotto P, Raangs EC, Couto N, Rosema S, Lokate M, Zhou X, Friedrich AW, Rossen JWA, Harmsen HJM, Bathoorn E, Chlebowicz-Fliss MA. Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium. BMC Genomics 2021; 22:758. [PMID: 34688274 PMCID: PMC8542323 DOI: 10.1186/s12864-021-08080-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome's structural composition but lacks the precision required for SNP-based typing and cgMLST. Here we compared prophages among 50 complete E. faecium genomes belonging to different lineages to explore whether a phage signature would be usable for typing and identifying an outbreak caused by VRE. As a proof of principle, we investigated if long-read sequencing data would allow for identifying phage signatures and thereby outbreak-related isolates. RESULTS Analysis of complete genome sequences of publicly available isolates showed variation in phage content among different lineages defined by MLST. We identified phage present in multiple STs as well as phages uniquely detected within a single lineage. Next, in silico phage typing was applied to twelve MinION sequenced isolates belonging to two different genetic backgrounds, namely ST117/CT24 and ST80/CT16. Genomic comparisons of the long-read-based assemblies allowed us to correctly identify isolates of the same complex type based on global genome architecture and specific phage signature similarity. CONCLUSIONS For rapid identification of related VRE isolates, phage content analysis in long-read sequencing data is possible. This allows software development for real-time typing analysis of long-read sequencing data, which will generate results within several hours. Future studies are required to assess the discriminatory power of this method in the investigation of ongoing outbreaks over a longer time period.
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Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erwin C Raangs
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.,IDbyDNA Inc., Salt Lake City, UT, USA
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Abdelsattar AS, Dawoud A, Makky S, Nofal R, Aziz RK, El-Shibiny A. Bacteriophages: from isolation to application. Curr Pharm Biotechnol 2021; 23:337-360. [PMID: 33902418 DOI: 10.2174/1389201022666210426092002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Bacteriophages are considered as a potential alternative to fight pathogenic bacteria during the antibiotic resistance era. With their high specificity, they are being widely used in various applications: medicine, food industry, agriculture, animal farms, biotechnology, diagnosis, etc. Many techniques have been designed by different researchers for phage isolation, purification, and amplification, each of which has strengths and weaknesses. However, all aim at having a reasonably pure phage sample that can be further characterized. Phages can be characterized based on their physiological, morphological or inactivation tests. Microscopy, in particular, has opened a wide gate not only for visualizing phage morphological structure, but also for monitoring biochemistry and behavior. Meanwhile, computational analysis of phage genomes provides more details about phage history, lifestyle, and potential for toxigenic or lysogenic conversion, which translate to safety in biocontrol and phage therapy applications. This review summarizes phage application pipelines at different levels and addresses specific restrictions and knowledge gaps in the field. Recently developed computational approaches, which are used in phage genome analysis, are critically assessed. We hope that this assessment provides researchers with useful insights for selection of suitable approaches for Phage-related research aims and applications.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Rana Nofal
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, Cairo. Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
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Rangel-Pineros G, Sicheritz-Pontén T, Clokie MRJ. inPhocus: "Virus Amigos?" The Journey of the Development of Phage-Based Biocontrol in the Latin American Poultry and Aquaculture Industries. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:3-6. [PMID: 36148440 PMCID: PMC9041483 DOI: 10.1089/phage.2021.29012.grp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Guillermo Rangel-Pineros
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Akter M, Brown N, Clokie M, Yeasmin M, Tareq TM, Baddam R, Azad MAK, Ghosh AN, Ahmed N, Talukder KA. Prevalence of Shigella boydii in Bangladesh: Isolation and Characterization of a Rare Phage MK-13 That Can Robustly Identify Shigellosis Caused by Shigella boydii Type 1. Front Microbiol 2019; 10:2461. [PMID: 31787934 PMCID: PMC6853846 DOI: 10.3389/fmicb.2019.02461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/14/2019] [Indexed: 11/25/2022] Open
Abstract
Shigellosis, caused by Shigella boydii type 1, is understudied and underreported. For 3 years, GEMS study identified 5.4% of all Shigella as S. boydii. We showed the prevalent serotypes of S. boydii in Bangladesh and phage-based diagnosis of S. boydii type 1, a rapid and low-cost approach. Previously typed 793 clinical S. boydii strains were used for serotype distribution. Twenty-eight environmental water samples were collected for isolation of Shigella phages. Forty-eight serotypes of Shigella and other enteric bacteria were used for testing the susceptibility to phage MK-13. Electron microscopy, restriction enzyme analysis, whole genome sequencing (WGS), and annotation were performed for extensive characterization. S. boydii type 1 is the second most prevalent serotype among 20 serotypes of S. boydii in Bangladesh. We isolated a novel phage, MK-13, which specifically lyses S. boydii type 1, but doesn’t lyse other 47 serotypes of Shigella or other enteric bacteria tested. The phage belongs to the Myoviridae family and distinct from other phages indicated by electron microscopy and restriction enzyme analysis, respectively. MK-13 genome consists of 158 kbp of circularly permuted double-stranded DNA with G + C content of 49.45%, and encodes 211 open reading frames including four tRNA-coding regions. The genome has 98% identity with previously reported phage, ΦSboM-AG3, reported to have a broader host range infecting most of the S. boydii and other species of Shigella tested. To our knowledge, MK-13 is the first phage reported to be used as a diagnostic marker to detect S. boydii type 1, especially in remote settings with limited laboratory infrastructure.
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Affiliation(s)
- Mahmuda Akter
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nathan Brown
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Mahmuda Yeasmin
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tokee M Tareq
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ramani Baddam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Muhammad A K Azad
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Amar N Ghosh
- Division of Electron Microscopy, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Niyaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Kaisar A Talukder
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
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7
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Mohanty PS, Bansal AK, Naaz F, Arora M, Gupta UD, Gupta P, Sharma S, Singh H. Multiple strain infection of Mycobacterium leprae in a family having 4 patients: A study employing short tandem repeats. PLoS One 2019; 14:e0214051. [PMID: 30947261 PMCID: PMC6449029 DOI: 10.1371/journal.pone.0214051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/06/2019] [Indexed: 11/19/2022] Open
Abstract
Background Leprosy is a slow, chronic disorder caused by Mycobacterium leprae. India has achieved elimination of leprosy in December 2005 but new cases are being detected and continue to occur in some endemic pockets. The possible ways of transmission of leprosy is not fully understood and is believed that leprosy is transmitted from person to person in long term contact. Studying the transmission dynamics is further complicated by inability to grow M. leprae in culture medium and lack of animal models. More than one family members were found to be affected by leprosy in some highly endemic pockets. This study reported the transmission pattern of leprosy in a family having 4 patients. Methodology/Principal findings We investigated the transmission of leprosy in a single family having 4 patients using microsatellite typing. DNA was isolated from slit skin smear samples taken from the patients and the isolated DNA were amplified using microsatellite loci TA11CA3. The amplified products were sequenced using Sanger’s sequencing methods and the copy number variation in the microsatellite loci between strains were elucidated by multiple sequence alignment. The result showed that all the 4 members of the family acquired infection from 3 different strains of M. leprae from 3 different sources. The elder and middle daughters were infected by same types of strains having the repeat unit TA13CA3 and could have acquired the infection from social contacts of leprosy cases while the father and younger daughter were infected by strains with the repeat unit TA12CA3 and TA11CA3 and could have acquired infection from social contacts. Conclusions/Significance The study suggested that three family members viz, elder daughter, father and younger daughter could be infected by M. leprae from 3 different sources and the history of the disease and genetic analysis showed that the middle daughter acquired infection from her elder sister in due course of contact. This study implies that the transmission of leprosy not only occurred amongst the house hold members but also has been transmitted from social and neighborhood contacts in long term association with the them.
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Affiliation(s)
- Partha Sarathi Mohanty
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
- * E-mail:
| | - Avi Kumar Bansal
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Farah Naaz
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Mamta Arora
- Clinical Division, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Umesh Datta Gupta
- Department of Animal Experimentation, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Pushpa Gupta
- Department of Animal Experimentation, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Sandeep Sharma
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
| | - Haribhan Singh
- Department of Epidemiology, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, India
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8
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Kauffman KM, Polz MF. Streamlining standard bacteriophage methods for higher throughput. MethodsX 2018; 5:159-172. [PMID: 30622914 PMCID: PMC6318102 DOI: 10.1016/j.mex.2018.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
A universal tool in the culture-based study of bacterial viruses (bacteriophages, or phages) is the agar overlay, which is used in the isolation of new viruses, and in their quantification and purification. Here, simple optimizations that increase efficiency and throughput in agar overlay based isolation and cultivation of virus-host systems are presented. The agar overlay is streamlined to minimize steps and materials. Serial purification of viruses from viral colonies (plaques) is optimized to eliminate steps by combining purification by serial re-streaking with the optimized agar overlay approach. Finally, recommendations are made for efficient archival and storage of virus plaques. In sum, this work presents: •Tube-free Agar Overlays: rapid plaque assays with fewer steps and materials•Molten Streaking for Singles: rapid tube-free serial purification of viruses•Archiving Plaques: saving virus purification for later.
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Affiliation(s)
- Kathryn M. Kauffman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02141, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02141, USA
- The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02141, USA
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9
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Richter Ł, Janczuk-Richter M, Niedziółka-Jönsson J, Paczesny J, Hołyst R. Recent advances in bacteriophage-based methods for bacteria detection. Drug Discov Today 2017; 23:448-455. [PMID: 29158194 DOI: 10.1016/j.drudis.2017.11.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 12/20/2022]
Abstract
Fast and reliable bacteria detection is crucial for lowering the socioeconomic burden related to bacterial infections (e.g., in healthcare, industry or security). Bacteriophages (i.e., viruses with bacterial hosts) pose advantages such as great specificity, robustness, toughness and cheap preparation, making them popular biorecognition elements in biosensors and other assays for bacteria detection. There are several possible designs of bacteriophage-based biosensors. Here, we focus on developments based on whole virions as recognition agents. We divide the review into sections dealing with phage lysis as an analytical signal, phages as capturing elements in assays and phage-based sensing layers, putting the main focus on development reported within the past three years but without omitting the fundamentals.
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Affiliation(s)
- Łukasz Richter
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marta Janczuk-Richter
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | | | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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10
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Hobbs JL, Warshawsky B, Maki A, Zittermann S, Murphy A, Majury A, Middleton D. Nuggets of Wisdom: Salmonella Enteritidis Outbreaks and the Case for New Rules on Uncooked Frozen Processed Chicken. J Food Prot 2017; 80:703-709. [PMID: 28338343 DOI: 10.4315/0362-028x.jfp-16-431] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In 2014 and 2015, three Canadian Salmonella serotype Enteritidis outbreak investigations implicated uncooked, frozen, processed chicken products produced at the same establishment, namely establishment A. In November 2014, a sustained increase in the number of reported domestically acquired Salmonella Enteritidis cases in Ontario led to the first outbreak investigation, which implicated uncooked, frozen, processed chicken products produced at establishment A. In June 2015, the identification of pulsed-field gel electrophoresis patterns that had not been previously reported in Canada led to a national Salmonella Enteritidis investigation. Of 51 cases reported nationally, 35 were from Ontario. Uncooked, frozen, processed chicken products produced at establishment A were identified as the source of the outbreak, and public health action was taken as a result of this second investigation. In September 2015, a sustained increase in the number of domestically acquired Salmonella Enteritidis PT13a cases in Ontario led to a third outbreak investigation, which identified a total of 36 PT13a cases. Uncooked, frozen, processed chicken products produced at establishment A were again identified as the source of the outbreak. Outbreaks have been linked to uncooked, frozen, processed chicken products since the late 1990s. Information collected during the three outbreak investigations, and from other jurisdictions, suggests that the breaded and prebrowned appearance of the product, as well as factors related to product packaging and marketing, result in consumer misperception that this raw product is cooked. This misperception may result in mishandling and improper cooking. The three outbreaks described in this article highlight the potential ongoing risks to consumers from these products and support interventions to prevent contamination at the source level and infection at the consumer level.
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Affiliation(s)
- J Leigh Hobbs
- 1 Communicable Diseases Emergency Preparedness and Response, Public Health Ontario, Toronto, Ontario, Canada M5G 1V2
| | - Bryna Warshawsky
- 1 Communicable Diseases Emergency Preparedness and Response, Public Health Ontario, Toronto, Ontario, Canada M5G 1V2.,2 Department of Epidemiology and Biostatistics, Western University, London, Ontario, Canada N6A 3K7
| | - Anne Maki
- 3 Public Health Ontario Laboratory, Toronto, Ontario, Canada M5G 1M1
| | - Sandra Zittermann
- 3 Public Health Ontario Laboratory, Toronto, Ontario, Canada M5G 1M1
| | - Allana Murphy
- 3 Public Health Ontario Laboratory, Toronto, Ontario, Canada M5G 1M1
| | - Anna Majury
- 4 Public Health Ontario Laboratory, Kingston, Ontario, Canada K7L 4V8
| | - Dean Middleton
- 1 Communicable Diseases Emergency Preparedness and Response, Public Health Ontario, Toronto, Ontario, Canada M5G 1V2
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11
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Anany H, Chou Y, Cucic S, Derda R, Evoy S, Griffiths M. From Bits and Pieces to Whole Phage to Nanomachines: Pathogen Detection Using Bacteriophages. Annu Rev Food Sci Technol 2017; 8:305-329. [DOI: 10.1146/annurev-food-041715-033235] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- H. Anany
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt 11566
| | - Y. Chou
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - S. Cucic
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
| | - R. Derda
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - S. Evoy
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - M.W. Griffiths
- Canadian Institute for Food Safety, University of Guelph, Guelph, Ontario, Canada N1G 2W1;, ,
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Czajkowski R. Bacteriophages of Soft Rot Enterobacteriaceae-a minireview. FEMS Microbiol Lett 2015; 363:fnv230. [PMID: 26626879 DOI: 10.1093/femsle/fnv230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2015] [Indexed: 11/14/2022] Open
Abstract
Soft rot Enterobacteriaceae (Pectobacterium spp. and Dickeya spp., formerly pectinolytic Erwinia spp.) are ubiquitous necrotrophic bacterial pathogens that infect a large number of different plant species worldwide, including economically important crops. Despite the fact that these bacteria have been studied for more than 50 years, little is known of their corresponding predators: bacteriophages, both lytic and lysogenic. The aim of this minireview is to critically summarize recent ecological, biological and molecular research on bacteriophages infecting Pectobacterium spp. and Dickeya spp. with the main focus on current and future perspectives in that field.
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Affiliation(s)
- Robert Czajkowski
- Laboratory of Plant Protection and Biotechnology, Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
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Switt AIM, Sulakvelidze A, Wiedmann M, Kropinski AM, Wishart DS, Poppe C, Liang Y. Salmonella phages and prophages: genomics, taxonomy, and applied aspects. Methods Mol Biol 2015; 1225:237-87. [PMID: 25253259 DOI: 10.1007/978-1-4939-1625-2_15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Since this book was originally published in 2007 there has been a significant increase in the number of Salmonella bacteriophages, particularly lytic virus, and Salmonella strains which have been fully sequenced. In addition, new insights into phage taxonomy have resulted in new phage genera, some of which have been recognized by the International Committee of Taxonomy of Viruses (ICTV). The properties of each of these genera are discussed, along with the role of phage as agents of genetic exchange, as therapeutic agents, and their involvement in phage typing.
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Affiliation(s)
- Andrea I Moreno Switt
- Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Escuela de Medicina Veterinaria, Republica 440, 8370251, Santiago, Chile
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15
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Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol 2014; 15:538. [PMID: 25418119 PMCID: PMC4282151 DOI: 10.1186/s13059-014-0538-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.
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David MZ, Daum RS. Editorial Commentary: Applying a New Technology to an Old Question: Whole-Genome Sequencing and Staphylococcus aureus Acquisition in an Intensive Care Unit. Clin Infect Dis 2013; 58:619-21. [DOI: 10.1093/cid/cit812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mulvey MR, Finley R, Allen V, Ang L, Bekal S, El Bailey S, Haldane D, Hoang L, Horsman G, Louie M, Robberts L, Wylie J, McCracken M, Langner S, Ahmed R, Tabor H, Gilmour M. Emergence of multidrug-resistant Salmonella enterica serotype 4,[5],12:i:- involving human cases in Canada: results from the Canadian Integrated Program on Antimicrobial Resistance Surveillance (CIPARS), 2003-10. J Antimicrob Chemother 2013; 68:1982-6. [PMID: 23710071 DOI: 10.1093/jac/dkt149] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Over the last decade, a marked increase in Salmonella enterica serotype 4,[5],12:i:- with a core resistance to ampicillin, streptomycin, sulphonamides and tetracycline (ASSuT) has been observed in Europe. This study describes the emergence and characterization of isolates of multidrug-resistant Salmonella 4,[5],12:i:- in Canada. METHODS Human clinical isolates of Salmonella 4,[5],12:i:- were identified by provincial laboratories from 2003 to 2010. Serotyping and phage typing were performed by standardized methodologies. MIC values were determined using broth microdilution. PCR was used to determine the presence of resistance genes. Multilocus sequence typing was performed on a selected number of isolates. RESULTS A total of 26 251 Salmonella were submitted as part of the Canadian Integrated Program on Antibiotic Resistance Surveillance (CIPARS). Of these, Salmonella 4,[5],12:i:- accounted for a total of 766 isolates (2.9%), and the number increased significantly from 42 (1.4%) in 2003 to 164 (4.8%) in 2010. The ASSuT+ phenotype was observed in 11.9% (n = 91) of Salmonella 4,[5],12:i:- isolates and increased from two isolates in 2003 to 35 isolates in 2010. Two sequence types (STs) were observed. ST34 was mainly associated with the ASSuT isolates (n = 24; 38%), which contained blaTEM, strA-strB, tet(B) and sul2. ST19 was more likely to be associated with the ACSSuT phenotype and contained blaTEM, floR, strA-strB, sul2 and tet(A) or blaPSE-1, floR, aadA2, sul1 and tet(G). CONCLUSIONS The prevalence of Salmonella 4,[5],12:i:- has significantly increased from 2003 to 2010 and it is now the fifth most common serotype reported in Canada causing human disease. Similar antimicrobial resistance patterns, phage types and STs have been observed in Europe.
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Łobocka M, Hejnowicz MS, Dąbrowski K, Gozdek A, Kosakowski J, Witkowska M, Ulatowska MI, Weber-Dąbrowska B, Kwiatek M, Parasion S, Gawor J, Kosowska H, Głowacka A. Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era. Adv Virus Res 2012; 83:143-216. [PMID: 22748811 DOI: 10.1016/b978-0-12-394438-2.00005-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.
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Affiliation(s)
- Małgorzata Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Borysowski J, Lobocka M, Międzybrodzki R, Weber-Dabrowska B, Górski A. Potential of bacteriophages and their lysins in the treatment of MRSA: current status and future perspectives. BioDrugs 2012; 25:347-55. [PMID: 22050337 DOI: 10.2165/11595610-000000000-00000] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacteriophages (phages) are viruses that specifically infect and kill bacteria. Lysins are enzymes of bacteriophage origin that cleave covalent bonds in peptidoglycan, thereby inducing rapid lysis of a bacterial cell. As potential antibacterial agents, phages and lysins have some important features in common, especially the capacity to kill antibiotic-resistant bacteria, a narrow antibacterial range, and lack of toxic effects on mammalian cells. In this article we present the staphylococcal phages and their lysins that can be used to combat methicillin-resistant Staphylococcus aureus (MRSA), one of today's most dangerous pathogens. We also discuss the use of phages as vectors specifically delivering different antibacterial agents to bacterial cells. Experimental data show that both phages and lysins could be effective in the treatment of MRSA.
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Affiliation(s)
- Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Warsaw Medical University, Poland.
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Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives. Appl Environ Microbiol 2011; 77:7877-85. [PMID: 21856826 DOI: 10.1128/aem.05527-11] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For more than 80 years, subtyping of Salmonella enterica has been routinely performed by serotyping, a method in which surface antigens are identified based on agglutination reactions with specific antibodies. The serotyping scheme, which is continuously updated as new serovars are discovered, has generated over time a data set of the utmost significance, allowing long-term epidemiological surveillance of Salmonella in the food chain and in public health control. Conceptually, serotyping provides no information regarding the phyletic relationships inside the different Salmonella enterica subspecies. In epidemiological investigations, identification and tracking of salmonellosis outbreaks require the use of methods that can fingerprint the causative strains at a taxonomic level far more specific than the one achieved by serotyping. During the last 2 decades, alternative methods that could successfully identify the serovar of a given strain by probing its DNA have emerged, and molecular biology-based methods have been made available to address phylogeny and fingerprinting issues. At the same time, accredited diagnostics have become increasingly generalized, imposing stringent methodological requirements in terms of traceability and measurability. In these new contexts, the hand-crafted character of classical serotyping is being challenged, although it is widely accepted that classification into serovars should be maintained. This review summarizes and discusses modern typing methods, with a particular focus on those having potential as alternatives for classical serotyping or for subtyping Salmonella strains at a deeper level.
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Matthews TD, Rabsch W, Maloy S. Chromosomal rearrangements in Salmonella enterica serovar Typhi strains isolated from asymptomatic human carriers. mBio 2011; 2:e00060-11. [PMID: 21652779 PMCID: PMC3107234 DOI: 10.1128/mbio.00060-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 04/29/2011] [Indexed: 11/20/2022] Open
Abstract
Host-specific serovars of Salmonella enterica often have large-scale chromosomal rearrangements that occur by recombination between rrn operons. Two hypotheses have been proposed to explain these rearrangements: (i) replichore imbalance from horizontal gene transfer drives the rearrangements to restore balance, or (ii) the rearrangements are a consequence of the host-specific lifestyle. Although recent evidence has refuted the replichore balance hypothesis, there has been no direct evidence for the lifestyle hypothesis. To test this hypothesis, we determined the rrn arrangement type for 20 Salmonella enterica serovar Typhi strains obtained from human carriers at periodic intervals over multiple years. These strains were also phage typed and analyzed for rearrangements that occurred over long-term storage versus routine culturing. Strains isolated from the same carrier at different time points often exhibited different arrangement types. Furthermore, colonies isolated directly from the Dorset egg slants used to store the strains also had different arrangement types. In contrast, colonies that were repeatedly cultured always had the same arrangement type. Estimated replichore balance of isolated strains did not improve over time, and some of the rearrangements resulted in decreased replicore balance. Our results support the hypothesis that the restricted lifestyle of host-specific Salmonella is responsible for the frequent chromosomal rearrangements in these serovars.
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Affiliation(s)
- T. David Matthews
- Center for Microbial Sciences, Department of Biology, San Diego State University, San Diego, California, USA, and
| | - Wolfgang Rabsch
- Division of Bacterial Infections and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch-Institute, Wernigerode Branch, Wernigerode, Germany
| | - Stanley Maloy
- Center for Microbial Sciences, Department of Biology, San Diego State University, San Diego, California, USA, and
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Abstract
The routine methods used in the Enteric Reference Laboratory for the study of enterobacterial plasmids are described. The results of their application to plasmids of diverse origin, and their value for the categorization of those plasmids, are presented and discussed.
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Sinell HJ, Kusch D, Untermann F. Zum Vorkommen von koagulasepositiven Staphylokokken in Hackfleisch: Lysisspektrum, biochemische Eigenschaften und Enterotoxinbildung*. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1439-0450.1970.tb01455.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Characterization of antimicrobial resistance, molecular and phage types ofSalmonella entericaserovar Typhi isolations. Epidemiol Infect 2010; 138:1414-26. [DOI: 10.1017/s0950268810000221] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SUMMARYIsolation rates in Canada ofSalmonella entericaserovar Typhi increased from 0·29 to 0·55 isolations/100 000 population during 2000–2006. Although no ciprofloxacin resistance was detected, nalidixic acid resistance increased from 41% to 80%. Multidrug-resistantS. Typhi represented 18% of the strains tested. Pulsed-field gel electrophoresis (PFGE) analysis of 222 isolates resulted in 91 distinct patterns clustering into four major genetic similarity groups. The five most frequently occurring PFGE patterns accounted for 46% of the isolates. Drug-resistant isolates predominantly occurred in one PFGE similarity group. There were 39 phage types identified in 826 isolates analysed with 60% described by five phage types; 134 were untypable. The phage types associated with multidrug resistance were phage types 53, B1, D1, E1, E9, G3 and M1. Improved integration of epidemiological and laboratory case data will facilitate the protection of public health in Canada during an era of increasing travel and globalization.
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Dutil L, Irwin R, Finley R, Ng LK, Avery B, Boerlin P, Bourgault AM, Cole L, Daignault D, Desruisseau A, Demczuk W, Hoang L, Horsman GB, Ismail J, Jamieson F, Maki A, Pacagnella A, Pillai DR. Ceftiofur resistance in Salmonella enterica serovar Heidelberg from chicken meat and humans, Canada. Emerg Infect Dis 2010; 16:48-54. [PMID: 20031042 PMCID: PMC2874360 DOI: 10.3201/eid1601.090729] [Citation(s) in RCA: 295] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Use of this drug in chickens may limit effectiveness of cephalosporins in treating human infections. The Canadian Integrated Program for Antimicrobial Resistance Surveillance describes a strong correlation (r = 0.9, p<0.0001) between ceftiofur-resistant Salmonella enterica serovar Heidelberg isolated from retail chicken and incidence of ceftiofur-resistant Salmonella serovar Heidelberg infections in humans across Canada. In Québec, changes of ceftiofur resistance in chicken Salmonella Heidelberg and Escherichia coli isolates appear related to changing levels of ceftiofur use in hatcheries during the study period, from highest to lowest levels before and after a voluntary withdrawal, to increasing levels after reintroduction of use (62% to 7% to 20%, and 34% to 6% to 19%, respectively). These events provide evidence that ceftiofur use in chickens results in extended-spectrum cephalosporin resistance in bacteria from chicken and humans. To ensure the continued effectiveness of extended-spectrum cephalosporins for treating serious infections in humans, multidisciplinary efforts are needed to scrutinize and, where appropriate, limit use of ceftiofur in chicken production in Canada.
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Affiliation(s)
- Lucie Dutil
- Public Health Agency of Canada, Saint-Hyacinthe, Quebec, Canada.
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Leon-Velarde CG, Zosherafatein L, Odumeru JA. Application of an automated immunomagnetic separation–enzyme immunoassay for the detection of Salmonella enterica subspecies enterica from poultry environmental swabs. J Microbiol Methods 2009; 79:13-7. [DOI: 10.1016/j.mimet.2009.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 07/08/2009] [Accepted: 07/08/2009] [Indexed: 10/20/2022]
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Bergan T. A new bacteriophage typing set for Pseudomonas aeruginosa. 2. Characterization and comparisons of new and previous typing sets. ACTA PATHOLOGICA ET MICROBIOLOGICA SCANDINAVICA. SECTION B: MICROBIOLOGY AND IMMUNOLOGY 2009; 80:189-201. [PMID: 4624531 DOI: 10.1111/j.1699-0463.1972.tb00149.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Phage typing is a rapid, economical, reliable, and reproducible technique, requiring no specialized equipment, for fingerprinting disease-causing agents for epidemiological investigation and surveillance.
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Affiliation(s)
- Irina Chirakadze
- George Eliava Institute of Bacteriophage, Microbiology and Virology (Eliava IBMV), Tbilisi, Georgia
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Farzan A, Friendship RM, Dewey CE, Muckle AC, Gray JT, Funk J. Distribution of Salmonella serovars and phage types on 80 Ontario swine farms in 2004. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2008; 72:1-6. [PMID: 18214155 PMCID: PMC2117361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 04/10/2007] [Indexed: 05/25/2023]
Abstract
The objective of this study was to describe the distribution of Salmonella spp. on Ontario grower-finisher pig farms. Eighty swine farms were visited from January through July 2004. On each farm, fecal samples were collected from 5 pens, 2 rectal samples and 1 pooled sample from fresh manure on the floor per pen. Salmonella was isolated from 91 (11%) of the 800 rectal samples and 73 (18%) of the 397 pooled samples. Overall, Salmonella was recovered from 37 (46%) of the 80 farms. On each positive farm, Salmonella was cultured from 1 to 7 pigs or 1 to 5 pens. Of the 37 farms, 18, 13, 5, and 1 yielded 1, 2, 3, and 4 serovars, respectively. The most common serovars were S. Typhimurium var. Copenhagen, S. Infantis, S. Typhimurium, S. Derby, S. Agona, S. Havana, and S. enterica subsp. I:Rough-O. The 3 most frequent phage types were PT 104, PT 104a, and PT 104b. There was a statistically fair agreement between samples collected directly from pigs and pooled pen samples in determining the Salmonella status at the pen and farm level (kappa = 0.6, P < 0.0001). However, in 62 pens, Salmonella status, serovars, or phage types differed between the pig and pooled pen samples. The distribution of Salmonella on the swine farms in this study indicates that, in developing an intervention strategy, priority should be given to farms positive for S. Typhimurium var. Copenhagen. Also, the variation in Salmonella status between pig and pooled pen samples deserves consideration in a sampling strategy.
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Affiliation(s)
- Abdolvahab Farzan
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1.
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Rosengren LB, Waldner CL, Reid-Smith RJ, Checkley SL, McFall ME, Rajić A. Antimicrobial resistance of fecal Salmonella spp. isolated from all phases of pig production in 20 herds in Alberta and Saskatchewan. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2008; 72:151-9. [PMID: 18505204 PMCID: PMC2276900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Salmonella spp. (n = 468), isolated from the feces of sows, nursery, and grow-finish pigs in 20 farrow-to-finish herds in Alberta and Saskatchewan, were tested for susceptibility to 16 antimicrobials. No resistance was identified to amikacin, amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, ciprofloxacin or nalidixic acid, and less than 1% of the isolates were resistant to cefoxitin and gentamicin. Isolates were most commonly resistant to tetracycline (35%) and sulfamethoxazole (27%). Overall, 59% of the Salmonella were susceptible to all 16 drugs (pansusceptible). Isolates from sows were more likely to be pansusceptible than isolates from nursery or grow-finish pigs. Resistance to 2 or more drugs occurred in 29% of the isolates and was significantly more likely to occur in Salmonella from nursery pigs than from sows. The odds of resistance to 4 of the drugs, streptomycin, ampicillin, kanamycin and cephalothin, were significantly higher in isolates from nursery pigs than grow-finish pigs, while the odds of resistance to 2 drugs, tetracycline and streptomycin, were higher in Salmonella from nursery pigs than from sows. More age-specific risk factor studies are needed to investigate these differences between production phases.
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Affiliation(s)
- Leigh B Rosengren
- Department of Large Animal Clinical Sciences, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4.
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Aragaw K, Molla B, Muckle A, Cole L, Wilkie E, Poppe C, Kleer J, Hildebrandt G. The characterization of Salmonella serovars isolated from apparently healthy slaughtered pigs at Addis Ababa abattoir, Ethiopia. Prev Vet Med 2007; 82:252-61. [PMID: 17658640 DOI: 10.1016/j.prevetmed.2007.05.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 05/09/2007] [Accepted: 05/27/2007] [Indexed: 11/21/2022]
Abstract
We looked for Salmonella in all 278 apparently healthy pigs slaughtered between September 2004 and May 2005 at the only pig-slaughtering slaughterhouse in Addis Ababa, Ethiopia. We used standard methods and tested caecal contents, mesenteric lymph nodes, and carcass swabs from each pig (missing only one carcass swab). Of the 278 pigs, 120 (43%) were positive; of the 833 samples 173 (21%) were positive. Thirty-three percent of the isolates were multi-resistant (including 46/48 isolates of S. Hadar, but none of the 39 isolates of S. Eastbourne or of the 37 of S. Saintpaul). Resistance to streptomycin (32.4%), tetracycline (31.8%) and nitrofurantoin (27.2%) was relatively high. The most common pattern of MDR observed was to nitrofurantoin, streptomycin and tetracycline (Resistance type NitStrTet). Our results indicate that salmonellae are prevalent in pigs slaughtered at Addis Ababa abattoir and a large proportion of the isolates were multi-drug resistant.
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Affiliation(s)
- K Aragaw
- Department of Veterinary Medicine, Awassa College of Agriculture, Debub University, Awassa, Ethiopia
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Bucher O, Holley RA, Ahmed R, Tabor H, Nadon C, Ng LK, D'Aoust JY. Occurrence and characterization of Salmonella from chicken nuggets, strips, and pelleted broiler feed. J Food Prot 2007; 70:2251-8. [PMID: 17969605 DOI: 10.4315/0362-028x-70.10.2251] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Raw, frozen chicken nuggets and strips have been identified as a significant risk factor in contracting foodborne salmonellosis. Cases of salmonellosis as a result of consuming partly cooked chicken nuggets may be due in part to Salmonella strains originating in broiler feed. This study was undertaken to determine the occurrence and characterize the strains of Salmonella contaminating chicken nuggets, strips, and pelleted feeds, in an attempt to demonstrate whether the same Salmonella strains present in broiler feed could be isolated from raw, frozen chicken nuggets and strips available for human consumption. Salmonellae were recovered using the Health Canada MFHPB-20 method for the isolation and identification of Salmonella from foods. Strains were characterized by serotyping, phage typing, antimicrobial resistance typing (R-typing), and by pulsed-field gel electrophoresis (PFGE). Salmonellae were isolated from 25-g samples in 27% (n=92) of nugget and strip samples, 95% (n=20) of chicken nugget meat samples, and from 9% (n=111) of pelleted feed samples. Salmonella Heidelberg, Salmonella Enteritidis, and Salmonella Orion were the most commonly isolated serovars from chicken nuggets and strips, nugget and strip meat, and pelleted broiler feeds, respectively. Salmonella Enteritidis phage type (PT) 13a with PFGE pattern SENXAI.0006 and R-type sensitive as well as Salmonella Enteritidis PT13a with PFGE pattern SENXAI.0068 and R-type sensitive were isolated from pelleted feed, and chicken nugget and strip meat in two separate instances. Data showed that Salmonella strains isolated from broiler feed were indistinguishable from strains isolated from packaged raw, frozen chicken nuggets and strips. However, results did not rule out the possibility that breeding stock or contamination during processing may have contributed to chicken meat contamination by Salmonella.
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Affiliation(s)
- O Bucher
- Department of Food Science, University of Manitoba, Winnipeg, Manitoba, Canada
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Molla W, Molla B, Alemayehu D, Muckle A, Cole L, Wilkie E. Occurrence and antimicrobial resistance of Salmonella serovars in apparently healthy slaughtered sheep and goats of central Ethiopia. Trop Anim Health Prod 2007; 38:455-62. [PMID: 17243472 DOI: 10.1007/s11250-006-4325-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The present study was undertaken to determine the occurrence, distribution and antimicrobial resistance pattern of Salmonella serovars in apparently healthy slaughtered sheep and goats in central Ethiopia. A total 1224 samples consisting of faeces, mesenteric lymph nodes, liver, spleen, and abdominal and diaphragmatic muscle samples were collected from 104 sheep and 100 goats. Salmonella was isolated from 12 of 104 (11.5%) sheep and 3 of 100 (3%) goats. Of the total 624 and 600 samples examined from sheep and goats, 18 (2.9%) and 4 (0.7%), respectively, were Salmonella positive. The 22 Salmonella isolates belonged to 9 different serovars. The common serovars isolated were S. typhimurium, followed by S. heidelberg, S. reading, S. give, and S. poona. Seven of the 22 isolates (31.8%) were multidrug-resistant to various antimicrobials.
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Affiliation(s)
- W Molla
- Faculty of Veterinary Medicine, Gondar University, Gondar, Ethiopia
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38
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Kropinski AM, Sulakvelidze A, Konczy P, Poppe C. Salmonella phages and prophages--genomics and practical aspects. Methods Mol Biol 2007; 394:133-75. [PMID: 18363236 DOI: 10.1007/978-1-59745-512-1_9] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Numerous bacteriophages specific to Salmonella have been isolated or identified as part of host genome sequencing projects. Phylogenetic analysis of the sequenced phages, based on related protein content using CoreGenes, reveals that these viruses fall into five groupings (P27-like, P2-like, lambdoid, P22-like, and T7-like) and three outliers (epsilon15, KS7, and Felix O1). The P27 group is only represented by ST64B; the P2 group contains Fels-2, SopEphi, and PSP3; the lambdoid Salmonella phages include Gifsy-1, Gifsy-2, and Fels-1. The P22-like viruses include epsilon34, ES18, P22, ST104, and ST64T. The only member of the T7-like group is SP6. The properties of each of these phages are discussed, along with their role as agents of genetic exchange and as therapeutic agents and their involvement in phage typing.
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Affiliation(s)
- Andrew M Kropinski
- Host and Pathogen Determinants, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario
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39
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McLaughlin JB, Castrodale LJ, Gardner MJ, Ahmed R, Gessner BD. Outbreak of multidrug-resistant Salmonella typhimurium associated with ground beef served at a school potluck. J Food Prot 2006; 69:666-70. [PMID: 16541701 DOI: 10.4315/0362-028x-69.3.666] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An outbreak of gastroenteritis occurred among at least 47 persons attending a school potluck. Illness was associated with consumption of ground beef (estimated odds ratio, 16.3; 95% confidence interval, 2.2 to 338.3). Salmonella Typhimurium isolated from infected individuals and the implicated ground beef revealed identical pulsed-field gel electrophoresis patterns and was multidrug resistant. The implicated ground beef was improperly handled during the cooking process and stored above the U.S. Food and Drug Administration cooling temperature standard for >15 h before being served. This outbreak demonstrates the limitations of food safety regulations in settings where foods are prepared in the home environment for communal potlucks, bake sales, or other such gatherings held at schools, churches, or other institutions. Public health authorities should encourage school and other institutional administrators to develop policies that require dissemination of safe food preparation guidelines to prospective food handlers when such events are scheduled.
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Affiliation(s)
- Joseph B McLaughlin
- Alaska Department of Health and Social Services, 3601 C Street, Suite 540, Anchorage, Alaska 99503, USA.
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40
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Molla B, Berhanu A, Muckle A, Cole L, Wilkie E, Kleer J, Hildebrandt G. Multidrug Resistance and Distribution of Salmonella Serovars in Slaughtered Pigs. ACTA ACUST UNITED AC 2006; 53:28-33. [PMID: 16460353 DOI: 10.1111/j.1439-0450.2006.00900.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present study was undertaken to estimate the occurrence and distribution of multidrug resistance (MDR) among Salmonella serovars isolated from slaughtered pigs at Debre Zeit, Ethiopia. A total of 501 different samples were examined of which 42 (41.6%) of 101 mesenteric lymph nodes, 22 (21.8%) of 101 tongues, 17 (16.8%) of 101 caecal contents, 11 (11.1%) of 99 livers and two (2%) of 99 muscle (diaphragm and abdomen) samples were Salmonella positive. Of the 94 Salmonella isolates representing 15 different serovars, 69 (73.4%) were multidrug resistant (resistance to two or more antimicrobials). Among the Salmonella serovars a high level of MDR was observed in S. Hadar, S. Kentucky, S. Blockley and S. Enteritidis mainly to tetracycline (88.6%), streptomycin (82.9%), nitrofurantoin (74.3%), nalidixic acid and ciprofloxacin (42.9% each), sulfisoxazole (21.1%) and spectinomycin (20%). The pattern of MDR varied from two to eight antimicrobials among the resistant Salmonella serovars. The common profiles of resistance among the MDR serovars were the combined resistance to nitrofurantoin, streptomycin and tetracycline (R type NitStrTet, 51.4%), ciprofloxacin, nalidixic acid and nitrofurantoin (R type CipNalNit, 10%), ciprofloxacin, nalidixic acid, spectinomycin, streptomycin, sulfisoxazole and tetracycline (R type CipNalSptStrSulTet, 14.3%) and to ciprofloxacin, kanamycin, nalidixic acid, neomycin, nitrofurantoin, streptomycin and tetracycline (R type CipKanNalNeoNitStrTet, 10%). Results of the present study indicate the widespread occurrence and distribution of MDR Salmonella serovars in slaughtered pigs which could be a potential source of human MDR Salmonella infections.
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Affiliation(s)
- B Molla
- Department of Microbiology and Veterinary Public Health, Faculty of Veterinary Medicine, Addis Ababa University, Debre Zeit, Ethiopia.
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41
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Kothapalli S, Nair S, Alokam S, Pang T, Khakhria R, Woodward D, Johnson W, Stocker BAD, Sanderson KE, Liu SL. Diversity of genome structure in Salmonella enterica serovar Typhi populations. J Bacteriol 2005; 187:2638-50. [PMID: 15805510 PMCID: PMC1070368 DOI: 10.1128/jb.187.8.2638-2650.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.
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Affiliation(s)
- Sushma Kothapalli
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
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42
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Rajic A, Keenliside J, McFall ME, Deckert AE, Muckle AC, O'Connor BP, Manninen K, Dewey CE, McEwen SA. Longitudinal study of Salmonella species in 90 Alberta swine finishing farms. Vet Microbiol 2005; 105:47-56. [PMID: 15607083 DOI: 10.1016/j.vetmic.2004.10.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 09/27/2004] [Accepted: 10/18/2004] [Indexed: 11/19/2022]
Abstract
The aim of this study was to determine the farm prevalence of Salmonella in 90 Alberta finishing swine farms over a 5-month period, to evaluate Salmonella distribution in the farm environment and to describe Salmonella serovar diversity on these farms. Ten veterinary practitioners selected 90 Alberta swine farms based on an annual production of > or =2000 market pigs per farm and the willingness of the producers to participate in the study. Between May and September 2000, twenty samples were collected from finishing swine and the environment of each farm. The annual production of selected farms represented approximately 25% of the market swine production in Alberta. Participating farms were geographically representative of major swine production areas in Alberta. Sixty (66.7%) farms had at least one Salmonella-positive sample, with confidence interval (CI) of 57.1-77.2%. Salmonella were detected in 14.3% of fecal and 20.1% of environmental samples. The number of Salmonella-positive samples per farm ranged from 1 to 19. Among environmental samples, Salmonella were most frequently recovered from boots (38.6%) and the main drain (31.8%). Twenty-two serovars were detected on the 60 Salmonella-positive farms. Serovars Typhimurium (78 isolates), Derby (71 isolates) and Infantis (47 isolates) were the most common. A single serovar was detected on 58 farms, while 2, 3 and >3 serovars were detected on 15, 10 and 7 farms, respectively. The Salmonella farm status changed frequently over the 5-month period indicating the dynamic nature of Salmonella infections on these farms.
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Affiliation(s)
- Andrijana Rajic
- Food Safety Division, Alberta Agriculture, Food and Rural Development, Edmonton, Alta., Canada.
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43
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Molla B, Mohammed A, Salah W. Salmonella prevalence and distribution of serotypes in apparently healthy slaughtered camels (Camelus dromedarius) in Eastern Ethiopia. Trop Anim Health Prod 2004; 36:451-8. [PMID: 15449834 DOI: 10.1023/b:trop.0000035013.01459.c9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The present study was undertaken to determine the prevalence and distribution of Salmonella from apparently healthy slaughtered camels in Eastern Ethiopia. A total of 714 samples (faeces, mesenteric, lymph nodes, spleen, liver, abdominal and diaphragmatic muscles) from 119 slaughtered camels were analysed. Salmonellae were detected from 116 (16.2%) of the 714 samples examined. Eighteen (15.1%) faeces, 19 (15.9%) mesenteric lymph nodes, 14 (11.8%) livers and 17 (14.3%) spleen samples (n = 119 for each) were positive for Salmonella. Salmonellae were found in 20.1% of the abdominal and diaphragmatic muscles. A total of sixteen different serotypes were identified of which Salmonella saintpaul (38.8%) and S. braenderup (22.4%) were the most prevalent followed by S. muenchen (8.6%), S. kottbus (6.0%) and S. havana (5.2%). Other serotypes, including S. typhimurium, S. heidelberg and S. enteritidis were also detected from Ethiopian camels.
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Affiliation(s)
- B Molla
- Department of Microbiology, Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Addis Ababa University, Debre Zeit, Ethiopia.
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44
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Sabour PM, Gill JJ, Lepp D, Pacan JC, Ahmed R, Dingwell R, Leslie K. Molecular typing and distribution of Staphylococcus aureus isolates in Eastern Canadian dairy herds. J Clin Microbiol 2004; 42:3449-55. [PMID: 15297482 PMCID: PMC497614 DOI: 10.1128/jcm.42.8.3449-3455.2004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Revised: 04/11/2004] [Accepted: 05/07/2004] [Indexed: 11/20/2022] Open
Abstract
Macrorestriction analysis of SmaI-digested chromosomal DNA, using pulsed field gel electrophoresis (PFGE) was performed to type and estimate genetic relationships among 288 Staphylococcus aureus isolates recovered from 58 Eastern Canadian dairy herds. In addition, a subset of the collection was phage typed and evaluated for sensitivity to 10 antimicrobial compounds. Of 288 isolates recovered, 29 distinct PFGE types were identified. Based on estimates of genetic relationships, the PFGE types were assigned to six lineage groups, designated A through F. Of all of the isolates, ca. 93% were assigned to lineage groups A, D, or F. In 58.6% of herds, only a single PFGE type was recovered, while the remainder had two to four types. Of the 212 isolates evaluated for antimicrobial resistance, 24.5% were resistant to one or more antimicrobials. Resistance to penicillin (9.9%) was most common, followed by resistance to sulfadimethoxine (7.5%). Isolates resistant to multiple antibiotics were rare. A total of 63% of isolates responded to phages from groups 1 and 3, and 32.8% could not be typed with any of the phage strains used. The other 4.1% belonged to a variety of phage types. Most of the PFGE lineage group A and F isolates corresponded to phage groups 3 and 1, respectively, and most group D isolates were not typeable. PFGE typing had better discriminatory power than phage typing in defining the relatedness of the S. aureus isolates. Distribution of PFGE types and phage types was independent across regions and within herds.
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Affiliation(s)
- P M Sabour
- Food Safety and Quality Research, Agriculture and Agri-Food Canada, 93 Stone Rd. West, Guelph, Ontario N1G 5C9, Canada.
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45
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Leon-Velarde CG, Cai HY, Larkin C, Bell-Rogers P, Stevens RWC, Odumeru JA. Evaluation of methods for the identification of Salmonella enterica serotype Typhimurium DT104 from poultry environmental samples. J Microbiol Methods 2004; 58:79-86. [PMID: 15177906 DOI: 10.1016/j.mimet.2004.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 03/08/2004] [Accepted: 03/08/2004] [Indexed: 11/17/2022]
Abstract
An increase in the prevalence of Salmonella enterica serotype Typhimurium DT104 has been reported worldwide. This study examined the prevalence of this microorganism in poultry environmental samples from commercial layer flocks and pullet environments as well as the sensitivity and specificity of a PCR-based method, and multiple antibiotic resistance profile of Salmonella serogroup B isolates in relation to the serotype and phagetype reference method for the identification of Salmonella Typhimurium DT104. A total of 435 Salmonella isolates were obtained from poultry house environmental samples tested during a 20-month period representing a prevalence of 5.5%. Of these, 313 (72%) isolates were identified as Salmonella serogroup B isolates. These isolates were tested by a PCR-based assay, and for resistance to five antibiotics: ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline (ACSSuT) for the rapid identification of Salmonella Typhimurium DT104. Upon comparing the antibiotic resistance and PCR results with serotype and phage type data, the sensitivity and specificity for the identification of Salmonella Typhimurium DT104 of both methods were found to be 100%, and 99.6%, respectively. Both methods can be completed within 24 h after obtaining an isolate, while serotyping and phagetyping required more than 5 days to complete.
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Affiliation(s)
- Carlos G Leon-Velarde
- Laboratory Services Division, University of Guelph, 95 Stone Rd. West, Guelph, ON, Canada N1H 8J7
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46
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Trattner S, Greenspan H, Tepper G, Abboud S. Automatic identification of bacterial types using statistical imaging methods. IEEE TRANSACTIONS ON MEDICAL IMAGING 2004; 23:807-820. [PMID: 15250633 DOI: 10.1109/tmi.2004.827481] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The objective of the current study is to develop an automatic tool to identify microbiological data types using computer-vision and statistical modeling techniques. Bacteriophage (phage) typing methods are used to identify and extract representative profiles of bacterial types out of species such as the Staphylococcus aureus. Current systems rely on the subjective reading of profiles by a human expert. This process is time-consuming and prone to errors, especially as technology is enabling the increase in the number of phages used for typing. The statistical methodology presented in this work, provides for an automated, objective and robust analysis of visual data, along with the ability to cope with increasing data volumes.
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Affiliation(s)
- Sigal Trattner
- Department of Biomedical Engineering, Faculty of Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel.
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47
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Nair S, Alokam S, Kothapalli S, Porwollik S, Proctor E, Choy C, McClelland M, Liu SL, Sanderson KE. Salmonella enterica serovar Typhi strains from which SPI7, a 134-kilobase island with genes for Vi exopolysaccharide and other functions, has been deleted. J Bacteriol 2004; 186:3214-23. [PMID: 15126484 PMCID: PMC400635 DOI: 10.1128/jb.186.10.3214-3223.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica serovar Typhi has a 134-kb island of DNA identified as salmonella pathogenicity island 7 (SPI7), inserted between pheU and 'pheU (truncated), two genes for tRNA(Phe). SPI7 has genes for Vi exopolysaccharide, for type IVB pili, for putative conjugal transfer, and for sopE bacteriophage. Pulsed-field gel electrophoresis following digestion with the endonuclease I-CeuI, using DNA from a set of 120 wild-type strains of serovar Typhi assembled from several sources, identified eight strains in which the I-CeuI G fragment, which contains SPI7, had a large deletion. In addition, agglutination tests with Vi antiserum and phage typing with Vi phages show that all eight strains are Vi negative. We therefore tested these strains for deletion of SPI7 by multiplex PCR, by microarray analysis, and by sequencing of PCR amplicons. Data show that seven of the eight strains are precise deletions of SPI7: a primer pair flanking SPI7 results in a PCR amplicon containing a single pheU gene; microarrays show that all SPI7 genes are deleted. Two of the strains produce amplicons which have A derived from pheU at bp 27, while five have C derived from 'pheU at this position; thus, the position of the crossover which results in the deletion can be inferred. The deletion in the eighth strain, TYT1669, removes 175 kb with junction points in genes STY4465 and STY4664; the left junction of SPI7 and adjacent genes, as well as part of SPI7 including the viaB operon for Vi exopolysaccharide, was removed, while the right junction of SPI7 was retained. We propose that these deletions occurred during storage following isolation.
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Affiliation(s)
- Satheesh Nair
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4.
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48
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Larkin C, Poppe C, McNab B, McEwen B, Mahdi A, Odumeru J. Antibiotic resistance of Salmonella isolated from hog, beef, and chicken carcass samples from provincially inspected abattoirs in Ontario. J Food Prot 2004; 67:448-55. [PMID: 15035356 DOI: 10.4315/0362-028x-67.3.448] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The emergence of antimicrobial-resistant Salmonella organisms, especially Salmonella Typhimurium DT104, has been reported in many countries, including the United States and Canada. The purposes of this study were to determine the antimicrobial resistance patterns of Salmonella isolated from hog, beef, and chicken carcasses from provincially inspected abattoirs in Ontario and to determine the agreement between the agar dilution method and the microbroth dilution method for measurement of antimicrobial resistance of the isolates. Antimicrobial resistance of Salmonella isolates from hogs (n = 71), beef (n = 24), and chicken (n = 295) to amikacin, ampicillin, cephalothin, chloramphenicol, ciprofloxacin, gentamicin, streptomycin, sulfamethoxazole, and tetracycline was determined using the two methods. None of the 390 isolates were resistant to ciprofloxacin at levels of 0.125 microg/ml. All chicken and hog isolates were sensitive to amikacin, whereas all beef isolates were sensitive to both amikacin and gentamicin. Multiple antimicrobial resistance (resistance to more than one antimicrobial) was found in 29% of bovine isolates and 42% of porcine isolates using both methods for testing and in 42% by the agar dilution and 33% by the microbroth dilution methods in the chicken isolates. Overall, there was good agreement between the two test methods for resistance to most of the antimicrobials, with disagreement found in the results in 1.3% of the isolates for ampicillin and sulfamethoxazole, 8.2% for streptomycin, 5.6% for cephalothin, and 1.0% of the isolates for tetracycline. The lack of agreement between the two test methods was found mostly among the chicken isolates.
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Affiliation(s)
- C Larkin
- Laboratory Services Division, University of Guelph, Guelph, Ontario, Canada N1H 8J7
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49
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Alemayehu D, Molla B, Muckle A. Prevalence and antimicrobial resistance pattern of Salmonella isolates from apparently healthy slaughtered cattle in Ethiopia. Trop Anim Health Prod 2003; 35:309-19. [PMID: 14509538 DOI: 10.1023/a:1025189204496] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The prevalence and antimicrobial resistance pattern of Salmonella isolates was determined from apparently healthy slaughtered cattle at Debre Zeit (Ethiopia). A total of 323 cattle were examined for the presence of Salmonella in faeces, mesenteric lymph nodes, abdominal and diaphragmatic muscles. Salmonellae were cultured from 23 (7.1%) of the animals. Salmonellae were isolated from 2 (3.1%) and 3 (4.5%) of 65 pooled faecal and mesenteric lymph node samples, respectively. Nine (2.8%) abdominal muscle and 10 (3.1%) diaphragmatic muscle samples (n = 323 of each) were contaminated by Salmonella. About 60% of the serovars identified in the abdominal and diaphragmatic muscles were also detected from faeces and mesenteric lymph node samples. The five different serovars isolated were Salmonella mishmarhaemek (48%) S. typhimurium (20%). S. enteritidis (12%), S. guildford (12%) and S. dublin (48%). The antimicrobial resistance profiles of 25 of the Salmonella isolates with 17 antimicrobials showed that 52%, (13/25) of them were resistant to three or more antimicrobials. Both strains of Salmonella (S. mishmarhaemek and S. typhimurium) showed multiple resistance to ampicillin, sulfamethoxazole and ticarcillin.
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Affiliation(s)
- D Alemayehu
- Department of Microbiology, Infectious Diseases and Veterinary Public Health, Faculty of Veterinary Medicine, Addis Ababa University, Debre Zeit, Ethiopia
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50
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Demczuk W, Soule G, Clark C, Ackermann HW, Easy R, Khakhria R, Rodgers F, Ahmed R. Phage-based typing scheme for Salmonella enterica serovar Heidelberg, a causative agent of food poisonings in Canada. J Clin Microbiol 2003; 41:4279-84. [PMID: 12958257 PMCID: PMC193816 DOI: 10.1128/jcm.41.9.4279-4284.2003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Heidelberg is perhaps the second most frequent Salmonella serovar isolated from humans and the most common isolated from animals in Canada. This pathogen has shown increasing resistance to antimicrobial agents and mimics the multidrug resistance observed in S. enterica serovar Typhimurium strain DT 104. However, unlike for serovar Typhimurium, a rapid and inexpensive subtyping method has not been available for large-scale surveillance efforts. We developed a phage typing scheme and subtyped 2,523 strains of serovar Heidelberg from outbreaks, sporadic infections, and environmental sources in Canada between January 1991 and December 2000. All strains were sensitive to one or more phages and could be subdivided into 49 phage types. A total of 196 isolates from 13 major outbreaks could be subtyped into six phage types, while 86 strains from family outbreaks were assigned to seven phage types. All strains were typeable, and epidemiologically related strains isolated from patients and implicated foods had identical phage types, antibiograms, and pulsed-field gel electrophoresis (PFGE) patterns. Combining PFGE with phage typing increased the discriminatory power of the analysis beyond that of either method alone. We concluded that this phage typing scheme, in conjunction with PFGE, enhances subtyping of serovar Heidelberg strains. Furthermore, this phage typing scheme is a rapid, economical, stable, and reliable epidemiologic tool for tracing the origin of food-borne disease and for the surveillance of sporadic infections.
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Affiliation(s)
- Walter Demczuk
- National Laboratory for Enteric Pathogens, National Microbiology Laboratory, Health Canada, Winnipeg, Manitoba, Canada
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