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Andrews N, McCabe E, Wall P, Buckley JF, Fanning S. Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis (MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments. J Food Prot 2023; 86:100147. [PMID: 37619693 DOI: 10.1016/j.jfp.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Listeria monocytogenes is a serious human pathogen and an enduring challenge to control for the ready-to-eat food processing industry. Cost-effective tools that can be deployed by commercial or in-house laboratories to rapidly investigate and resolve contamination events in the built food processing environment are of value to the food industry. Multilocus variable number tandem-repeat analysis (MLVA) is a molecular subtyping method, which along with other same-generation methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) is being superseded in disease tracking and outbreak investigations by whole-genome sequencing (WGS). In this paper, it is demonstrated that MLVA can continue to play a valuable role as a valid, fast, simple, and cost-effective method to identify and track Listeria monocytogenes subtypes in factory environments, with the method being highly congruent with MLST. Although MLVA does not have the discriminatory power of WGS to identify truly persistent clones, with careful interpretation of results alongside isolate metadata, it remains a powerful tool in situations and locations where WGS may not be readily available to food business operators.
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Affiliation(s)
- Nicholas Andrews
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Patrick Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - James F Buckley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT5 6AG, United Kingdom.
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Osanloo L, Zeighami H, Haghi F, Shapouri R, Shokri R. Molecular Typing of Multidrug-Resistant Acinetobacter baumannii Isolates from Clinical Specimens by ERIC-PCR and MLVA. Curr Microbiol 2023; 80:355. [PMID: 37752362 DOI: 10.1007/s00284-023-03459-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023]
Abstract
Acinetobacter baumannii, a Gram-negative and oxidase-negative bacterium, is a major cause of nosocomial infections, leading to high mortality rates in hospitalized patients. The use of 2 prominent molecular typing methods (i.e., enterobacterial repetitive intergenic consensus-polymerase chain reaction [ERIC-PCR] and multiple-locus variable-number tandem repeat [VNTR] analysis [MLVA]) for genotyping A. baumannii isolates has proven to be an effective approach in assessing the clonal relation of these isolates and managing their outbreaks. A total of 100 A. baumannii isolates were collected from immunocompromised patients hospitalized in the intensive care unit (ICU) of a hospital in Zanjan City, Iran. Their antibiotic resistance ability (especially aminoglycoside resistance) was studied by disc diffusion tests. The genetic typing of A. baumannii was studied using ERIC-PCR and MLVA methods. All isolates were resistant to 3 or more antibiotics and regarded as multidrug-resistant (MDR). Additionally, 32% of the isolates were resistant to all antibiotics tested, and 91% were extensively drug-resistant (XDR). The increased rate of aminoglycoside-resistant A. baumannii in ICU patients, with an increased incidence of aminoglycoside-modifying enzymes of aac (6')-Ib, ant (3″)-I, and aph (2″)-Id. ERIC-PCR has likewise shown an increased level of diversity in A. baumannii isolates. According to the ERIC-PCR patterns, isolates were classified as 4 clusters, while according to the MLVA patterns, isolates were classified as 9 distinct clusters. ERIC-PCR and MLVA assays serve as useful genotyping methods to assess the genetic variety or clonal relatedness of A. baumannii isolates.
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Affiliation(s)
- Leili Osanloo
- Department of Microbiology, Biology Research Center, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Habib Zeighami
- Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Fakhri Haghi
- Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Reza Shapouri
- Department of Microbiology, Biology Research Center, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Rasoul Shokri
- Department of Microbiology, Biology Research Center, Zanjan Branch, Islamic Azad University, Zanjan, Iran
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Identification of Listeria species and Multilocus Variable-Number Tandem Repeat Analysis (MLVA) Typing of Listeria innocua and Listeria monocytogenes Isolates from Cattle Farms and Beef and Beef-Based Products from Retail Outlets in Mpumalanga and North West Provinces, South Africa. Pathogens 2023; 12:pathogens12010147. [PMID: 36678495 PMCID: PMC9862459 DOI: 10.3390/pathogens12010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
In this study, Listeria isolates (214) were characterized as follows: L. innocua (77.10%), L. monocytogenes (11.21%), L. welshimeri (5.61%), L. grayi (1.40%), L. seeligeri (0.93%), and L. species (3.73%) that were not identified at the species level, from beef and beef based products from retail and farms in Mpumalanga and North West provinces of South Africa. MLVA was further used to type Listeria innocua isolates (165) and Listeria monocytogenes isolates (24). The L. monocytogenes isolates were also serogrouped using PCR. The MLVA protocol for L. monocytogenes typing included six tandem repeat primer sets, and the MLVA protocol for L. innocua included the use of three tandem repeats primer sets. The L. monocytogenes serogroups were determined as follows: 4b-4d-4e (IVb) (37.50%), 1/2a-3a (IIa) (29.16%), 1/2b-3b (IIb) (12.50%), 1/2c-3c (IIc) (8.33%), and IVb-1 (4.16%). MLVA could cluster isolates belonging to each specie, L. monocytogenes, and L. innocua isolates, into MLVA-related strains. There were 34 and 10 MLVA types obtained from the MLVA typing of L. innocua and L. monocytogenes, respectively. MLVA clustered the L. monocytogenes isolates irrespective of sample category, serogroups, and geographical origin. Similarly, the L. innocua isolates clustered irrespective of meat category and geographical origin. MLVA was able to cluster isolates based on MLVA relatedness. The clustering of isolates from farms and retailers indicates transmission of Listeria spp. MLVA is an affordable, simple, and discriminatory method that can be used routinely to type L. monocytogenes and L. innocua isolates.
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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Gana J, Gcebe N, Pierneef R, Moerane R, Adesiyun AA. Multiple-Locus Variable-Number Tandem Repeat Analysis Genotypes of Listeria monocytogenes Isolated from Farms, Abattoirs, and Retail in Gauteng Province, South Africa. J Food Prot 2022; 85:1249-1257. [PMID: 35588459 DOI: 10.4315/jfp-22-081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/29/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT The use of multiple-locus variable-number analysis (MLVA) of tandem repeats (TRs) for subtyping Listeria monocytogenes has proven to be reliable and fast. This study determined the MLVA genotypes of 60 isolates of L. monocytogenes recovered from cattle farms, abattoirs, and retail outlets in Gauteng province, South Africa. The distribution of the 60 L. monocytogenes isolates analyzed by type of sample was as follows: raw beef (28, 46.7%), ready-to-eat beef products (9, 15.0%), beef carcass swabs (9, 15.0%), cattle environment (6, 10.0%), and cattle feces (8, 13.3%). The serogroups of the isolates were determined using PCR and the MLVA genotypes based on six selected loci. The frequency of the 60 serogroups detected was as follows: 1/2a-3a (IIa) (27, 45.0%); 4b-4d-4e (1Vb) (24, 40.0%); 1/2c-3c (IIc) (8, 13.3%); and 1/2b-3b (IIb) (1, 1.7%). MLVA successfully clustered genetically related isolates and differentiated nonrelated isolates, irrespective of their sources, sample types, and serogroups, as demonstrated by 16 MLVA pattern types detected. For serogroup 4b-4d-4e (IVb), there was no variation in TRs LM-TR2, LM-TR4, and LM-TR6, which each contained only one allele (02, 00, and 93, respectively). However, across the sources and sample types of isolates, there was variation in serogroup 4b-4d-4e (IVb): LM-TR1 contained 00, 03, and 05; LM-TR3 contained 14, 20, and 22; and LM-TR5 contained 14, 21, and 25. Similar patterns of variation in the TRs were detected in the other serogroups (1/2a-3a, 1/2b-3b, and 1/2c-3c). BioNumeric data analysis identified at least five types in Gauteng province. MLVA epidemiologically clustered the related isolates and differentiated unrelated isolates. HIGHLIGHTS
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Affiliation(s)
- James Gana
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa.,Department of Agricultural Education, Federal College of Education, Kontagora, Niger State, Nigeria
| | - Nomakorinte Gcebe
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, South Africa
| | - Rian Pierneef
- Agricultural Research Council-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
| | - Rebone Moerane
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Abiodun A Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa.,Department of Paraclinical Sciences, School of Veterinary Medicine, The University of West Indies, St. Augustine, Trinidad and Tobago
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Genotyping of Listeria monocytogenes isolates by high-resolution melting curve (HRM) analysis of tandem repeat locus. Braz J Infect Dis 2022; 26:102348. [PMID: 35341738 PMCID: PMC9387474 DOI: 10.1016/j.bjid.2022.102348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
Listeria monocytogenes is responsible for causing listeriosis, a type of food poisoning with high mortality. This bacterium is mainly transmitted to humans through the consumption of contaminated foods. Detection of L. monocytogenes through molecular methods is crucial for food safety and clinical diagnosis. Present techniques are characterized by low discrimination power and high cost, as well as being time-consuming and taking several days to give the final result. In our study, MLVA-HRM (Multiple-Locus Variable-number tandem repeats Analysis ‒ High-Resolution Melting) was investigated as an alternative method for a fast and precise method for the genotyping of L. monocytogenes isolates. Forty-eight isolates of L. monocytogenes obtained from the microbial bank of Department of Microbiology, Iran University of Medical Sciences, were typed by MLVA-HRM analysis using five Variable Numbers of Tandem Repeat (VNTR) loci. A total of 43 different types were obtained. This research demonstrated the usefulness of the MLVA-HRMA method and its ability to discriminate L. monocytogenes isolates. Since this method is easier and more efficient than existing methods, it can be widely used in food processing plants and diagnostic laboratories as a fast and accurate method.
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Neoh HM, Tan XE, Sapri HF, Tan TL. Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives. INFECTION GENETICS AND EVOLUTION 2019; 74:103935. [PMID: 31233781 DOI: 10.1016/j.meegid.2019.103935] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/01/2022]
Abstract
Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.
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Affiliation(s)
- Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.
| | - Xin-Ee Tan
- Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Hassriana Fazilla Sapri
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
| | - Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
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Fang R, Jiang B, Xie J, Wang Z, Liang W, Yang Z, Lin LU, Peng Y, Nie K, Zeng Z, Huang B. An Optimized Multilocus Variable-Number Tandem Repeat Analysis Typing Scheme for Listeria monocytogenes from Three Western Provinces in China. J Food Prot 2018; 81:1956-1962. [PMID: 30457387 DOI: 10.4315/0362-028x.jfp-18-064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Listeria monocytogenes is a foodborne pathogen worldwide. Multilocus variable-number tandem repeat analysis (MLVA) has been used for listeriosis surveillance and outbreak investigations. MLVA typing schemes have been proposed, but their usefulness for typing isolates from the People's Republic of China has not been assessed. To this aim, all L. monocytogenes strains (79) isolated from 1,445 raw meat and abattoir environmental samples of three western provinces in China were characterized with PCR serogrouping, multilocus sequence typing, and MLVA. The isolates were typed into the four PCR serogroups IIb (38.0%), IIc (26.6%), IIa (24.0%), and IVb (11.4%), with a Simpson's index (SI) of 0.7235. With multilocus sequence typing, they were typed into 18 sequence types (STs), including two new STs, ST1029 and ST1011, with an SI of 0.8880. With the 14 MLVA loci from the previous five schemes, the isolates were typed into 39 MLVA genotypes, with an SI of 0.9656. The typing data indicated that MLVA had the highest typing capability among the three methods. A subsequent optimization analysis identified an optimal combination of eight loci (LMV2, LMV9, LMV1, Lm10, Lm11, Lm15, Lm23, and LMTR6) producing the same SI as that of the 14 loci. The present optimized combination shared only six loci with the optimal nine-loci combination proposed in Australia, verifying for the first time that the optimal combinations varied with the isolates' sets. The current optimal typing scheme was ideal for L. monocytogenes isolates from western China.
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Affiliation(s)
- Rendong Fang
- 1 College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Bing Jiang
- 1 College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Jianhua Xie
- 2 Chongqing Animal Disease Prevention and Control Center, Chongqing Research Center for Prevention and Control of Swine Infectious Diseases, and Laboratory of Quality & Safety Risk Assessment for Animal Products on Biohazards, Ministry of Agriculture, Chongqing 401120, People's Republic of China
| | - Zichun Wang
- 2 Chongqing Animal Disease Prevention and Control Center, Chongqing Research Center for Prevention and Control of Swine Infectious Diseases, and Laboratory of Quality & Safety Risk Assessment for Animal Products on Biohazards, Ministry of Agriculture, Chongqing 401120, People's Republic of China
| | - Wangwang Liang
- 2 Chongqing Animal Disease Prevention and Control Center, Chongqing Research Center for Prevention and Control of Swine Infectious Diseases, and Laboratory of Quality & Safety Risk Assessment for Animal Products on Biohazards, Ministry of Agriculture, Chongqing 401120, People's Republic of China
| | - Zelin Yang
- 2 Chongqing Animal Disease Prevention and Control Center, Chongqing Research Center for Prevention and Control of Swine Infectious Diseases, and Laboratory of Quality & Safety Risk Assessment for Animal Products on Biohazards, Ministry of Agriculture, Chongqing 401120, People's Republic of China
| | - L U Lin
- 2 Chongqing Animal Disease Prevention and Control Center, Chongqing Research Center for Prevention and Control of Swine Infectious Diseases, and Laboratory of Quality & Safety Risk Assessment for Animal Products on Biohazards, Ministry of Agriculture, Chongqing 401120, People's Republic of China
| | - Yuanyi Peng
- 1 College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Kui Nie
- 1 College of Animal Science and Technology, Southwest University, Beibei, Chongqing 400715, People's Republic of China
| | - Zheng Zeng
- 2 Chongqing Animal Disease Prevention and Control Center, Chongqing Research Center for Prevention and Control of Swine Infectious Diseases, and Laboratory of Quality & Safety Risk Assessment for Animal Products on Biohazards, Ministry of Agriculture, Chongqing 401120, People's Republic of China
| | - Bixing Huang
- 3 Public Health Virology, Queensland Health Forensic and Scientific Services, Department of Health, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia (ORCID: http://orcid/org/0000-0002-7025-2292 )
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Martín B, Bover-Cid S, Aymerich T. MLVA subtyping of Listeria monocytogenes isolates from meat products and meat processing plants. Food Res Int 2017; 106:225-232. [PMID: 29579922 DOI: 10.1016/j.foodres.2017.12.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 01/30/2023]
Abstract
Listeria monocytogenes is widely distributed in meat products and the meat-processing industry thus posing a risk to consumers. The aim of this study was to evaluate the suitability of the multilocus variable-number tandem-repeat analysis (MLVA) for use as a L. monocytogenes subtyping technique for surveillance and routine control in meat products and meat processing plants. A collection of 113 isolates (including control strains and isolates from meat products and meat processing plants) were subject to MLVA analysis using two different platforms for fragment sizing: 1.) ABI 3730xl DNA analyzer (Life Technologies) as the reference method and 2.) The QIAxcel Advanced System (Qiagen). Although discrepancies in fragment sizing were observed it was possible to standardize results in order to assign the same allele for a given fragment independently of the platform used for fragment sizing. A total of 27 different MLVA profiles were obtained considering all the isolates (N=113), 24 of them corresponding to the meat industry isolates (N=106). MLVA and multilocus sequence typing (MLST) results were compared and yielded Simpson's diversity indices of 0.907 and 0.872, respectively. The congruence between both typing methods was measured with the adjusted Wallace coefficient (AW). Using MLVA as the primary method, AW=0.946 suggested that MLVA can predict the sequence type with high accuracy. Given its discriminatory power and high throughput, MLVA could be considered a rapid, reliable, and high-throughput alternative to existing subtyping methods for surveillance and control of L. monocytogenes in the meat-processing industry.
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Affiliation(s)
- Belén Martín
- IRTA, Food Safety Program, Finca Camps i Armet, 17121 Monells, Spain
| | - Sara Bover-Cid
- IRTA, Food Safety Program, Finca Camps i Armet, 17121 Monells, Spain
| | - Teresa Aymerich
- IRTA, Food Safety Program, Finca Camps i Armet, 17121 Monells, Spain.
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10
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Prevalence and methodologies for detection, characterization and subtyping of Listeria monocytogenes and L. ivanovii in foods and environmental sources. FOOD SCIENCE AND HUMAN WELLNESS 2017. [DOI: 10.1016/j.fshw.2017.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Complete Genome Sequences of 12 Isolates of Listeria monocytogenes Belonging to Serotypes 1/2a, 1/2b, and 4b Obtained from Food Products and Food-Processing Environments in Canada. GENOME ANNOUNCEMENTS 2017; 5:5/19/e00258-17. [PMID: 28495767 PMCID: PMC5427202 DOI: 10.1128/genomea.00258-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Listeria monocytogenes is the etiological agent for an often fatal foodborne illness known as listeriosis. Here, we present the complete genome sequences of 12 L. monocytogenes isolates representing the three most common serotypes of this pathogen (1/2a, 1/2b, and 4b), collected in Canada from different food products and environmental sources.
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12
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Doijad S, Weigel M, Barbuddhe S, Blom J, Goesmann A, Hain T, Chakraborty T. Phylogenomic grouping of Listeria monocytogenes. Can J Microbiol 2015; 61:637-46. [DOI: 10.1139/cjm-2015-0281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.
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Affiliation(s)
- Swapnil Doijad
- Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392
| | - Markus Weigel
- Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392
| | - Sukhadeo Barbuddhe
- National Institute of Biotic Stress Management, Raipur, Chhattisgarh, India
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany 35392
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany 35392
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392
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Liu F, Liu H, Liao Y, Wei J, Zhou X, Xing D. Multiplex detection and genotyping of pathogenic bacteria on paper-based biosensor with a novel universal primer mediated asymmetric PCR. Biosens Bioelectron 2015; 74:778-85. [PMID: 26226347 DOI: 10.1016/j.bios.2015.06.054] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/21/2015] [Accepted: 06/23/2015] [Indexed: 01/06/2023]
Abstract
Traditionary multiplex asymmetric polymerase chain reaction (PCR) can be applied to detect multiplex target organisms simultaneously, but complex optimizations of primer concentrations and staggered additions of primers are required to achieve equal amplification of multiplex genes. To overcome this shortcoming, we propose a novel method based on multiplex asymmetric PCR and paper-based nucleic acid diagnostics (PBNAD). In the asymmetric PCR, a universal primer was introduced to break the bottlenecks of low sensitivity and self-inhibition among different sets of primers. Amplification using the novel multiplex asymmetric PCR boosted the quantity of single-stranded amplicons, and the amplified products contained the same sequence at the 5' end. Therefore, only one gold nanoparticle-based signal probe was needed for the simultaneous detection of three genes using the PBNAD platform, and the detection signals could be observed with the naked eye. With this highly efficient, novel multiplex asymmetric PCR, as little as 1 pg/μL genomic DNA can be detected. This method can also be applied to genotyping for reliable epidemiological investigations. This proof-of-concept study highlights the potential of the PBNAD platform for cost- and labor-effective applications in the detection of pathogenic bacteria.
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Affiliation(s)
- Fang Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Hongxing Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yuhui Liao
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Jitao Wei
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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Genotypic characterization, invasion index and antimicrobial resistance pattern in Listeria monocytogenes strains isolated from clinical samples. JOURNAL OF ACUTE DISEASE 2015. [DOI: 10.1016/s2221-6189(15)30024-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Chui L, Li V. Technical and Software Advances in Bacterial Pathogen Typing. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Dugat T, Chastagner A, Lagrée AC, Petit E, Durand B, Thierry S, Corbière F, Verheyden H, Chabanne L, Bailly X, Leblond A, Vourc'h G, Boulouis HJ, Maillard R, Haddad N. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants. Parasit Vectors 2014; 7:439. [PMID: 25228371 PMCID: PMC4262125 DOI: 10.1186/1756-3305-7-439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/02/2014] [Indexed: 11/26/2022] Open
Abstract
Background Anaplasma phagocytophilum is a tick-borne intragranulocytic alpha-proteobacterium. It is the causative agent of tick-borne fever in ruminants, and of human granulocytic anaplasmosis in humans, two diseases which are becoming increasingly recognized in Europe and the USA. However, while several molecular typing tools have been developed over the last years, few of them are appropriate for in-depth exploration of the epidemiological cycle of this bacterium. Therefore we have developed a Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique for A. phagocytophilum. Methods Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples: 67 from cattle, 7 from sheep, 15 from roe deer, 4 from red deer, 1 from a reindeer, 2 from horses, 1 from a dog, and 26 from ticks. Results From these samples, we obtained 84 different profiles, with a diversity index of 0.96 (0.99 for vertebrate samples, i.e. without tick samples). Our technique confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. As expected, greater diversity was obtained between rather than within cattle herds. Conclusions Our technique has great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-439) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Renaud Maillard
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR ENVA Anses UPEC USC INRA, Maisons-Alfort, France.
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Draft Genome Sequence of Listeria monocytogenes Strain LI0521 (syn. HPB7171), Isolated in 1983 during an Outbreak in Massachusetts Caused by Contaminated Cheese. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00729-14. [PMID: 25059873 PMCID: PMC4110231 DOI: 10.1128/genomea.00729-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Listeria monocytogenes, a pathogenic food-borne bacterium, is the causative agent of both sporadic and outbreak cases of human listeriosis. Here, we present the genome sequence of L. monocytogenes reference strain LI0521, isolated during an outbreak involving contaminated cheese, which has been used as the model during several proteomic studies.
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18
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Gorski L, Walker S, Liang AS, Nguyen KM, Govoni J, Carychao D, Cooley MB, Mandrell RE. Comparison of subtypes of Listeria monocytogenes isolates from naturally contaminated watershed samples with and without a selective secondary enrichment. PLoS One 2014; 9:e92467. [PMID: 24651315 PMCID: PMC3961389 DOI: 10.1371/journal.pone.0092467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 02/21/2014] [Indexed: 11/19/2022] Open
Abstract
Two enrichment methods for Listeria monocytogenes using Immuno Magnetic Separation (IMS) were tested to determine if they selected the same subtypes of isolates. Both methods used a non-selective primary enrichment and one included subculture in Fraser Broth, while the other involved direct plating of IMS beads. Sixty-two naturally contaminated watershed samples from the Central California Coast were used as a source of L. monocytogenes, and subtype diversity was measured by serotype and Multiple Number Variable Tandem Repeat Analysis (MLVA). Three different serotypes were detected from both methods with serotype 4b strains making up 87% of the isolates, serotype 1/2a making up 8%, and serotype 1/2b making up 5%. The data suggest that serotype 1/2a strains were more likely to be isolated from the Fraser Broth culture method. Sixty-two different MLVA types were detected and the more common MLVA types were detected by both culture methods. Forty-three MLVA types were detected only from one culture method or the other, while 19 types were detected from both culture methods. The most common MLVA type-12 was detected in 33 of the 62 water samples, and represented 31% of the isolates from both culture methods. This limited study provides evidence that using both enrichment culture methods allowed for detection of a greater diversity of isolates among the samples than the use of one method alone, and that a wide diversity of L. monocytogenes strains exist in this watershed.
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Affiliation(s)
- Lisa Gorski
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Samarpita Walker
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Anita S. Liang
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Kimberly M. Nguyen
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Jessica Govoni
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Michael B. Cooley
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Robert E. Mandrell
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
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