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Structures and stability of simple DNA repeats from bacteria. Biochem J 2020; 477:325-339. [PMID: 31967649 PMCID: PMC7015867 DOI: 10.1042/bcj20190703] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 01/12/2023]
Abstract
DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.
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Methicillin-resistant Staphylococcus aureus tracking spread among health-care workers and hospitalized patients in critical wards at a university hospital, Tehran, Iran. New Microbes New Infect 2018; 27:29-35. [PMID: 30534385 PMCID: PMC6278718 DOI: 10.1016/j.nmni.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/04/2018] [Accepted: 11/08/2018] [Indexed: 11/22/2022] Open
Abstract
Health-care workers may serve as a reservoir for dissemination of methicillin-resistant Staphylococcus aureus (MRSA) to patients in hospital settings. The present study aimed to screen MRSA in nasal swabs of health-care workers and clinical specimens from patients and investigate the possible relationship between these isolates at a university hospital in Tehran, Iran. Additionally, we aimed to identify potential risk factors for MRSA colonization in health-care workers. Staphylococcus aureus strains were isolated from health-care workers and inpatients who completed a questionnaire on risk factors. Cefoxitin disc diffusion test was also used for detection of MRSA. Moreover, all of the MRSA isolates were subjected to pulsed-field gel electrophoresis (PFGE). Colonization rate of MRSA among health-care workers was 22.5%. Furthermore, out of 24 S. aureus isolates obtained from patients, nine (37.5%) were MRSA. Regarding risk factors, the prevalence of nasal MRSA carriage among hospital personnel who used masks was significantly lower than in those without masks (p 0.007). Using PFGE, 10 clusters and 14 singletons were identified among the MRSA isolates. In this regard, most of the MRSA isolates recovered from health-care carriers and patients in intensive care wards, especially general intensive care units, were grouped in certain clusters, indicating intra-ward transmission of the mentioned isolates in these restricted areas. We concluded that screening and decolonization of carriers, contact precautions, prudent use of antibiotics and implementation of active surveillance are recommended strategies for the prevention and control of MRSA transmission in hospital settings.
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Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) and Tandem Repeat Sequence Typing (TRST), helpful tools for subtyping Staphylococcus lugdunensis. Sci Rep 2018; 8:11669. [PMID: 30076395 PMCID: PMC6076266 DOI: 10.1038/s41598-018-30144-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus lugdunensis is an emergent virulent coagulase-negative Staphylococcus that is increasingly responsible for severe infections. In an attempt to generate informative sequence data for subtyping S. lugdunensis, we selected and sequenced seven polymorphic variable number of tandem repeats (VNTRs) to develop two new methods: a classic length-based multiple-locus VNTR analysis (MLVA) method and a tandem repeat sequence typing (TRST) method. We assessed their performances compared to two existing methods, multilocus sequence typing (MLST) and multivirulence-locus sequence typing (MVLST) for 128 isolates from diverse clinical settings and geographical origins. The clustering achieved by the four methods was highly congruent, with MLVA discriminating within clonal complexes as defined by MLST. Indeed, MLVA was highly discriminant compared to MLST and MVLST in terms of number of genotypes as well as diversity indexes. Sequencing of the seven VNTRs showed that they were stable, and analysis of sequence polymorphisms provided superior discriminatory power. The typeability, reproducibility, and epidemiological concordance of these new methods were excellent. Of note, no link between clustering and clinical settings was identified. This study demonstrates that MLVA and TRST provide valuable information for molecular epidemiological study of S. lugdunensis, and represent promising tools to distinguish between strains of homogenous lineages in this clonal species.
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Campoccia D, Montanaro L, Arciola CR. Current Methods for Molecular Epidemiology Studies of Implant Infections. Int J Artif Organs 2018; 32:642-54. [DOI: 10.1177/039139880903200914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Over the last few decades, the number of surgical procedures involving prosthetic materials has greatly multiplied, along with the rising medical and economic impact of implant-associated infections. The need to appropriately counteract and deal with this phenomenon has led to growing efforts to elucidate the etiology, pathogenesis and epidemiology of these types of infections, characterized by opportunistic pathogens. Molecular epidemiology studies have progressively emerged as a leading multitask tool to identify and fingerprint bacterial strains, unveil the complex clonal nature of important pathogens, detect outbreak events, track the origin of the infections, assess the clinical significance of individual strain types, survey their distribution, recognize associations of strain types with specific virulence determinants and/or pathological conditions, assess the role played by the specific components of the virulon, and reveal the phylogeny and the mechanisms through which new strain types have emerged. Despite the many advances that have been made thanks to these flourishing new approaches to molecular epidemiology, a number of critical aspects remain challenging. In this paper, we briefly discuss the current limitations and possible developments of molecular epidemiology methods in the investigation and surveillance of implant infections.
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Affiliation(s)
- Davide Campoccia
- Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy
| | - Lucio Montanaro
- Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy
- Department of Experimental Pathology, University of Bologna, Bologna - Italy
| | - Carla Renata Arciola
- Research Unit on Implant Infections, Rizzoli Orthopedic Institute, Bologna - Italy
- Department of Experimental Pathology, University of Bologna, Bologna - Italy
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Grinberg A, Biggs PJ, Zhang J, Ritchie S, Oneroa Z, O'Neill C, Karkaba A, Velathanthiri NS, Coombs GW. Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection. J Infect 2017; 75:326-335. [PMID: 28782565 DOI: 10.1016/j.jinf.2017.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/29/2017] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains. METHODS We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets. RESULTS Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%). CONCLUSIONS In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk.
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Affiliation(s)
- Alex Grinberg
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand.
| | - Patrick J Biggs
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Ji Zhang
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Stephen Ritchie
- University of Auckland, Faculty of Medical and Health Sciences, Molecular Medicine and Pathology, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Zachary Oneroa
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Charlotte O'Neill
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Ali Karkaba
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Niluka S Velathanthiri
- Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Private Bag 11,222, Palmerston North, 4442, New Zealand
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA, Australia
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Mehraj J, Witte W, Akmatov MK, Layer F, Werner G, Krause G. Epidemiology of Staphylococcus aureus Nasal Carriage Patterns in the Community. Curr Top Microbiol Immunol 2016; 398:55-87. [PMID: 27370344 DOI: 10.1007/82_2016_497] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Staphylococcus aureus (S. aureus) is a Gram-positive opportunistic pathogen that colonizes frequently and asymptomatically the anterior nares of humans and animals. It can cause different kinds of infections and is considered to be an important nosocomial pathogen. Nasal carriage of S. aureus can be permanent or intermittent and may build the reservoir for autogenous infections and cross-transmission to other individuals. Most of the studies on the epidemiology of S. aureus performed in the past were focused on the emergence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) in healthcare settings. There are, however, a number of more recent epidemiological studies have aimed at analysing carriage patterns over time in the community settings providing new insights on risk factors for colonization and important data for the development of strategies to prevent infections. This chapter aims to give a review of current epidemiological studies on S. aureus carriage patterns in the general community and put them into perspective with recent, yet unpublished, investigations on the S. aureus epidemiology in the general population in northern Germany.
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Affiliation(s)
- Jaishri Mehraj
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Hannover Medical School, Hannover, Germany
| | - Wolfgang Witte
- The Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Manas K Akmatov
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Franziska Layer
- The Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Guido Werner
- The Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany. .,Hannover Medical School, Hannover, Germany.
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van den Berg S, de Vogel CP, van Belkum A, Bakker-Woudenberg IAJM. Mild Staphylococcus aureus Skin Infection Improves the Course of Subsequent Endogenous S. aureus Bacteremia in Mice. PLoS One 2015; 10:e0129150. [PMID: 26060995 PMCID: PMC4464736 DOI: 10.1371/journal.pone.0129150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 01/02/2023] Open
Abstract
Staphylococcus aureus carriers with S. aureus bacteremia may have a reduced mortality risk compared to non-carriers. A role for the immune system is suggested. Here, we study in mice the effect of mild S. aureus skin infection prior to endogenous or exogenous S. aureus bacteremia, and evaluate protection in relation to anti-staphylococcal antibody levels. Skin infections once or twice by a clinical S. aureus isolate (isolate P) or S. aureus strain 8325-4 were induced in mice free of S. aureus and anti-staphylococcal antibodies. Five weeks later, immunoglobulin G (IgG) levels in blood against 25 S. aureus antigens were determined, and LD50 or LD100 bacteremia caused by S. aureus isolate P was induced. S. aureus skin infections led to elevated levels of anti-staphylococcal IgG in blood. One skin infection improved the course of subsequent severe endogenous bacteremia only. A second skin infection further improved animal survival rate, which was associated with increased pre-bacteremia IgG levels against Efb, IsaA, LukD, LukE, Nuc, PrsA and WTA. In conclusion, S. aureus isolate P skin infection in mice reduces the severity of subsequent endogenous S. aureus bacteremia only. Although cellular immune effects cannot be rules out, anti-staphylococcal IgG against specified antigens may contribute to this effect.
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Affiliation(s)
- Sanne van den Berg
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
- * E-mail:
| | - Corné P. de Vogel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Alex van Belkum
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
- bioMérieux, Microbiology R&D, La Balme les Grottes, France
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Bergonier D, Sobral D, Feßler AT, Jacquet E, Gilbert FB, Schwarz S, Treilles M, Bouloc P, Pourcel C, Vergnaud G. Staphylococcus aureus from 152 cases of bovine, ovine and caprine mastitis investigated by Multiple-locus variable number of tandem repeat analysis (MLVA). Vet Res 2014; 45:97. [PMID: 25315988 PMCID: PMC4195859 DOI: 10.1186/s13567-014-0097-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 09/05/2014] [Indexed: 11/29/2022] Open
Abstract
Staphylococcus aureus is one of the main etiological agents of mastitis in ruminants. In the present retrospective study, we evaluated the potential interest of a previously described automated multiple loci Variable Number of Tandem Repeats (VNTR) Assay (MLVA) comprising 16 loci as a first line tool to investigate the population structure of S. aureus from mastitis. We determined the genetic diversity of S. aureus strains from cases of clinical and subclinical mastitis in dairy cattle (n = 118, of which 16 were methicillin-resistant), sheep (n = 18) and goats (n = 16). The 152 strains could be subdivided into 115 MLVA genotypes (including 14 genotypes for the ovine strains and 15 genotypes for the caprine strains). This corresponds to a discriminatory index (D) value of 0.9936. Comparison with published MLVA data obtained using the same protocol applied to strains from diverse human and animal origins revealed a low number (8.5%) of human-related MLVA genotypes among the present collection. Eighteen percent of the S. aureus mastitis collection belonged to clonal complexes apparently not associated with other pathological conditions. Some of them displayed a relatively low level of diversity in agreement with a restricted ecological niche. These findings provide arguments suggesting that specific S. aureus lineages particularly adapted to ruminant mammary glands have emerged and that MLVA is a convenient tool to provide a broad overview of the population, owing to the availability via internet of databases compiling published MLVA genotypes.
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Affiliation(s)
- Dominique Bergonier
- INRA, UMR1225, IHAP, 31076, Toulouse, France. .,Université de Toulouse, INP, ENVT, UMR1225, IHAP, 31076, Toulouse, France. .,UMT INRA-ENVT-Institut de l'Élevage "Small Ruminants Health Management", 31076, Toulouse, France.
| | - Daniel Sobral
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France. .,Ceeram (Centre Européen d'Expertise et de Recherche sur les Agents Microbiens), 44240, La Chapelle sur Erdre, France.
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute, 31535, Neustadt-Mariensee, Germany.
| | - Eric Jacquet
- ICSN, CNRS, UPR2301, IMAGIF qPCR-Platform, 91198, Gif-sur-Yvette, France.
| | | | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute, 31535, Neustadt-Mariensee, Germany.
| | - Michaël Treilles
- Laboratoire départemental d'analyses de la Manche (LDA50), 50000, Saint-Lô, France.
| | - Philippe Bouloc
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France.
| | - Christine Pourcel
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France.
| | - Gilles Vergnaud
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91400, Orsay, France. .,CNRS, Orsay, France. .,ENSTA ParisTech, 91762, Palaiseau, France.
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Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ. Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers. BMC Microbiol 2014; 14:161. [PMID: 24946775 PMCID: PMC4071214 DOI: 10.1186/1471-2180-14-161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. RESULTS The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. CONCLUSIONS This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control.
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Affiliation(s)
| | | | | | | | | | | | | | - Adriana J Bernal
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia.
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Rešková Z, Koreňová J, Kuchta T. Effective application of multiple locus variable number of tandem repeats analysis to tracing Staphylococcus aureus in food-processing environment. Lett Appl Microbiol 2013; 58:376-83. [PMID: 24283534 DOI: 10.1111/lam.12200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/12/2013] [Accepted: 11/22/2013] [Indexed: 11/27/2022]
Abstract
UNLABELLED A total of 256 isolates of Staphylococcus aureus were isolated from 98 samples (34 swabs and 64 food samples) obtained from small or medium meat- and cheese-processing plants in Slovakia. The strains were genotypically characterized by multiple locus variable number of tandem repeats analysis (MLVA), involving multiplex polymerase chain reaction (PCR) with subsequent separation of the amplified DNA fragments by an automated flow-through gel electrophoresis. With the panel of isolates, MLVA produced 31 profile types, which was a sufficient discrimination to facilitate the description of spatial and temporal aspects of contamination. Further data on MLVA discrimination were obtained by typing a subpanel of strains by multiple locus sequence typing (MLST). MLVA coupled to automated electrophoresis proved to be an effective, comparatively fast and inexpensive method for tracing S. aureus contamination of food-processing factories. SIGNIFICANCE AND IMPACT OF THE STUDY Subspecies genotyping of microbial contaminants in food-processing factories may facilitate identification of spatial and temporal aspects of the contamination. This may help to properly manage the process hygiene. With S. aureus, multiple locus variable number of tandem repeats analysis (MLVA) proved to be an effective method for the purpose, being sufficiently discriminative, yet comparatively fast and inexpensive. The application of automated flow-through gel electrophoresis to separation of DNA fragments produced by multiplex PCR helped to improve the accuracy and speed of the method.
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Affiliation(s)
- Z Rešková
- Department of Microbiology and Molecular Biology, Food Research Institute, Bratislava, Slovakia
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11
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Impact of strain typing methods on assessment of relationship between paired nares and wound isolates of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 2012; 51:224-31. [PMID: 23135945 DOI: 10.1128/jcm.02423-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anterior nares are the site of choice for the Veterans Administration methicillin-resistant Staphylococcus aureus (MRSA) surveillance program; however, a correlation between nares colonization and concomitant wound infections has not been well established. The purpose of this study was 3-fold: to determine the relatedness of MRSA isolates from 40 paired wound and nares specimens by four different strain typing methods, to determine concordance of typing methods, and to establish a baseline of MRSA types at this medical center. Isolates were typed by repetitive PCR (rep-PCR) (DiversiLab System; DL) and SpectraCell Raman analysis (SCRA) (commercially available methods that can be performed within a clinical lab), pulsed-field gel electrophoresis (PFGE), and an antibiotic susceptibility profile (AB). Whole-genome optical mapping (WGM) (OpGen, Inc.) was performed on selected isolates. All methods agreed that 26 pairs were indistinguishable and four pairs were different. Discrepant results were as follows: 4 where only SCRA was discordant, 3 where only AB was discordant, 2 where both DL and AB were discordant, and 1 where both DL and SCRA were discordant. All WGM agreed with PFGE. After discrepancy resolution, 80% of the pairs were indistinguishable and 20% were different. A total of 56% of nares results were nonpredictive if negative nares and positive wound cultures are included. Methods agreed 85 to 93% of the time; however, congruence of isolates to a clade was lower. Baseline analysis of types showed that 15 pairs were unique to single patients (30 strains, 38%; 47% of the matching pairs). Twenty-five strains (30%) represented a single clade identical by PFGE, SCRA, and DL, decreasing specificity. Typing method and institutional type frequency are important in assessing MRSA strain relatedness.
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12
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Ng KH, Ho CK, Phon-Amnuaisuk S. A hybrid distance measure for clustering expressed sequence tags originating from the same gene family. PLoS One 2012; 7:e47216. [PMID: 23071763 PMCID: PMC3469558 DOI: 10.1371/journal.pone.0047216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/10/2012] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Clustering is a key step in the processing of Expressed Sequence Tags (ESTs). The primary goal of clustering is to put ESTs from the same transcript of a single gene into a unique cluster. Recent EST clustering algorithms mostly adopt the alignment-free distance measures, where they tend to yield acceptable clustering accuracies with reasonable computational time. Despite the fact that these clustering methods work satisfactorily on a majority of the EST datasets, they have a common weakness. They are prone to deliver unsatisfactory clustering results when dealing with ESTs from the genes derived from the same family. The root cause is the distance measures applied on them are not sensitive enough to separate these closely related genes. METHODOLOGY/PRINCIPAL FINDINGS We propose a hybrid distance measure that combines the global and local features extracted from ESTs, with the aim to address the clustering problem faced by ESTs derived from the same gene family. The clustering process is implemented using the DBSCAN algorithm. We test the hybrid distance measure on the ten EST datasets, and the clustering results are compared with the two alignment-free EST clustering tools, i.e. wcd and PEACE. The clustering results indicate that the proposed hybrid distance measure performs relatively better (in terms of clustering accuracy) than both EST clustering tools. CONCLUSIONS/SIGNIFICANCE The clustering results provide support for the effectiveness of the proposed hybrid distance measure in solving the clustering problem for ESTs that originate from the same gene family. The improvement of clustering accuracies on the experimental datasets has supported the claim that the sensitivity of the hybrid distance measure is sufficient to solve the clustering problem.
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Affiliation(s)
- Keng-Hoong Ng
- Faculty of Computing and Informatics, Multimedia University, Cyberjaya, Malaysia.
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Sangal V, Girvan EK, Jadhav S, Lawes T, Robb A, Vali L, Edwards GF, Yu J, Gould IM. Impacts of a long-term programme of active surveillance and chlorhexidine baths on the clinical and molecular epidemiology of meticillin-resistant Staphylococcus aureus (MRSA) in an Intensive Care Unit in Scotland. Int J Antimicrob Agents 2012; 40:323-31. [DOI: 10.1016/j.ijantimicag.2012.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/05/2012] [Accepted: 06/07/2012] [Indexed: 11/26/2022]
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Desai D, Ellington MJ, Arnold C, Desai M. Mapping the genetic diversity within major clonal complexes of meticillin-resistant Staphylococcus aureus utilizing genome-wide fluorescent amplified fragment length polymorphism markers. J Med Microbiol 2012; 61:1673-1680. [PMID: 22935850 DOI: 10.1099/jmm.0.049429-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity between major meticillin-resistant Staphylococcus aureus (MRSA) lineages was probed using fluorescent amplified fragment length polymorphism (FAFLP) as a random genome sampling tool. Genomic DNA was digested with endonucleases BglII and Csp6I and a subset of the restricted fragments were amplified using the primer pair BglII+A and Csp6I+0. Sixty-seven FAFLP profiles consisting of 46-68 amplified fragments ranging in size from 50 to 600 bp were exhibited amongst the 71 isolates analysed. Cluster analysis of FAFLP data revealed concordance with spa typing and MLST clonal complexes (CC), with isolates of each CC grouping in the same FAFLP cluster. Furthermore, FAFLP could differentiate subtypes within the homogeneous CC22 isolates and also between MLST sequence types 8 and 239. The discriminatory power of FAFLP was 0.998 compared to values of 0.975 and 0.909 for spa typing and MLST, respectively. Thus, FAFLP analysis proved to be a rapid, reproducible and high-resolution tool that displayed the microheterogeneity within MRSA lineages. Using FAFLP data, lineage-specific fragments were identified and sequenced; these encoded toxins, antibiotic resistance determinants and bacteriophage resistance factors. Lineage-specific sequence variations were observed, which may provide insights into the evolution and fitness of successful lineages. This will also aid in the development of rapid and high-throughput diagnostic PCR-based assays for the identification of MRSA lineages in resource-poor settings.
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Affiliation(s)
- Darshana Desai
- Microbiology Services Division Colindale, Health Protection Agency - Department for Bioanalysis and Horizon Technologies, London NW9 5EQ, UK
| | - Matthew J Ellington
- Microbiology Services Division, Cambridge Laboratory, Health Protection Agency, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QW, UK
| | - Catherine Arnold
- Microbiology Services Division Colindale, Health Protection Agency - Department for Bioanalysis and Horizon Technologies, London NW9 5EQ, UK
| | - Meeta Desai
- Microbiology Services Division Colindale, Health Protection Agency - Department for Bioanalysis and Horizon Technologies, London NW9 5EQ, UK
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15
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Wang X, Huang B, Blair B, Eglezos S, Bates J. Selection of optimal combinations of loci by the Optimal Combination Finder computer program from a group of variable number tandem repeat loci for use in Staphylococcus aureus food poisoning case investigations. J Med Microbiol 2012; 61:631-639. [DOI: 10.1099/jmm.0.040287-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xian Wang
- Shijiazhuang Center for Disease Control and Prevention, 3 Likang Street, Shijiazhuang, Hebei Province, PR China
| | - Bixing Huang
- Queensland Public Health Microbiology Laboratory, Forensic and Scientific Services, 39 Kessels Road, Coopers Plains, QLD 4108, Australia
| | - Barry Blair
- Queensland Public Health Microbiology Laboratory, Forensic and Scientific Services, 39 Kessels Road, Coopers Plains, QLD 4108, Australia
| | - Sofroni Eglezos
- EML Consulting Services QLD, 1/148 Tennyson Memorial Avenue, Tennyson, QLD 4105, Australia
| | - John Bates
- Queensland Public Health Microbiology Laboratory, Forensic and Scientific Services, 39 Kessels Road, Coopers Plains, QLD 4108, Australia
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16
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Evaluation of Neisseria gonorrhoeae multiple-locus variable-number tandem-repeat analysis, N. gonorrhoeae Multiantigen sequence typing, and full-length porB gene sequence analysis for molecular epidemiological typing. J Clin Microbiol 2011; 50:180-3. [PMID: 22075591 DOI: 10.1128/jcm.05386-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance characteristics of Neisseria gonorrhoeae multilocus variable-number tandem-repeat analysis were evaluated, by comparison with N. gonorrhoeae multiantigen sequence typing and full-length porB sequence typing. Assessment of the relatedness of intra- and interpatient isolates showed that all three genotyping techniques display a high resolution and typeability.
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17
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Willems RJL, Hanage WP, Bessen DE, Feil EJ. Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance. FEMS Microbiol Rev 2011; 35:872-900. [PMID: 21658083 DOI: 10.1111/j.1574-6976.2011.00284.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Infections caused by multiresistant Gram-positive bacteria represent a major health burden in the community as well as in hospitalized patients. Staphylococcus aureus, Enterococcus faecalis and Enterococcus faecium are well-known pathogens of hospitalized patients, frequently linked with resistance against multiple antibiotics, compromising effective therapy. Streptococcus pneumoniae and Streptococcus pyogenes are important pathogens in the community and S. aureus has recently emerged as an important community-acquired pathogen. Population genetic studies reveal that recombination prevails as a driving force of genetic diversity in E. faecium, E. faecalis, S. pneumoniae and S. pyogenes, and thus, these species are weakly clonal. Although recombination has a relatively modest role driving the genetic variation of the core genome of S. aureus, the horizontal acquisition of resistance and virulence genes plays a key role in the emergence of new clinically relevant clones in this species. In this review, we discuss the population genetics of E. faecium, E. faecalis, S. pneumoniae, S. pyogenes and S. aureus. Knowledge of the population structure of these pathogens is not only highly relevant for (molecular) epidemiological research but also for identifying the genetic variation that underlies changes in clinical behaviour, to improve our understanding of the pathogenic behaviour of particular clones and to identify novel targets for vaccines or immunotherapy.
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Affiliation(s)
- Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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18
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Lazarevic V, Beaume M, Corvaglia A, Hernandez D, Schrenzel J, François P. Epidemiology and virulence insights from MRSA and MSSA genome analysis. Future Microbiol 2011; 6:513-32. [DOI: 10.2217/fmb.11.38] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen responsible for a wide diversity of infections ranging from localized to life threatening diseases. From 1961 and the emergence of methicillin-resistant S. aureus (MRSA), this bacterium has shown a particular capacity to survive and adapt to drastic environmental changes and since the beginning of the 1990s it has spread worldwide. Until recently, S. aureus was considered as the prototype of a nosocomial pathogen but it has now been recognized as an agent responsible for outbreaks in the community. Several recent reports suggest that the epidemiology of MRSA is changing. Understanding of pathogenicity, virulence and emergence of epidemic clones within MRSA populations is not clearly defined, despite several attempts to identify common molecular features between strains that share similar epidemiological and/or virulence behavior. These studies included: pattern profiling of bacterial adhesins, analysis of clonal complex groups, molecular genotyping and enterotoxin content analysis. To date, all approaches failed to find a correlation between molecular determinants and clinical outcomes. We hypothesize that the capacity of the bacterium to become more invasive or virulent is determined by genetics. The utilization of massively parallel methods of analysis is therefore ideal to study the contribution of genetics. Therefore, this article focuses on the entire genome including coding sequences as well as noncoding sequences. This high resolution approach allows the monitoring micro- and macroevolution of MRSA and identification of specific genomic markers of evolution of invasive or highly virulent phenotypes.
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Affiliation(s)
- Vladimir Lazarevic
- Genomic Research Laboratory, Geneva University Hospitals, CH-1211 Geneva 14, Switzerland
| | - Marie Beaume
- Genomic Research Laboratory, Geneva University Hospitals, CH-1211 Geneva 14, Switzerland
| | - Anna Corvaglia
- Department of Microbiology & Molecular Medicine, University Medical Centre, University of Geneva, 1211 Geneva 4, Switzerland
| | - David Hernandez
- Genomic Research Laboratory, Geneva University Hospitals, CH-1211 Geneva 14, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Geneva University Hospitals, CH-1211 Geneva 14, Switzerland
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19
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van der Mee-Marquet N, Francois P, Domelier-Valentin AS, Coulomb F, Decreux C, Hombrock-Allet C, Lehiani O, Neveu C, Ratovohery D, Schrenzel J, Quentin R. Emergence of Unusual Bloodstream Infections Associated with Pig-Borne-Like Staphylococcus aureus ST398 in France. Clin Infect Dis 2011; 52:152-3. [DOI: 10.1093/cid/ciq053] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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20
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Evaluation of multiple-locus variable-number tandem-repeat analysis for typing a polyclonal hospital-acquired methicillin-resistant Staphylococcus aureus population in an area where such infections are endemic. J Clin Microbiol 2010; 48:2991-4. [PMID: 20519480 DOI: 10.1128/jcm.02220-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple-locus variable-number tandem-repeat analysis (MLVA) was performed with 292 methicillin-resistant Staphylococcus aureus (MRSA) isolates previously characterized by pulsed-field gel electrophoresis, multilocus sequence typing, and staphylococcal cassette chromosome mec typing. Quantitative correspondence analyses showed the best correlation between data when an >or=80% cutoff was applied to MLVA. We confirmed the validity of MLVA for identification of related strains in a polyclonal MRSA population.
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21
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Improved multiple-locus variable-number tandem-repeat assay for Staphylococcus aureus genotyping, providing a highly informative technique together with strong phylogenetic value. J Clin Microbiol 2009; 47:3121-8. [PMID: 19710277 DOI: 10.1128/jcm.00267-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe an improved multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme for genotyping Staphylococcus aureus. We compare its performance to those of multilocus sequence typing (MLST) and spa typing in a survey of 309 strains. This collection includes 87 epidemic methicillin-resistant S. aureus (MRSA) strains of the Harmony collection, 75 clinical strains representing the major MLST clonal complexes (CCs) (50 methicillin-sensitive S. aureus [MSSA] and 25 MRSA), 135 nasal carriage strains (133 MSSA and 2 MRSA), and 13 published S. aureus genome sequences. The results show excellent concordance between the techniques' results and demonstrate that the discriminatory power of MLVA is higher than those of both MLST and spa typing. Two hundred forty-two genotypes are discriminated with 14 VNTR loci (diversity index, 0.9965; 95% confidence interval, 0.9947 to 0.9984). Using a cutoff value of 45%, 21 clusters are observed, corresponding to the CCs previously defined by MLST. The variability of the different tandem repeats allows epidemiological studies, as well as follow-up of the evolution of CCs and the identification of potential ancestors. The 14 loci can conveniently be analyzed in two steps, based upon a first-line simplified assay comprising a subset of 10 loci (panel 1) and a second subset of 4 loci (panel 2) that provides higher resolution when needed. In conclusion, the MLVA scheme proposed here, in combination with available on-line genotyping databases (including http://mlva.u-psud.fr/), multiplexing, and automatic sizing, can provide a basis for almost-real-time large-scale population monitoring of S. aureus.
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22
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Lazzi C, Bove CG, Sgarbi E, Gatti M, Monica G, La Gioia F, Torriani S, Sandra T, Neviani E. Application of AFLP fingerprint analysis for studying the biodiversity of Streptococcus thermophilus. J Microbiol Methods 2009; 79:48-54. [PMID: 19647766 DOI: 10.1016/j.mimet.2009.07.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 07/22/2009] [Indexed: 11/16/2022]
Abstract
Streptococcus thermophilus is a lactic acid bacteria (LAB) widely used in milk fermentation processes as a starter culture. In this work the genetic diversity of S. thermophilus isolates from different sources was analyzed using Amplified Fragment Length Polymorphism fingerprinting (AFLP). Since this is the first report that indicates the application of AFLP in order to study genotypic polymorphism in S. thermophilus species, an optimization of experimental conditions was carried out to decide the optimal AFLP analysis protocol. Furthermore the fingerprinting resolutions of AFLP and RAPD (Random Amplified Polymorphic DNA) were evaluated and compared. The overall data suggest that genotypic characterization performed by AFLP provide a better view of microbial diversity of S. thermophilus, indicating that RAPD is less discriminating than AFLP. The successful use of AFLP analysis in the characterization of S. thermophilus strains reported in this study suggests the potential uses for this technique to define the whole-genome diversity of each specific strain, as an alternative to the fingerprinting methods used till now.
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Affiliation(s)
- Camilla Lazzi
- Dipartimento di Genetica, Biologia dei Microrganismi, Antropologia, Evoluzione, Università degli Studi di Parma, Viale Usberti 11/A, 43100 Parma, Italy.
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23
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Report of the Task Force on Zoonoses Data Collection on the availability of molecular typing methods for Salmonella, Campylobacter, verotoxigenic Escherichia coli, Listeria monocytogenes and Staphylococcus aureus isolates from food, animals and feedingstuffs in European Union Member States (and in some other reporting countries). EFSA J 2009. [DOI: 10.2903/j.efsa.2009.272r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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