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Feng SY, Hauck Y, Morgene F, Mohammedi R, Mirouze N. The complex regulation of competence in Staphylococcus aureus under microaerobic conditions. Commun Biol 2023; 6:512. [PMID: 37173437 PMCID: PMC10182052 DOI: 10.1038/s42003-023-04892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.
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Affiliation(s)
- Shi Yuan Feng
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Yolande Hauck
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Fedy Morgene
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Roza Mohammedi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France
| | - Nicolas Mirouze
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-Sur-Yvette, France.
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2
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Su YC, Hung WW, Lin JM, Chang CC, Chen YH, Lai YL, Tseng SP, Lu PL, Yamamoto T, Teng LJ, Hung WC. Tracking the evolution of the two successful CC59 methicillin-resistant Staphylococcus aureus clones in Taiwan: the divergence time of the two clades is estimated to be the 1980s. Int J Antimicrob Agents 2020; 56:106047. [PMID: 32544568 DOI: 10.1016/j.ijantimicag.2020.106047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 05/31/2020] [Accepted: 06/06/2020] [Indexed: 02/06/2023]
Abstract
Clonal complex 59 (CC59) is the dominant community-associated methicillin-resistant Staphylococcus aureus (MRSA) strain in Taiwan and includes the Asian-Pacific clone with Panton-Valentine leukocidin (PVL)-negative/staphylococcal cassette chromosome mec (SCCmec) IVg and the Taiwan clone characterised as PVL-positive/SCCmec V (5C2&5). Nevertheless, data on the evolutionary history of the two dominant CC59 MRSA clones in Taiwan are scarce. In this study, a total of 258 CC59 S. aureus strains from Taiwan were classified by multiple-locus variable-number tandem repeat analysis (MLVA), which revealed two major clusters (MT1 and MT2) with distinct mobile genetic elements (MGEs). However, sequencing and PCR mapping of the β-lactamase-producing plasmid revealed no difference among all CC59 S. aureus strains. Bayesian evolutionary analysis of 18 of the CC59 S. aureus strains based on core genome alignment revealed two clades: (i) Clade A, which shared the samples with MT1, had the features of mainly harbouring gentamicin-resistant MES6272-2 or MES4578, φSA3 translocation in νSaβ and SCCmec IVg; and (ii) Clade B, which shared the samples with MT2, had the features of mainly harbouring streptomycin-resistant MESPM1, PVL phage and SCCmec V (5C2&5). Based on the time-calibrated phylogenetic tree, the estimated time of divergence of the two clades was in the 1980s. These results suggest that the CC59 S. aureus progenitor acquired a β-lactamase-producing plasmid and then developed the varied genetic backgrounds, which were associated with the acquisition and maintenance of distinct MGEs, leading to differences in antimicrobial susceptibility profiles and molecular virulence determinants.
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Affiliation(s)
- Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Wen Hung
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Jia-Mi Lin
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Chia Chang
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - You-Han Chen
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Lin Lai
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Liang Lu
- Division of Infection, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tatsuo Yamamoto
- Department of Epidemiology, Genomics, and Evolution, International Medical Education and Research Center, Niigata, Japan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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3
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Sakmanoglu A, Sayin Z, Pinarkara Y, Uslu A, Ucan US, Erganis O. Evaluation of random amplified polymorphic DNA and multiple-locus variable number tandem repeat analyses for Mycoplasma cynos. J Microbiol Methods 2019; 161:1-7. [PMID: 30981711 DOI: 10.1016/j.mimet.2019.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/30/2019] [Accepted: 04/04/2019] [Indexed: 11/25/2022]
Abstract
Mycoplasma spp. can cause diseases of the respiratory system as well as urogenital infections, infertility, and anemia. The members of this genus have a low G + C content compared to other bacteria. Because primers used in the random amplified polymorphic DNA (RAPD) technique are only 10 bp long and have high GC content, this method can be inadequate for genotyping Mycoplasma spp. isolates. The aim of this study was to develop and evaluate multiple-locus variable number tandem repeat analysis (MLVA) and two-primer RAPD (TP-RAPD) procedures for subtyping Mycoplasma cynos isolates. A total of 55 M. cynos isolates obtained from 162 bronchoalveolar lavage fluid samples from shelter and pet dogs were used in this study. Seventy-four tandem repeat regions were detected in the M. cynos genome, and two of these loci were determined to be suitable and used for development of the MLVA scheme. The results of variable number tandem repeat (VNTR) analysis and TP-RAPD-PCR were compared with RAPD-PCR. The discriminatory power of TP-RAPD-PCR (Hunter-Gaston diversity index [HGDI] = 0.84) was higher than those of RAPD-PCR (HGDI = 0.727), VNTR1 (HGDI = 0.8), and VNTR3 (HGDI = 0.757). We observed that the TP-RAPD-PCR and MLVA methods provide clearer data and are more successful in determining genetic diversity, in contrast to the RAPD-PCR method for this species.
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Affiliation(s)
- Aslı Sakmanoglu
- Department of Microbiology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey.
| | - Zafer Sayin
- Department of Microbiology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey.
| | - Yasemin Pinarkara
- Department of Food Technology, Sarayonu Vocational School, Selcuk University, 42430, Konya, Turkey.
| | - Ali Uslu
- Department of Microbiology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey.
| | - Uckun Sait Ucan
- Department of Microbiology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey.
| | - Osman Erganis
- Department of Microbiology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey.
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4
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Partial prediction of the duration and the clinical status of Staphylococcus aureus bovine intramammary infections based on the phenotypic and genotypic analysis of isolates. Vet Microbiol 2019; 228:188-195. [DOI: 10.1016/j.vetmic.2018.11.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/29/2018] [Accepted: 11/24/2018] [Indexed: 01/24/2023]
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5
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Côté-Gravel J, Malouin F. Symposium review: Features of Staphylococcus aureus mastitis pathogenesis that guide vaccine development strategies. J Dairy Sci 2018; 102:4727-4740. [PMID: 30580940 DOI: 10.3168/jds.2018-15272] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 10/07/2018] [Indexed: 12/25/2022]
Abstract
Bovine mastitis affects animal health and welfare and milk production and quality, and it challenges the economic success of dairy farms. Staphylococcus aureus is one of the most commonly found pathogens in clinical mastitis but it also causes subclinical, persistent, and difficult-to-treat intramammary infections. Because of the failure of conventional antibiotic treatments and increasing pressure and concern from experts and consumers over the use of antibiotics in the dairy industry, many attempts have been made over the years to develop a vaccine for the prevention and control of Staph. aureus intramammary infections. Still, no commercially available vaccine formulation demonstrates sufficient protection and cost-effective potential. Multiple factors account for the lack of protection, including inadequate vaccine targets, high diversity among mastitis-provoking strains, cow-to-cow variation in immune response, and a failure to elicit an immune response that is appropriate for protection against a highly complex pathogen. The purpose of this review is to summarize key concepts related to the pathogenesis of Staph. aureus, and its interaction with the host, as well as to describe recent vaccine development strategies for prevention and control of Staph. aureus mastitis.
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Affiliation(s)
- Julie Côté-Gravel
- Centre d'Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada, J1K 2R1
| | - François Malouin
- Centre d'Étude et de Valorisation de la Diversité Microbienne (CEVDM), Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Canada, J1K 2R1.
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New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations. Appl Environ Microbiol 2017; 83:AEM.03095-16. [PMID: 28003195 DOI: 10.1128/aem.03095-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/13/2016] [Indexed: 12/31/2022] Open
Abstract
Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is considered one of the most harmful plant diseases in the world. Special attention should be paid to R. pseudosolanacearum phylotype I due to its large host range, its worldwide distribution, and its high evolutionary potential. So far, the molecular epidemiology and population genetics of this bacterium are poorly understood. Until now, the genetic structure of the RSSC has been analyzed on the worldwide and regional scales. Emerging questions regarding evolutionary forces in RSSC adaptation to hosts now require genetic markers that are able to monitor RSSC field populations. In this study, we aimed to evaluate the multilocus variable-number tandem-repeat analysis (MLVA) approach for its ability to discriminate genetically close phylotype I strains and for population genetics studies. We developed a new MLVA scheme (MLVA-7) allowing us to genotype 580 R. pseudosolanacearum phylotype I strains extracted from susceptible and resistant hosts and from different habitats (stem, soil, and rhizosphere). Based on specificity, polymorphism, and the amplification success rate, we selected seven fast-evolving variable-number tandem-repeat (VNTR) markers. The newly developed MLVA-7 scheme showed higher discriminatory power than the previously published MLVA-13 scheme when applied to collections sampled from the same location on different dates and to collections from different locations on very small scales. Our study provides a valuable tool for fine-scale monitoring and microevolution-related study of R. pseudosolanacearum phylotype I populations.IMPORTANCE Understanding the evolutionary dynamics of adaptation of plant pathogens to new hosts or ecological niches has become a key point for the development of innovative disease management strategies, including durable resistance. Whereas the molecular mechanisms underlying virulence or pathogenicity changes have been studied thoroughly, the population genetics of plant pathogen adaptation remains an open, unexplored field, especially for plant-pathogenic bacteria. MLVA has become increasingly popular for epidemiosurveillance and molecular epidemiology studies of plant pathogens. However, this method has been used mostly for genotyping and identification on a regional or global scale. In this study, we developed a new MLVA scheme, targeting phylotype I of the soilborne Ralstonia solanacearum species complex (RSSC), specifically to address the bacterial population genetics on the field scale. Such a MLVA scheme, based on fast-evolving loci, may be a tool of choice for field experimental evolution and spatial genetics studies.
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Zurita J, Barba P, Ortega-Paredes D, Mora M, Rivadeneira S. Local circulating clones of Staphylococcus aureus in Ecuador. Braz J Infect Dis 2016; 20:525-533. [PMID: 27638417 PMCID: PMC9427608 DOI: 10.1016/j.bjid.2016.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/22/2016] [Accepted: 08/02/2016] [Indexed: 01/18/2023] Open
Abstract
The spread of pandemic Staphylococcus aureus clones, mainly methicillin-resistant S. aureus (MRSA), must be kept under surveillance to assemble an accurate, local epidemiological analysis. In Ecuador, the prevalence of the USA300 Latin American variant clone (USA300-LV) is well known; however, there is little information about other circulating clones. The aim of this work was to identify the sequence types (ST) using a Multiple-Locus Variable number tandem repeat Analysis 14-locus genotyping approach. We analyzed 132 S. aureus strains that were recovered from 2005 to 2013 and isolated in several clinical settings in Quito, Ecuador. MRSA isolates composed 46.97% (62/132) of the study population. Within MRSA, 37 isolates were related to the USA300-LV clone (ST8-MRSA-IV, Panton-Valentine Leukocidin [PVL] +) and 10 were related to the Brazilian clone (ST239-MRSA-III, PVL−). Additionally, two isolates (ST5-MRSA-II, PVL−) were related to the New York/Japan clone. One isolate was related to the Pediatric clone (ST5-MRSA-IV, PVL−), one isolate (ST45-MRSA-II, PVL−) was related to the USA600 clone, and one (ST22-MRSA-IV, PVL−) was related to the epidemic UK-EMRSA-15 clone. Moreover, the most prevalent MSSA sequence types were ST8 (11 isolates), ST45 (8 isolates), ST30 (8 isolates), ST5 (7 isolates) and ST22 (6 isolates). Additionally, we found one isolate that was related to the livestock associated S. aureus clone ST398. We conclude that in addition to the high prevalence of clone LV-ST8-MRSA-IV, other epidemic clones are circulating in Quito, such as the Brazilian, Pediatric and New York/Japan clones. The USA600 and UK-EMRSA-15 clones, which were not previously described in Ecuador, were also found. Moreover, we found evidence of the presence of the livestock associated clone ST398 in a hospital environment.
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Affiliation(s)
- Jeannete Zurita
- Pontificia Universidad Católica del Ecuador, Facultad de Medicina, Quito, Ecuador; Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador.
| | - Pedro Barba
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - David Ortega-Paredes
- Pontificia Universidad Católica del Ecuador, Facultad de Medicina, Quito, Ecuador; Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Marcelo Mora
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
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8
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Hung WC, Wan TW, Kuo YC, Yamamoto T, Tsai JC, Lin YT, Hsueh PR, Teng LJ. Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages. PLoS One 2016; 11:e0162526. [PMID: 27606427 PMCID: PMC5015870 DOI: 10.1371/journal.pone.0162526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 08/24/2016] [Indexed: 12/04/2022] Open
Abstract
Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). As the most prominent community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major clones characterized as PVL-negative SCCmec IV (carrying the staphylococcal cassette chromosome mec IV but Panton-Valentine leukocidin-negative) and PVL-positive SCCmec V (5C2&5). We investigated the drug resistance, phylogeny and the distribution and sequence variation of SCCmec, staphylococcal bacteriophage φSA3, genomic island νSaβ and MES (an enterococcal mobile genetic element conferring multidrug resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping revealed that all of the CC59/SCCmec V (5C2&5) MRSA strains had acquired MESPM1 or its segregants, and obtained a φSA3-related fragment in νSaβ. In contrast, MES6272-2 and MES4578, which showed gentamicin resistance that was not encoded by MESPM1, were dominant in SCCmec IVg MRSA. Translocation of a whole φSA3 into νSaβ instead of only a φSA3-related fragment was common in SCCmec IVg MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is the major) still carried MES and νSaβ structures similar to those in SCCmec V (5C2&5) MRSA. A minimum spanning tree constructed by multiple-locus variable-number tandem repeat analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA grouped respectively in two major clades. The CC59 MSSA was equally distributed among the two clades, while the non-subtype-g SCCmec IV MRSA mostly clustered with SCCmec V (5C2&5) MRSA. Our findings strongly suggest that CC59 MSSA acquired divergent mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The evolutionary history of CC59 S. aureus explains how mobile genetic elements increase the antimicrobial resistance and virulence and contribute to the success of CA-MRSA in Taiwan.
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Affiliation(s)
- Wei-Chun Hung
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Chia Kuo
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tatsuo Yamamoto
- Department of Epidemiology, Genomics, and Evolution, International Medical Education and Research Center, Niigata, Japan
| | - Jui-Chang Tsai
- Institute of Medical Device and Imaging, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail:
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9
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Boss R, Cosandey A, Luini M, Artursson K, Bardiau M, Breitenwieser F, Hehenberger E, Lam T, Mansfeld M, Michel A, Mösslacher G, Naskova J, Nelson S, Podpečan O, Raemy A, Ryan E, Salat O, Zangerl P, Steiner A, Graber HU. Bovine Staphylococcus aureus: Subtyping, evolution, and zoonotic transfer. J Dairy Sci 2015; 99:515-28. [PMID: 26601578 DOI: 10.3168/jds.2015-9589] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/27/2015] [Indexed: 11/19/2022]
Abstract
Staphylococcus aureus is globally one of the most important pathogens causing contagious mastitis in cattle. Previous studies using ribosomal spacer (RS)-PCR, however, demonstrated in Swiss cows that Staph. aureus isolated from bovine intramammary infections are genetically heterogeneous, with Staph. aureus genotype B (GTB) and GTC being the most prominent genotypes. Furthermore, Staph. aureus GTB was found to be contagious, whereas Staph. aureus GTC and all the remaining genotypes were involved in individual cow disease. In addition to RS-PCR, other methods for subtyping Staph. aureus are known, including spa typing and multilocus sequence typing (MLST). They are based on sequencing the spa and various housekeeping genes, respectively. The aim of the present study was to compare the 3 analytic methods using 456 strains of Staph. aureus isolated from milk of bovine intramammary infections and bulk tanks obtained from 12 European countries. Furthermore, the phylogeny of animal Staph. aureus was inferred and the zoonotic transfer of Staph. aureus between cattle and humans was studied. The analyzed strains could be grouped into 6 genotypic clusters, with CLB, CLC, and CLR being the most prominent ones. Comparing the 3 subtyping methods, RS-PCR showed the highest resolution, followed by spa typing and MLST. We found associations among the methods but in many cases they were unsatisfactory except for CLB and CLC. Cluster CLB was positive for clonal complex (CC)8 in 99% of the cases and typically positive for t2953; it is the cattle-adapted form of CC8. Cluster CLC was always positive for tbl 2645 and typically positive for CC705. For CLR and the remaining subtypes, links among the 3 methods were generally poor. Bovine Staph. aureus is highly clonal and a few clones predominate. Animal Staph. aureus always evolve from human strains, such that every human strain may be the ancestor of a novel animal-adapted strain. The zoonotic transfer of IMI- and milk-associated strains of Staph. aureus between cattle and humans seems to be very limited and different hosts are not considered as a source for mutual, spontaneous infections. Spillover events, however, may happen.
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Affiliation(s)
- R Boss
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland
| | - A Cosandey
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland; Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - M Luini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Via Einstein, 26900 Lodi, Italy
| | - K Artursson
- Department of Bacteriology, National Veterinary Institute, SE-751 89 Uppsala, Sweden
| | - M Bardiau
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, University of Liège, Avenue de Cureghem 6, 4000 Liège, Belgium
| | - F Breitenwieser
- Milchprüfring Baden-Württemberg e. V., Marie-Curie-Strasse 19, 73230 Kirchheim/Teck, Germany
| | - E Hehenberger
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - Th Lam
- GD Animal Health, Arnsbergstraat 7, PO Box 9, 7400 AA Deventer, the Netherlands
| | - M Mansfeld
- Carinthian Institute for Veterinary Disease Control, Kirchengasse 43, 9020 Klagenfurt, Austria
| | - A Michel
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - G Mösslacher
- Animal Health Organisation Upper Austria, Bahnhofplatz 1, 4021 Linz, Austria
| | - J Naskova
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland
| | - S Nelson
- Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Ullevalsvn 72, PO Box 8146 Dep, N-0033 Oslo, Norway
| | - O Podpečan
- Ambulatory Clinic for Large Animals, University of Ljubljana, Veterinary Faculty, Gerbičeva ul. 60, 1000 Ljubljana, Slovenia
| | - A Raemy
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - E Ryan
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - O Salat
- Veterinary Clinic of Haute Auvergne, Allauzier, 15100 Saint Flour, France
| | - P Zangerl
- Federal Institute for Alpine Dairying BAM, 6200 Jenbach, Austria
| | - A Steiner
- Clinic for Ruminants, Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Bremgartenstrasse 109a, P.O. Box 8466, 3001 Berne, Switzerland
| | - H U Graber
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, 3003 Berne, Switzerland.
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10
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Lindquist MR, López-Núñez JC, Jones MA, Cox EJ, Pinkelman RJ, Bang SS, Moser BR, Jackson MA, Iten LB, Kurtzman CP, Bischoff KM, Liu S, Qureshi N, Tasaki K, Rich JO, Cotta MA, Saha BC, Hughes SR. Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates. Appl Microbiol Biotechnol 2015; 99:9723-43. [PMID: 26272089 PMCID: PMC4628078 DOI: 10.1007/s00253-015-6852-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/12/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-products. We irradiated Y. lipolytica NRRL YB-567 with UV-C to enhance ammonia (for fertilizer) and lipid (for biodiesel) production on low-cost protein and carbohydrate substrates. The resulting strains were screened for ammonia and oil production using color intensity of indicators on plate assays. Seven mutant strains were selected (based on ammonia assay) and further evaluated for growth rate, ammonia and oil production, soluble protein content, and morphology when grown on liver infusion medium (without sugars), and for growth on various substrates. Strains were identified among these mutants that had a faster doubling time, produced higher maximum ammonia levels (enzyme assay) and more oil (Sudan Black assay), and had higher maximum soluble protein levels (Bradford assay) than wild type. When grown on plates with substrates of interest, all mutant strains showed similar results aerobically to wild-type strain. The mutant strain with the highest oil production and the fastest doubling time was evaluated on coffee waste medium. On this medium, the strain produced 0.12 g/L ammonia and 0.20 g/L 2-phenylethanol, a valuable fragrance/flavoring, in addition to acylglycerols (oil) containing predominantly C16 and C18 residues. These mutant strains will be investigated further for potential application in commercial biodiesel production.
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Affiliation(s)
- Mitch R Lindquist
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Juan Carlos López-Núñez
- National Coffee Research Centre - Cenicafe, National Federation of Coffee Growers of Colombia - FNC, Cenicafé Planalto Km 4 vía Antigua Chinchiná, Manizales, Caldas, Colombia
| | - Marjorie A Jones
- 4160 Department of Chemistry, Illinois State University, 214 Julian Hall, Normal, IL, 61790-4160, USA
| | - Elby J Cox
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Rebecca J Pinkelman
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, 501 East Saint Joseph Street, Rapid City, SD, 57701-3995, USA
| | - Sookie S Bang
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, 501 East Saint Joseph Street, Rapid City, SD, 57701-3995, USA
| | - Bryan R Moser
- USDA, ARS, NCAUR, Bio-oils Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael A Jackson
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Loren B Iten
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Cletus P Kurtzman
- USDA, ARS, NCAUR, Bacterial Foodborne Pathogens and Mycology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth M Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Siqing Liu
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Nasib Qureshi
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth Tasaki
- Mitsubishi Chemical, USMC Research & Innovation, 410 Palos Verdes Blvd, Redondo Beach, CA, 90277, USA
| | - Joseph O Rich
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael A Cotta
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Badal C Saha
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Stephen R Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA.
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11
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Roussel S, Felix B, Vingadassalon N, Grout J, Hennekinne JA, Guillier L, Brisabois A, Auvray F. Staphylococcus aureus strains associated with food poisoning outbreaks in France: comparison of different molecular typing methods, including MLVA. Front Microbiol 2015; 6:882. [PMID: 26441849 PMCID: PMC4566840 DOI: 10.3389/fmicb.2015.00882] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/11/2015] [Indexed: 11/15/2022] Open
Abstract
Staphylococcal food poisoning outbreaks (SFPOs) are frequently reported in France. However, most of them remain unconfirmed, highlighting a need for a better characterization of isolated strains. Here we analyzed the genetic diversity of 112 Staphylococcus aureus strains isolated from 76 distinct SFPOs that occurred in France over the last 30 years. We used a recently developed multiple-locus variable-number tandem-repeat analysis (MLVA) protocol and compared this method with pulsed field gel electrophoresis (PFGE), spa-typing and carriage of genes (se genes) coding for 11 staphylococcal enterotoxins (i.e., SEA, SEB, SEC, SED, SEE, SEG, SEH, SEI, SEJ, SEP, SER). The strains known to have an epidemiological association with one another had identical MLVA types, PFGE profiles, spa-types or se gene carriage. MLVA, PFGE and spa-typing divided 103 epidemiologically unrelated strains into 84, 80, and 50 types respectively demonstrating the high genetic diversity of S. aureus strains involved in SFPOs. Each MLVA type shared by more than one strain corresponded to a single spa-type except for one MLVA type represented by four strains that showed two different-but closely related-spa-types. The 87 enterotoxigenic strains were distributed across 68 distinct MLVA types that correlated all with se gene carriage except for four MLVA types. The most frequent se gene detected was sea, followed by seg and sei and the most frequently associated se genes were sea-seh and sea-sed-sej-ser. The discriminatory ability of MLVA was similar to that of PFGE and higher than that of spa-typing. This MLVA protocol was found to be compatible with high throughput analysis, and was also faster and less labor-intensive than PFGE. MLVA holds promise as a suitable method for investigating SFPOs and tracking the source of contamination in food processing facilities in real time.
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Affiliation(s)
- Sophie Roussel
- Université Paris-Est, ANSES, Food Safety Laboratory, European Union Reference Laboratory for Coagulase Positive Staphylococci, Maisons-AlfortFrance
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12
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Ranjbar R, Memariani M, Memariani H. Diversity of Variable Number Tandem Repeat Loci in Shigella Species Isolated from Pediatric Patients. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2015; 4:174-81. [PMID: 26629486 PMCID: PMC4644529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Multilocus variable number tandem repeat (VNTR) analysis (MLVA) is a new typing method with several advantages compared to other methods. Dissemination of Shigella is highly significant in developing countries. Whilst Shigella is becoming increasingly important as an etiologic agent of pediatric shigellosis in Iran, little is known about the genetic diversity of the local strains. Therefore, the aim of this study was to describe the genetic diversity of Shigella species isolated from pediatric patients in Tehran, Iran. A total of 53 Shigella isolates were obtained from 1070 patients with diarrhea (less than 12 years of age). All isolates were identified by routine biochemical and serological tests. The confirmed Shigella isolates were further serogrouped (by the slide agglutination) using slide agglutination method. MLVA assay with the seven loci resolved 53 Shigella isolates into 36 different genotypes. Almost all the isolates were classified into five clonal complexes. Furthermore, our MLVA assay could effectively distinguish the four Shigella species. This study has provided valuable insights into the genetic heterogeneity of Shigella species in Tehran, Iran. Our findings can be helpful for further epidemiological surveillance of Shigella species in this country in the future.
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Affiliation(s)
- Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Mojtaba Memariani
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Corresponding author: Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran. E-mail:
| | - Hamed Memariani
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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Ranjbar R, Memariani M. Multilocus variable-number tandem-repeat analysis for genotyping of Shigella sonnei strains isolated from pediatric patients. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2015; 8:225-32. [PMID: 26328045 PMCID: PMC4553163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 11/10/2014] [Indexed: 10/29/2022]
Abstract
AIM The aims of this study were to characterize Iranian Shigella sonnei strains isolated from pediatric cases and evaluate the utility of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) for genotyping of local S. sonnei strains. BACKGROUND S. sonnei has become the dominant species in certain parts of Iran. Although PFGE is still a gold standard for genotyping and source tracking of food-borne pathogens, it is laborious, expensive, time-consuming, and often difficult to interpret. However, MLVA is a PCR-based method, which is rapid, relatively inexpensive and easy to perform. PATIENTS AND METHODS A total of 47 S. sonnei isolates were obtained from sporadic cases of pediatric shigellosis in Tehran, Iran, during the years 2002-2003 (n=10) and 2008-2010 (n=37). The patients suffered from acute diarrhea and had evidence of more than three episodes of watery, loose, or bloody stools per day. A MLVA scheme based on 7 VNTR loci was established to assess the diversity of 47 S. sonnei isolates. RESULTS Based on the results, it was clear that the S. sonnei isolates were heterogeneous. Overall, 47 S. sonnei isolates were discriminated into 21 different genotypes. Analysis of the MLVA profiles using a minimum spanning tree (MST) algorithm showed the usefulness of the MLVA assay in discriminating S. sonnei isolates collected over different time periods. However, no correlation was found between the MLVA genotypes and age, gender or clinical symptoms of the patients. CONCLUSION It is assumed that our S. sonnei isolates are derived from a limited number of clones that undergo minor genetic changes in the course of time. The present study has provided some valuable insights into the genetic relatedness of S. sonnei in Tehran, Iran.
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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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15
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Du XF, Xiao M, Liang HY, Sun Z, Jiang YH, Chen GY, Meng XY, Zou GL, Zhang L, Liu YL, Zhang H, Sun HL, Jiang XF, Xu YC. An improved MLVF method and its comparison with traditional MLVF, spa typing, MLST/SCCmec and PFGE for the typing of methicillin-resistant Staphylococcus aureus. Int J Mol Sci 2014; 15:725-42. [PMID: 24406728 PMCID: PMC3907834 DOI: 10.3390/ijms15010725] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/12/2013] [Accepted: 12/20/2013] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has become an important nosocomial pathogen, causing considerable morbidity and mortality. During the last 20 years, a variety of genotyping methods have been introduced for screening the prevalence of MRSA. In this study, we developed and evaluated an improved approach capillary gel electrophoresis based multilocus variable-number tandem-repeat fingerprinting (CGE/MLVF) for rapid MRSA typing. A total of 42 well-characterized strains and 116 non-repetitive clinical MRSA isolates collected from six hospitals in northeast China between 2009 and 2010 were tested. The results obtained by CGE/MLVF against clinical isolates were compared with traditional MLVF, spa typing, Multilocus sequence typing/ staphylococcal cassette chromosome mec (MLST/SCCmec) and pulse field gel electrophoresis (PFGE). The discriminatory power estimated by Simpson's index of diversity was 0.855 (28 types), 0.855 (28 patterns), 0.623 (11 types), 0.517 (8 types) and 0.854 (28 patterns) for CGE/MLVF, traditional MLVF, spa typing, MLST/SCCmec and PFGE, respectively. All methods tested showed a satisfied concordance in clonal complex level calculated by adjusted Rand's coefficient. CGE/MLVF showed better reproducibility and accuracy than traditional MLVF and PFGE methods. In addition, the CGE/MLVF has potential to produce portable results. In conclusion, CGE/MLVF is a rapid and easy to use MRSA typing method with lower cost, good reproducibility and high discriminatory power for monitoring the outbreak and clonal spread of MRSA isolates.
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Affiliation(s)
- Xue-Fei Du
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Meng Xiao
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Hong-Yan Liang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Zhe Sun
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Yue-Hong Jiang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Guo-Yu Chen
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Xiao-Yu Meng
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Gui-Ling Zou
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Li Zhang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Ya-Li Liu
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Hui Zhang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Hong-Li Sun
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Xiao-Feng Jiang
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
| | - Ying-Chun Xu
- Department of Clinical Laboratory, the Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang, Harbin 150001, Heilongjiang, China.
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16
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Loncaric I, Künzel F, Licka T, Simhofer H, Spergser J, Rosengarten R. Identification and characterization of methicillin-resistant Staphylococcus aureus (MRSA) from Austrian companion animals and horses. Vet Microbiol 2014; 168:381-7. [DOI: 10.1016/j.vetmic.2013.11.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 01/24/2023]
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17
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Lv G, Xu B, Wei P, Song J, Zhang H, Zhao C, Qin L, Zhao B. Molecular characterization of foodborne-associated Staphylococcus aureus strains isolated in Shijiazhuang, China, from 2010 to 2012. Diagn Microbiol Infect Dis 2013; 78:462-8. [PMID: 24582576 DOI: 10.1016/j.diagmicrobio.2013.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/07/2013] [Accepted: 12/08/2013] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen commonly identified from food poisoning-associated foodstuffs. From 1996 to the present, S. aureus isolates have been found to exhibit increasing resistance to antimicrobial drugs. The aim of this study was to assess the molecular epidemiology properties of various S. aureus isolates through molecular typing and to investigate their characterization based on their production of enterotoxins and hemolysins and their resistance to antibiotics. A total of 78 coagulase-positive staphylococcal strains isolated from food or clinical samples were analyzed. Eight VNTR loci were used to genotype the 78 isolates, and this analysis resulted in 39 different multilocus variable number tandem repeat analysis (MLVA) profiles. The isolates recovered from a single outbreak exhibited the same MLVA profile. According to CLSI, 97.4% of the isolates were resistant to penicillin, whereas only 3.8% were methicillin-resistant Staphylococcus aureus strains. Through multiplex PCR, 87.2% of the isolates were shown to be enterotoxigenic (SEs), and the most common genes present were sea, sem, seg, seu, and sek. In conclusion, this study demonstrates the prevalence of staphylococcal enterotoxins, the contents of virulent factors, and the characteristics of β-lactam antibiotic resistance in 78 S. aureus isolates. These findings emphasize the need to prevent the presence of S. aureus strains and SE production in foods. Our results also demonstrate that MLVA is a useful and powerful method for epidemiological studies of S. aureus. In contrast to multilocus sequence typing, the MLVA method is a simpler and more rapid method for epidemiological typing with a higher discriminatory power.
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Affiliation(s)
- GuoPing Lv
- College of Life Science, Hebei Normal University, Shijiazhuang 050000, China; Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - BaoHong Xu
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - PeiNan Wei
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - Jie Song
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - HongYing Zhang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - Chuan Zhao
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China
| | - LiYun Qin
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang 050000, China.
| | - BaoHua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang 050000, China.
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Loncaric I, Künzel F. Sequence type 398 meticillin-resistant Staphylococcus aureus infection in a pet rabbit. Vet Dermatol 2013; 24:370-2, e84. [PMID: 23551846 DOI: 10.1111/vde.12023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2013] [Indexed: 01/09/2023]
Abstract
BACKGROUND Meticillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen of humans and many animal species, and has become established as a veterinary pathogen. CASE REPORT In this case report we describe an MRSA infection in a dwarf rabbit, treatment of the infection and, subsequently, the genetic analysis of the isolated strain. The pet rabbit was presented to an animal hospital due to recurrent swellings on the head and on the neck. Bacteriological examination yielded Staphylococcus aureus, which was resistant to β-lactam antibiotics. The isolate was confirmed as an MRSA by mecA PCR, Panton-Valentine leukocidin (PVL) negative, and typed as multilocus sequence type (ST)398/staphylococcal protein A (spa) type t011/staphylococcal cassette chromosome mec (SCCmec) type SCCmecIVa. The rabbit was treated with rifampicin for 2 weeks. After 2.5 weeks the rabbit was clinically normal and control swabs were negative for MRSA. CONCLUSIONS AND CLINICAL IMPORTANCE This study is the first to report MRSA in a rabbit in Austria. This study contributes to the growing evidence that MRSA ST398 could be isolated from a variety of animals.
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Affiliation(s)
- Igor Loncaric
- Department of Pathobiology, Institute for Bacteriology, Mycology and Hygiene, University of Veterinary Medicine, Vienna, Austria.
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19
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Suspected goat-to-human transmission of methicillin-resistant Staphylococcus aureus sequence type 398. J Clin Microbiol 2013; 51:1625-6. [PMID: 23447633 DOI: 10.1128/jcm.03052-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transmission of methicillin-resistant Staphylococcus aureus (MRSA) between animals and humans is widely recognized. In this study, we describe the first case of infection of a goat and suspected transmission of MRSA ST398 to a human, which resulted in colonization of animal owners by MRSA sequence type 398.
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20
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N'guessan CA, Brisse S, Le Roux-Nio AC, Poussier S, Koné D, Wicker E. Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot. J Microbiol Methods 2013; 92:366-74. [PMID: 23376194 DOI: 10.1016/j.mimet.2013.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 11/25/2022]
Abstract
Ralstonia solanacearum is an important soil borne bacterial plant pathogen causing bacterial wilt on many important crops. To better monitor epidemics, efficient tools that can identify and discriminate populations are needed. In this study, we assessed variable number of tandem repeats (VNTR) genotyping as a new tool for epidemiological surveillance of R. solanacearum phylotypes, and more specifically for the monitoring of the monomorphic ecotypes "Moko" (banana-pathogenic) and "brown rot" (potato-pathogenic under cool conditions). Screening of six R. solanacearum genome sequences lead to select 36 VNTR loci that were preliminarily amplified on 24 strains. From this step, 26 single-locus primer pairs were multiplexed, and applied to a worldwide collection of 337 strains encompassing the whole phylogenetic diversity, with revelation on a capillary-electrophoresis genotype. Four loci were monomorphic within all phylotypes and were not retained; the other loci were highly polymorphic but displayed a clear phylotype-specificity. Phylotype-specific MLVA schemes were thus defined, based on 13 loci for phylotype I, 12 loci for phylotype II, 11 loci for phylotype III and 6 for phylotype IV. MLVA typing was significantly more discriminative than egl-based sequevar typing, particularly on monomorphic "brown rot" ecotype (phylotype IIB/sequevar 1) and "Moko disease" clade 4 (Phylotype IIB/sequevar 4). Our results raise promising prospects for studies of population genetic structures and epidemiological monitoring.
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Brandt KM, Mellmann A, Ballhausen B, Jenke C, van der Wolf PJ, Broens EM, Becker K, Köck R. Evaluation of multiple-locus variable number of tandem repeats analysis for typing livestock-associated methicillin-resistant Staphylococcus aureus. PLoS One 2013; 8:e54425. [PMID: 23349886 PMCID: PMC3549956 DOI: 10.1371/journal.pone.0054425] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 12/11/2012] [Indexed: 11/30/2022] Open
Abstract
Background The increasing occurrence of livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) associated with the clonal complex (CC) 398 within the past years shows the importance of standardized and comparable typing methods for the purposes of molecular surveillance and outbreak detection. Multiple-locus variable number of tandem repeats analysis (MLVA) has recently been described as an alternative and highly discriminative tool for S. aureus. However, until now the applicability of MLVA for the typing of LA-MRSA isolates from different geographic origin has not been investigated in detail. We therefore compared MLVA and S. aureus protein A (spa) typing for characterizing porcine MRSA from distinct Dutch and German farms. Methodology/Principal Findings Overall, 134 MRSA isolates originating from 21 different pig-farms in the Netherlands and 36 farms in Germany comprising 21 different spa types were subjected to MLVA-typing. Amplification and subsequent automated fragment sizing of the tandem repeat loci on a capillary sequencer differentiated these 134 isolates into 20 distinct MLVA types. Whereas overall MLVA and spa typing showed the same discriminatory power to type LA-MRSA (p = 0.102), MLVA was more discriminatory than spa typing for isolates associated with the prevalent spa types t011 and t034 (Simpson’s Index of Diversity 0.564 vs. 0.429, respectively; p<0.001). Conclusion Although the applied MLVA scheme was not more discriminatory than spa typing in general, it added valuable information to spa typing results for specific spa types (t011, t034) which are highly prevalent in the study area, i.e. Dutch-German border area. Thus, both methods may complement each other to increase the discriminatory power to resolute highly conserved clones such as CC398 (spa types t011, t034) for the detection of outbreaks and molecular surveillance of zoonotic MRSA.
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Affiliation(s)
- Karin M. Brandt
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Britta Ballhausen
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Christian Jenke
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Els M. Broens
- Veterinary Microbiological Diagnostic Centre, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Robin Köck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- * E-mail:
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Whole genome sequencing in the prevention and control of Staphylococcus aureus infection. J Hosp Infect 2012; 83:14-21. [PMID: 23164609 PMCID: PMC7132511 DOI: 10.1016/j.jhin.2012.10.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 10/02/2012] [Indexed: 11/22/2022]
Abstract
BACKGROUND Staphylococcus aureus remains a leading cause of hospital-acquired infection but weaknesses inherent in currently available typing methods impede effective infection prevention and control. The high resolution offered by whole genome sequencing has the potential to revolutionise our understanding and management of S. aureus infection. AIM To outline the practicalities of whole genome sequencing and discuss how it might shape future infection control practice. METHODS We review conventional typing methods and compare these with the potential offered by whole genome sequencing. FINDINGS In contrast with conventional methods, whole genome sequencing discriminates down to single nucleotide differences and allows accurate characterisation of transmission events and outbreaks and additionally provides information about the genetic basis of phenotypic characteristics, including antibiotic susceptibility and virulence. However, translating its potential into routine practice will depend on affordability, acceptable turnaround times and on creating a reliable standardised bioinformatic infrastructure. CONCLUSION Whole genome sequencing has the potential to provide a universal test that facilitates outbreak investigation, enables the detection of emerging strains and predicts their clinical importance.
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Purves J, Blades M, Arafat Y, Malik SA, Bayliss CD, Morrissey JA. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution. BMC Genomics 2012; 13:515. [PMID: 23020678 PMCID: PMC3532100 DOI: 10.1186/1471-2164-13-515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/24/2012] [Indexed: 01/05/2023] Open
Abstract
Background Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Results Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. Conclusions The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.
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Evaluation of Fourier transform infrared (FT-IR) spectroscopy and chemometrics as a rapid approach for sub-typing Escherichia coli O157:H7 isolates. Food Microbiol 2012; 31:181-90. [DOI: 10.1016/j.fm.2012.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/06/2012] [Accepted: 02/20/2012] [Indexed: 11/19/2022]
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Frickmann H, Gawlik PP, Crusius S, Podbielski A. The current role of pulsed-field gel electrophoresis in methicillin-resistant Staphylococcus aureus (MRSA) typing and the retrospective identification of outbreaks. Eur J Microbiol Immunol (Bp) 2012; 2:128-33. [PMID: 24672681 DOI: 10.1556/eujmi.2.2012.2.5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 01/23/2012] [Indexed: 11/19/2022] Open
Abstract
The objective of this paper was to investigate whether retrospective pulsed-field gel electrophoresis (PFGE) of methicillin-resistant Staphylococcus aureus (MRSA) isolates at two-year intervals is suitable and sufficient to demonstrate changes in the clonal composition of MRSA isolates and to identify previously undetected local outbreaks. PFGE patterns of 400 MRSA isolates were collected between 2004 and 2008 at the University of Rostock Hospital in Germany, and were used to assess the prevalence of MRSA clones at different time points. Only minor changes were detected. The combined analysis of all isolates that were collected per year reduced the time needed to perform this laborious procedure. The retrospective identification of outbreaks may require shorter intervals. Improved infection prevention and control measures prevented further outbreaks in previously affected hospital departments. In conclusion, PGFE at two-year intervals is sufficient to detect changes in the clonal composition of local MRSA isolates. If time for identification is important during outbreak investigations, more rapid methods with a similarly high discriminatory power such as spa typing should be used.
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Cavanagh JP, Klingenberg C, Hanssen AM, Fredheim EA, Francois P, Schrenzel J, Flægstad T, Sollid JE. Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis. J Microbiol Methods 2012; 89:159-66. [DOI: 10.1016/j.mimet.2012.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/23/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
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High throughput multiple locus variable number of tandem repeat analysis (MLVA) of Staphylococcus aureus from human, animal and food sources. PLoS One 2012; 7:e33967. [PMID: 22567085 PMCID: PMC3342327 DOI: 10.1371/journal.pone.0033967] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/20/2012] [Indexed: 11/19/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen, a relevant pathogen in veterinary medicine, and a major cause of food poisoning. Epidemiological investigation tools are needed to establish surveillance of S. aureus strains in humans, animals and food. In this study, we investigated 145 S. aureus isolates recovered from various animal species, disease conditions, food products and food poisoning events. Multiple Locus Variable Number of Tandem Repeat (VNTR) analysis (MLVA), known to be highly efficient for the genotyping of human S. aureus isolates, was used and shown to be equally well suited for the typing of animal S. aureus isolates. MLVA was improved by using sixteen VNTR loci amplified in two multiplex PCRs and analyzed by capillary electrophoresis ensuring a high throughput and high discriminatory power. The isolates were assigned to twelve known clonal complexes (CCs) and –a few singletons. Half of the test collection belonged to four CCs (CC9, CC97, CC133, CC398) previously described as mostly associated with animals. The remaining eight CCs (CC1, CC5, CC8, CC15, CC25, CC30, CC45, CC51), representing 46% of the animal isolates, are common in humans. Interestingly, isolates responsible for food poisoning show a CC distribution signature typical of human isolates and strikingly different from animal isolates, suggesting a predominantly human origin.
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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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Kushnir AV, Muminov TA, Bayev AI, Khrapov EA, Filipenko ML. Molecular characterization of Neisseria gonorrhoeae isolates in Almaty, Kazakhstan, by VNTR analysis, Opa-typing and NG-MAST. INFECTION GENETICS AND EVOLUTION 2012; 12:570-6. [PMID: 22333840 DOI: 10.1016/j.meegid.2012.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 01/30/2012] [Accepted: 01/30/2012] [Indexed: 11/17/2022]
Abstract
In the present study, new variable number tandem repeats (VNTR) loci in the Neisseria gonorrhoeae genome were identified in silico. VNTR analysis scheme using PCR and agarose or polyacrylamide gel electrophoresis was developed based on nine VNTR loci with various degrees of polymorphism. The method was used to genotype a collection of 48 isolates, obtained from patients with gonorrhea in Almaty, Kazakhstan during the period from December 2008 to November 2009. This collection of isolates was also characterized by the opa-typing and multiantigen sequence typing (NG-MAST). The discriminatory power of the VNTR analysis translated by Hunter-Gaston Discrimination Index (HGDI) was similar to that of opa typing (HGDI=0.98 versus 0.97) and slightly higher than that of NG-MAST (HDGI=0.95). The adjusted Rand (AR) coefficients and Wallace coefficients showed that the overall concordance between the typing methods was not high. VNTR analysis described here is simple, inexpensive, easy to interpret, and it would be reliable for the comparison of data obtained in different laboratories. The proposed VNTR loci might be used for epidemiological studies of gonococcal infections.
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Affiliation(s)
- Anastasiya V Kushnir
- Group of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Lavrentjeva 8, Novosibirsk 630090, Russia.
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Evidence of diversity among epidemiologically related carbapenemase-producing Acinetobacter baumannii strains belonging to international clonal lineage II. J Clin Microbiol 2012; 50:590-7. [PMID: 22205821 DOI: 10.1128/jcm.05555-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii strains belonging to international clonal lineage II (ICL-II) have become predominant in intensive care units (ICUs) throughout Italy. Between 2005 and 2009, the carbapenem-hydrolyzing class D β-lactamase (CHDL) bla(OXA-23) gene became more prevalent than bla(OXA-58) among epidemic ICL-II strains showing extensive genetic similarity. These findings posed the question of whether CHDL gene replacement occurred in the homogeneous ICL-II population or a new OXA-23 clone(s) emerged and spread in ICUs. In this study, the changes in the ICL-II A. baumannii population and CHDL gene carriage were investigated in 30 genetically related isolates collected during the bla(OXA-58)-to-bla(OXA-23) transition period. Pulsotyping, randomly amplified polymorphic DNA (RAPD) analysis, and multilocus sequence typing (MLST) results were combined with multilocus variable-number tandem-repeat (VNTR) analysis (MLVA-8), siderotyping, and plasmid profiling to improve genotype-based discrimination between isolates. Pulsotyping, RAPD analysis, and MLST clustered isolates into a single type. MLVA-8 identified 19 types that clustered into three complexes. All OXA-23-producing isolates formed a single complex, while OXA-58 producers were split into two complexes. Southern blot analysis of the physical localization and genetic context of the CHDL genes showed that bla(OXA-58) was invariably located on plasmids, while bla(OXA-23) was present within Tn2006 on the chromosome or both the chromosome and plasmids. These data indicate that the apparently homogeneous population of CHDL-producing ICL-II strains was composed of several independent strains and that, between 2005 and 2009, distinct OXA-23 producers displaced the preexisting OXA-58 producers. Thus, MLVA-8 appears to be a suitable tool not only for investigating A. baumannii population structure but also for high-resolution epidemiological typing.
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From types to trees: reconstructing the spatial spread of Staphylococcus aureus based on DNA variation. Int J Med Microbiol 2011; 301:614-8. [PMID: 21983337 DOI: 10.1016/j.ijmm.2011.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tracing the spatial spread of pathogens is a key objective of molecular infectious disease epidemiology. Accordingly, a wide range of genotyping approaches have been used to monitor the dissemination of Staphylococcus aureus strains, from localized outbreaks to global spread. We provide a critical review of available methods, revealing that molecular markers currently in use for typing S. aureus acquire changes so slowly that they monitor evolutionary change over timescales that are largely irrelevant to epidemiology. Moreover, the more variable markers frequently do not reflect the pathogen's evolutionary history and, hence, provide potentially misleading information about spread. More recent work has demonstrated that staphylococcal evolution proceeds sufficiently fast that the dynamics of S. aureus spatial spread can be elucidated at great detail on the basis of genome-wide single-nucleotide polymorphisms.
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Haguenoer E, Baty G, Pourcel C, Lartigue MF, Domelier AS, Rosenau A, Quentin R, Mereghetti L, Lanotte P. A multi locus variable number of tandem repeat analysis (MLVA) scheme for Streptococcus agalactiae genotyping. BMC Microbiol 2011; 11:171. [PMID: 21794143 PMCID: PMC3163538 DOI: 10.1186/1471-2180-11-171] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 07/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Multilocus sequence typing (MLST) is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping. Results We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R). Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains. Conclusions The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.
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Affiliation(s)
- Eve Haguenoer
- Université François-Rabelais de Tours, UFR de Médecine, EA 3854 Bactéries et risque materno-fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, Tours, France
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Strain Typing Using Multiple “Variable Number of Tandem Repeat” Analysis and Genetic Element CRISPR. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Comparison of automated repetitive-sequence-based polymerase chain reaction and spa typing versus pulsed-field gel electrophoresis for molecular typing of methicillin-resistant Staphylococcus aureus. Diagn Microbiol Infect Dis 2011; 69:30-7. [PMID: 21146711 DOI: 10.1016/j.diagmicrobio.2010.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 09/03/2010] [Accepted: 09/09/2010] [Indexed: 11/23/2022]
Abstract
Automated repetitive polymerase chain reaction (PCR) (DiversiLab, bioMérieux, St. Laurent, Quebec, Canada) and single locus sequence typing of the Staphylococcus protein A (spa) gene with spa-type assignment by StaphType RIDOM software were compared to pulsed-field gel electrophoresis (PFGE) as the "gold standard" method for methicillin-resistant Staphylococcus aureus (MRSA) typing. Fifty-four MRSA isolates were typed by all methods: 10 of known PFGE CMRSA type and 44 clinical isolates. Correct assignment of CMRSA type or cluster occurred for 47 of 54 (87%) of the isolates when using a rep-PCR similarity index (SI) of ≥95%. Rep-PCR gave 7 discordant results [CMRSA1 (3), CMRSA2 (1), CMRSA4 (1), and CMRSA10 (2)], and some CMRSA clusters were not distinguished (CMRSA10/5/9, CMRSA 7/8, and CMRSA3/6). Several spa types occurred within a single PFGE or repetitive PCR types among the 19 different spa types found. spa type t037 was shared by CMRSA3 and CMRSA6 strains, and CMRSA9 and most CMRSA10 strains shared spa type t008. Time to results for PFGE, repetitive PCR, and spa typing was 3-4 days, 24 h, and 48 h, respectively. The annual costs of using spa or repetitive PCR were 2.4× and 1.9× higher, respectively, than PFGE but routine use of spa typing would lower annual labor costs by 0.10 full-time equivalents compared to PFGE. Repetitive PCR is a good method for rapid outbreak screening, but MRSA isolates that share the same repetitive PCR or PFGE patterns can be distinguished by spa typing.
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Identification of variable-number tandem-repeat (VNTR) sequences in Acinetobacter baumannii and interlaboratory validation of an optimized multiple-locus VNTR analysis typing scheme. J Clin Microbiol 2010; 49:539-48. [PMID: 21147956 DOI: 10.1128/jcm.02003-10] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/.
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Thierry S, Wang D, Arné P, Deville M, De Bruin B, Nieguitsila A, Pourcel C, Laroucau K, Chermette R, Huang W, Botterel F, Guillot J. Multiple-locus variable-number tandem repeat analysis for molecular typing of Aspergillus fumigatus. BMC Microbiol 2010; 10:315. [PMID: 21143842 PMCID: PMC3004892 DOI: 10.1186/1471-2180-10-315] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 12/08/2010] [Indexed: 11/30/2022] Open
Abstract
Background Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyping method to resolve closely related microbial isolates to provide information for establishing genetic patterns among isolates and to investigate disease outbreaks. The usefulness of MLVA was recently demonstrated for the avian major pathogen Chlamydophila psittaci. In the present study, we developed a similar method for another pathogen of birds: the filamentous fungus Aspergillus fumigatus. Results We selected 10 VNTR markers located on 4 different chromosomes (1, 5, 6 and 8) of A. fumigatus. These markers were tested with 57 unrelated isolates from different hosts or their environment (53 isolates from avian species in France, China or Morocco, 3 isolates from humans collected at CHU Henri Mondor hospital in France and the reference strain CBS 144.89). The Simpson index for individual markers ranged from 0.5771 to 0.8530. A combined loci index calculated with all the markers yielded an index of 0.9994. In a second step, the panel of 10 markers was used in different epidemiological situations and tested on 277 isolates, including 62 isolates from birds in Guangxi province in China, 95 isolates collected in two duck farms in France and 120 environmental isolates from a turkey hatchery in France. A database was created with the results of the present study http://minisatellites.u-psud.fr/MLVAnet/. Three major clusters of isolates were defined by using the graphing algorithm termed Minimum Spanning Tree (MST). The first cluster comprised most of the avian isolates collected in the two duck farms in France, the second cluster comprised most of the avian isolates collected in poultry farms in China and the third one comprised most of the isolates collected in the turkey hatchery in France. Conclusions MLVA displayed excellent discriminatory power. The method showed a good reproducibility. MST analysis revealed an interesting clustering with a clear separation between isolates according to their geographic origin rather than their respective hosts.
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Affiliation(s)
- Simon Thierry
- ENVA, UMR BIPAR, Ecopham, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, France
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Bacterial population genomics and infectious disease diagnostics. Trends Biotechnol 2010; 28:611-8. [PMID: 20961641 DOI: 10.1016/j.tibtech.2010.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 01/14/2023]
Abstract
New sequencing technologies have made the production of bacterial genome sequences increasingly easy, and it can be confidently forecasted that vast genomic databases will be generated in the next few years. Here, we detail how collections of bacterial genomes from a particular species (population genomics libraries) have already been used to improve the design of several diagnostic assays for bacterial pathogens. Genome sequencing itself is also becoming more commonly used for epidemiological, forensic and clinical investigations. There is an opportunity for the further development of bioinformatic tools to bring even further value to bacterial diagnostic genomics.
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te Witt R, van Belkum A, van Leeuwen WB. Molecular diagnostics and genotyping of MRSA: an update. Expert Rev Mol Diagn 2010; 10:375-80. [PMID: 20465491 DOI: 10.1586/erm.10.34] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Comparison of two multilocus variable-number tandem-repeat methods and pulsed-field gel electrophoresis for differentiating highly clonal methicillin-resistant Staphylococcus aureus isolates. J Clin Microbiol 2010; 48:3600-7. [PMID: 20702668 DOI: 10.1128/jcm.01039-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the United Kingdom, EMRSA-15 and EMRSA-16 account for the majority (∼90%) of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections. Currently, the standard typing technique, pulsed-field gel electrophoresis (PFGE), is laborious and insufficient for discriminating between closely related subtypes of EMRSA-15 and -16. The objective of the present study was to compare the usefulness of multilocus variable-number tandem-repeat fingerprinting (MLVF) and multilocus variable-number tandem-repeat analysis (MLVA) with PFGE for subtyping these highly clonal MRSA lineages. A panel of 85 MRSA isolates (41 EMRSA-15, 20 EMRSA-16, and 24 MRSA isolates with diverse PFGE patterns) was investigated. In addition, a further 29 EMRSA-15s with identical PFGE patterns from two geographically linked but epidemiologically distinct outbreaks and several sporadic cases were analyzed. PFGE, MLVF, and MLVA resolved 66 (Simpson's index of diversity [SID] = 0.984), 51 (SID = 0.95), and 42 (SID = 0.881) types, respectively, among the 85 MRSA isolates. MLVF was more discriminatory than MLVA for EMRSA-15 and -16 strains, but both methods had comparable discriminatory powers for distinguishing isolates in the group containing diverse PFGE types. MLVF was comparable to PFGE for resolving the EMRSA-15s but had a lower discriminatory power for the EMRSA-16s. MLVF and MLVA resolved the 29 isolates with identical PFGE patterns into seven and six subtypes, respectively. Importantly, both assays indicated that the two geographically related outbreaks were caused by distinct subtypes of EMRSA-15. Taken together, the data suggest that both methods are suitable for identifying and tracking specific subtypes of otherwise-indistinguishable MRSA. However, due to its greater discriminatory power, MLVF would be the most suitable alternative to PFGE for hospital outbreak investigations.
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Vu-Thien H, Hormigos K, Corbineau G, Fauroux B, Corvol H, Moissenet D, Vergnaud G, Pourcel C. Longitudinal survey of Staphylococcus aureus in cystic fibrosis patients using a multiple-locus variable-number of tandem-repeats analysis method. BMC Microbiol 2010; 10:24. [PMID: 20105324 PMCID: PMC2825195 DOI: 10.1186/1471-2180-10-24] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 01/27/2010] [Indexed: 11/30/2022] Open
Abstract
Background Staphylococcus aureus infection in patients with cystic fibrosis (CF) is frequent and may be due to colonization by a few pathogenic lineages. Systematic genotyping of all isolates, methicillin-susceptible S. aureus (MSSA) as well as methicillin-resistant S. aureus (MRSA) is necessary to identify such lineages and follow their evolution in patients. Multiple-locus variable-number tandem repeat analysis (MLVA/VNTR) was used to survey S. aureus clinical isolates in a French paediatric CF centre. Results During a 30 months period, 108 patients, aged 2 to 21 years, regularly followed up at the centre, provided sputum for culture. From 79 patients, a total of 278 isolates were genotyped by MLVA, resolving into 110 genotypes and 19 clonal complexes (CC) composed of similar or closely related isolates. 71% of the strains were distributed into four main CCs, in term of number of isolates and number of genotypes. Spa (Staphylococcus protein A) typing was performed on representative samples, showing an excellent concordance with MLVA. In 17 patients, strains from two to four different CCs were recovered over time. On six occasions, S. aureus isolates with the same genotype were shared by 2 different patients and they belonged to one of the four main clusters. Methicillin-resistance was observed in 60% of the isolates, 90% of which belonged to the main clonal complexes CC8, CC45 and CC5. In 5 patients, methicillin-resistance of S. aureus isolates was not associated with the mecA gene: for four patients, it was due to overproduction of β-lactamase, leading to BOR-SA (borderline S. aureus) isolates, while a strain showing probably a new modified penicillin-binding capacity (MOD-SA) was observed from one patient. Conclusion Systematic genotyping of S. aureus isolates recovered from sputum of CF children allows a thorough analysis of the strains responsible for sporadic as well as chronic colonization and the follow up of their evolution over time. We show here that more than 70% of these strains belong to 4 major CCs. MSSA as well as MRSA, BOR-SA and MOD-SA isolates can persist over several years, despite antibiotic treatments.
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Affiliation(s)
- Hoang Vu-Thien
- Université Paris Sud 11, CNRS, UMR 8621, Institut de Génétique et Microbiologie, Orsay 91405, France
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