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Nouws S, Bogaerts B, Verhaegen B, Denayer S, Laeremans L, Marchal K, Roosens NHC, Vanneste K, De Keersmaecker SCJ. Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks. Front Microbiol 2021; 12:750278. [PMID: 34795649 PMCID: PMC8593433 DOI: 10.3389/fmicb.2021.750278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
Through staphylococcal enterotoxin (SE) production, Staphylococcus aureus is a common cause of food poisoning. Detection of staphylococcal food poisoning (SFP) is mostly performed using immunoassays, which, however, only detect five of 27 SEs described to date. Polymerase chain reactions are, therefore, frequently used in complement to identify a bigger arsenal of SE at the gene level (se) but are labor-intensive. Complete se profiling of isolates from different sources, i.e., food and human cases, is, however, important to provide an indication of their potential link within foodborne outbreak investigation. In addition to complete se gene profiling, relatedness between isolates is determined with more certainty using pulsed-field gel electrophoresis, Staphylococcus protein A gene typing and other methods, but these are shown to lack resolution. We evaluated how whole genome sequencing (WGS) can offer a solution to these shortcomings. By WGS analysis of a selection of S. aureus isolates, including some belonging to a confirmed foodborne outbreak, its added value as the ultimate multiplexing method was demonstrated. In contrast to PCR-based se gene detection for which primers are sometimes shown to be non-specific, WGS enabled complete se gene profiling with high performance, provided that a database containing reference sequences for all se genes was constructed and employed. The custom compiled database and applied parameters were made publicly available in an online user-friendly interface. As an all-in-one approach with high resolution, WGS additionally allowed inferring correct isolate relationships. The different DNA extraction kits that were tested affected neither se gene profiling nor relatedness determination, which is interesting for data sharing during SFP outbreak investigation. Although confirming the production of enterotoxins remains important for SFP investigation, we delivered a proof-of-concept that WGS is a valid alternative and/or complementary tool for outbreak investigation.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Lasse Laeremans
- Organic Contaminants and Additives, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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Identification of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from burn patients by multiplex PCR. Burns 2014; 41:590-4. [PMID: 25441547 DOI: 10.1016/j.burns.2014.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/15/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MRCoNS) as important human pathogens are causes of nosocomial infections worldwide. Burn patients are at a higher risk of local and systemic infections with these microorganisms. OBJECTIVE A screening method for MRSA by using a multiplex polymerase chain reaction (PCR) targeting the 16S ribosomal RNA (rRNA), mecA, and nuc genes was developed. The aim of the present study was to investigate the potential of this PCR assay for the detection of MRSA strains in samples from burn patients. METHODS During an 11-month period, 230 isolates (53.11%) of Staphylococcus spp. were collected from burn patients. The isolates were identified as S. aureus by using standard culture and biochemical tests. DNA was extracted from bacterial colonies and multiplex PCR was used to detect MRSA and MRCoNS strains. RESULTS Of the staphylococci isolates, 149 (64.9%) were identified as S. aureus and 81 (35.21%) were described as CoNS. Among the latter, 51 (62.97%) were reported to be MRCoNS. From the total S. aureus isolates, 132 (88.6%) were detected as MRSA and 17 (11.4%) were methicillin-susceptible S. aureus (MSSA). The presence of the mecA gene in all isolates was confirmed by using multiplex PCR as a gold standard method. CONCLUSION This study presented a high MRSA rate in the region under investigation. The 16S rRNA-mecA-nuc multiplex PCR is a good tool for the rapid characterization of MRSA strains. This paper emphasizes the need for preventive measures and choosing effective antimicrobials against MRSA and MRCoNS infections in the burn units.
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Łobocka M, Hejnowicz MS, Dąbrowski K, Gozdek A, Kosakowski J, Witkowska M, Ulatowska MI, Weber-Dąbrowska B, Kwiatek M, Parasion S, Gawor J, Kosowska H, Głowacka A. Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era. Adv Virus Res 2012; 83:143-216. [PMID: 22748811 DOI: 10.1016/b978-0-12-394438-2.00005-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.
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Affiliation(s)
- Małgorzata Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Khaliq MF, Noorani MM, Siddiqui UA, Al Ibran E, Rao MH. Factors associated with duration of hospitalization and outcome in burns patients: a cross sectional study from Government Tertiary Care Hospital in Karachi, Pakistan. Burns 2012; 39:150-4. [PMID: 22694872 DOI: 10.1016/j.burns.2012.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 04/03/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVE Burns are important contributors toward mortality in trauma related injuries in Karachi, Pakistan. The aim of the present study was to delineate the factors contributing to the duration of hospitalization and mortality in such patients. METHODS We performed a single center retrospective study of patients admitted during a 2 year period (January 2009 till December 2010) in Burns Center, Karachi. Patients with incomplete record were excluded. Variables included were age and gender of the patient, the percent total body surface area (%TBSA) burn, the cause of the burn and the body parts affected along with the micro-organisms isolated from the burn wounds. The relationship of these variables with the duration of hospitalization and the outcome of patients was assessed by means of Pearson Chi Square test in SPSS version 14. RESULTS Mean age of patients was 26.64 years (± 13.430). More males (56.6%) were admitted than females (43.4%), giving a male to female ratio of 1.3:1. Mean percent total body surface area (%TBSA) burnt and mortality were 24.69% and 26.38% respectively with both having higher values in females (p<0.001). Males had a mean longer duration of hospitalization compared to females (35.94 days vs. 27.63 days). The most common micro-organism colonizing the wounds was found to be Staphylococcus aureus. Factors significantly (p<0.05) associated with increased duration of hospitalization and mortality include the age and gender of the patient, the cause of burn, inhalation injury, the region affected and %TBSA burnt. CONCLUSION The relationship of age and gender of the patient, the cause of burn, inhalation injury, the region affected and %TBSA burnt are important factors in determining the duration of hospitalization of the patients and whether the patients will survive or succumb to injuries.
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Wiśniewska K, Szewczyk A, Piechowicz L, Bronk M, Samet A, Swieć K. The use of spa and phage typing for characterization of clinical isolates of methicillin-resistant Staphylococcus aureus in the University Clinical Center in Gdańsk, Poland. Folia Microbiol (Praha) 2012; 57:243-9. [PMID: 22532090 PMCID: PMC3345334 DOI: 10.1007/s12223-012-0148-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 04/09/2012] [Indexed: 11/28/2022]
Abstract
The emergence of spa types and spa–clonal complexes (CC) among clinical methicillin-resistant Staphylococcus aureus isolates collected from the University Clinical Center in Gdańsk between 2008 and 2009 were investigated. Phage typing was used as the initial screening in the study. The basic set of phages and the additional set of phages were used. Most of the isolates (56 %) belonged to the phage group III. With the additional set of phages, eight types were found, with predominant one MR8 (50 %). Sixteen distinct spa types were observed. The most frequent were t003 (22 %), t151 (16 %), and t008 (12 %). The spa types were clustered into two spa-CC and eight singletons. The predominant CC010 (50 %) consisted of six types, with the most common t003 (36.7 %) and t151(26.7 %), and in 80 % was identified as staphylococcal chromosomal casette mec (SCCmec) type II. The second cluster has no founder (12 %) with only two spa types: t037 belonging to SCCmec type III and t029. In the most frequent singleton, spa type t008 alone was clustered in 12 % of the isolates. All singletons correspond to SCCmec type IV. The CC010 was distributed in most of the hospital wards, corresponded to Multilocus sequence typing type ST5/ST225 and was constantly present throughout the observed period. The isolates of CC010 generally belonged to the phage group III, and most of them (53.3 %) were resistant to erythromycin, clindamycin, and ciprofloxacin. The concordance between spa-clone and phage type was very high, but the same phage type MR8 was observed within different spa types of the predominant clone.
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Wildemauwe C, De Brouwer D, Godard C, Buyssens P, Dewit J, Joseph R, Vanhoof R. The use of spa and phage typing for characterization of a MRSA population in a Belgian hospital: Comparison between 2002 and 2007. ACTA ACUST UNITED AC 2010; 58:70-2. [DOI: 10.1016/j.patbio.2009.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
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Sharma RS, Mishra V, Mohmmed A, Babu CR. Phage specificity and lipopolysaccarides of stem- and root-nodulating bacteria (Azorhizobium caulinodans, Sinorhizobium spp., and Rhizobium spp.) of Sesbania spp. Arch Microbiol 2007; 189:411-8. [DOI: 10.1007/s00203-007-0322-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 10/02/2007] [Accepted: 10/24/2007] [Indexed: 11/25/2022]
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Wildemauwe C, Godard C, Joseph R, De Ryck R, Deplano A, Damée S, Van Bossuyt E, Vanhoof R, Struelens M. New phage type among methicillin-resistant Staphylococcus aureus associated with a local outbreak in Belgium during 2002. Clin Microbiol Infect 2006; 12:1036-8. [PMID: 16961645 DOI: 10.1111/j.1469-0691.2006.01516.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In total, 150 methicillin-resistant Staphylococcus aureus (MRSA) isolates collected during 2002 from a general Belgian hospital were phage-typed at routine test dilution x 100. The majority (45%) belonged to phage group (J)*, while 10% were classified as a new phage type 29/(42E)/54/(D11)*. The isolates belonging to this new type carried the aac(6')-aph(2'') and the aph(3') aminoglycoside resistance genes and showed high-level resistance to oxacillin. Molecular typing revealed that they belonged to the multiresistant clonal pulsed-field gel electrophoresis (PFGE) type D8. PFGE group D, characterised as genotype ST228-MRSA-I, has been present in Belgian hospitals since 1999.
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Affiliation(s)
- C Wildemauwe
- National Phage Typing Reference Centre, Pasteur Institute, Brussels, Belgium.
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Wildemauwe C, Godard C, De Beenhouwer H, Boel A, Damée S, Van Bossuyt E, Vanhoof R. A change in Belgian epidemic methicillin-resistant Staphylococcus aureus phage types in 2000: phenotypic and genotypic characterization of isolates from a general hospital. J Hosp Infect 2005; 60:307-11. [PMID: 15890433 DOI: 10.1016/j.jhin.2005.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2004] [Accepted: 01/10/2005] [Indexed: 10/25/2022]
Abstract
During 2000, new methicillin-resistant Staphylococcus aureus (MRSA) epidemic phage types became preponderant in Belgium. In the present study, phenotypic and genotypic characteristics of 130 MRSA isolates from a general Belgian hospital were investigated. The MRSA nature of the isolates was confirmed by coagulase test, oxacillin screen plate test and detection of the mecA gene by polymerase chain reaction. Phage typing categorized the MRSA strains into two main groups: the [O]* types and the [J]* types. SmaI macrorestriction analysis by pulsed-field gel electrophoresis gave the same pulsotype in the majority of strains. All strains of the [O]* and [J]* groups, except one, belonged to this pulsotype. Aminoglycoside-modifying-enzyme genes could only be detected in a minority of strains. Although the epidemic phage types of the mid-1990s appear to have been supplanted by the [O]* and [J]* groups, the MRSA population examined showed a remarkably uniform profile corresponding to the previous major clone B.
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Murchan S, Aucken HM, O'neill GL, Ganner M, Cookson BD. Emergence, spread, and characterization of phage variants of epidemic methicillin-resistant Staphylococcus aureus 16 in England and Wales. J Clin Microbiol 2004; 42:5154-60. [PMID: 15528709 PMCID: PMC525207 DOI: 10.1128/jcm.42.11.5154-5160.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Revised: 05/14/2004] [Accepted: 07/09/2004] [Indexed: 11/20/2022] Open
Abstract
Epidemic methicillin-resistant Staphylococcus aureus 16 (EMRSA-16) and EMRSA-15 are the two most important and prevalent EMRSA strains found in the United Kingdom and have also been found in a number of European countries and the United States. We describe for the first time the spread of an EMRSA strain (EMRSA-16) from its point of origin in one hospital to the surrounding hospitals and regions over the following 2 years. In the first 18 months after its original appearance, 136 hospitals referred EMRSA-16 isolates for typing, and interhospital and intraregional spread were reported: it was more prevalent in males between 60 and 80 years old and was isolated from sputum and throat more often than EMRSA-15. Important characteristics, e.g., carriage of the enterotoxin A (sea) and toxic shock syndrome toxin (tst) genes and production of urease, are described. Phage-variant strains of EMRSA-16 which share some of the characteristics of the classical strain, including toxin carriage and urease production, emerged, but without genotypic investigations, their relationship could only be inferred. A total of 129 clinical isolates from 52 hospitals, collected between March 1998 and April 1999 and representing classical EMRSA-16 (49 isolates) or phage variants (80 isolates), were compared by phage typing, pulsed-field gel electrophoresis (PFGE) following SmaI macrorestriction, antimicrobial susceptibility testing, urease production, and PCR detection of toxin gene carriage. PFGE analysis revealed 29 profiles, A1 to A29, with A1 representing the prototypic strain, NCTC 13143. All other profiles differed from A1 by 1 to 6 bands, but some differed from each other by up to 10 bands.
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Affiliation(s)
- S Murchan
- Laboratory of Healthcare-Associated Infection, Specialist and Reference Microbiology Division, Health Protection Agency, London, UK
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