1
|
Ravaioli S, Campoccia D, Mirzaei R, Mariani V, Bottau G, De Donno A, Montanaro L, Speziale P, Arciola CR. Searching for Virulence Factors among Staphylococcus lugdunensis Isolates from Orthopedic Infections: Correlation of β-hemolysin, hemolysin III, and slush Genes with Hemolytic Activity and Synergistic Hemolytic Activity. Int J Mol Sci 2023; 24:15724. [PMID: 37958706 PMCID: PMC10650139 DOI: 10.3390/ijms242115724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Staphylococcus lugdunensis is an emerging high-virulent pathogen. Here, the presence and expression of virulence genes (icaA, fbl, vwbl, fbpA, slush A, B and C, and genes of the putative β-hemolysin and hemolysin III) and the ability to induce synergistic hemolytic activity and hemolysis after 24, 48 and 72 h were investigated in a collection of twenty-two S. lugdunensis clinical isolates. The collection of isolates, mainly from implant orthopedic infections, had previously been grouped by ribotyping/dendrogram analysis and studied for biofilm matrices, biomasses and antibiotic resistances. Two isolates, constituting a unique small ribogroup sharing the same cluster, exhibited an amplicon size of the slush operon (S. lugdunensis synergistic hemolysin) which was shorter than the expected 977 bp. This outcome can predict the genetic lineage of the S. lugdunensis strains. One isolate (cra1342) presented two deletions: one of 90 bp in slush A and the other of 91 bp in slush B. Another isolate (N860314) showed a single 193 bp deletion, which encompassed part of the slush B terminal sequence and most of slush C. The isolate N860314 was devoid of hemolytic activity after 24 h, and the first consideration was that the deleted region deals with the coding of the active enzymatic site of the slush hemolysin. On the other hand, cra1342 and N860314 isolates with different slush deletions and with hemolytic activity after 24 and 48 h, respectively, could have replaced the hemolytic phenotype through other processes.
Collapse
Affiliation(s)
- Stefano Ravaioli
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (D.C.); (V.M.); (G.B.); (A.D.D.); (L.M.)
| | - Davide Campoccia
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (D.C.); (V.M.); (G.B.); (A.D.D.); (L.M.)
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Laboratory, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Valentina Mariani
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (D.C.); (V.M.); (G.B.); (A.D.D.); (L.M.)
| | - Giulia Bottau
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (D.C.); (V.M.); (G.B.); (A.D.D.); (L.M.)
| | - Andrea De Donno
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (D.C.); (V.M.); (G.B.); (A.D.D.); (L.M.)
| | - Lucio Montanaro
- Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy; (D.C.); (V.M.); (G.B.); (A.D.D.); (L.M.)
- Laboratory of Immunorheumatology and Tissue Regeneration, Laboratory of Pathology of Implant Infections, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Pietro Speziale
- Department of Molecular Medicine, Biochemistry Section, Viale Taramelli 3/b, 27100 Pavia, Italy;
| | - Carla Renata Arciola
- Laboratory of Immunorheumatology and Tissue Regeneration, Laboratory of Pathology of Implant Infections, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy
| |
Collapse
|
2
|
Lin LC, Cheng CW, Chang SC, Lu JJ. Molecular Epidemiological Survey of Staphylococcus lugdunensis Isolates With Variable Number of Repeats in the von Willebrand Factor-Binding Protein Gene. Front Cell Infect Microbiol 2021; 11:748640. [PMID: 34858874 PMCID: PMC8632046 DOI: 10.3389/fcimb.2021.748640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The von Willebrand factor binding protein in Staphylococcus lugdunensis (vWbl) comprises four major regions: the signal peptide (S), the non-repetitive (A) region, the repeat (R) region, and the wall-associated (W) region. Previous studies have demonstrated that the R region contains 10 copies of repeating sequences; however, we reveal that the copy number of repeats in the vWbl gene varies among different S. lugdunensis isolates. In this study, an epidemiological surveillance was conducted to determine whether the copy number of repeats in vWbl in different isolates of S. lugdunensis correlates with their infectivity. The number of repeats was estimated in a total of 212 isolates, consisting of 162 isolates of oxacillin-sensitive S. lugdunensis (OSSL) and 50 isolates of oxacillin-resistant S. lugdunensis (ORSL). Our data showed that 72.5% (116/162) of OSSL isolates contained 9 (25, 15.4%), 12 (43, 26.5%), or 13 (48, 29.6%) repeats, and 90% (45/50) of ORSL isolates had 9 (32, 64%) or 13 (13, 26%) repeats. In addition, 89.6% (26 of 29) of the sequence type (ST)27 strain had 12 repeats, and 86.8% (13 of 15) of the ST4 strain had 14 repeats. Twenty-seven of the 28 isolates with nine repeats were of the staphylococcal cassette chromosome mec (SCCmec) V or Vt type and belonged to ST3, and all isolates with 13 repeats were of SCCmec II type and belonged to ST6. All isolates with nine repeats had a stop codon at the 18th codon of the third repeat, suggesting that these isolates coded for nonfunctional vWbl. Further, western blot analysis confirmed that all strains translated vWbl, and only vWbl proteins coded by genes with nine repeats were exported outside the cell. These results suggest that number of vWbl repeats in S. lugdunensis have clonal specificities and may correlate with potential pathogenicity.
Collapse
Affiliation(s)
- Lee-Chung Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chun-Wen Cheng
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
3
|
Staphylococcus lugdunensis: a Skin Commensal with Invasive Pathogenic Potential. Clin Microbiol Rev 2020; 34:34/2/e00205-20. [PMID: 33361142 DOI: 10.1128/cmr.00205-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Staphylococcus lugdunensis is a species of coagulase-negative staphylococcus (CoNS) that causes serious infections in humans akin to those of S. aureus It was often misidentified as S. aureus, but this has been rectified by recent routine use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in diagnostic laboratories. It encodes a diverse array of virulence factors for adhesion, cytotoxicity, and innate immune evasion, but these are less diverse than those encoded by S. aureus It expresses an iron-regulated surface determinant (Isd) system combined with a novel energy-coupling factor (ECF) mechanism for extracting heme from hemoproteins. Small cytolytic S. lugdunensis synergistic hemolysins (SLUSH), peptides related to phenol-soluble modulins of S. aureus, act synergistically with β-toxin to lyse erythrocytes. S. lugdunensis expresses a novel peptide antibiotic, lugdunin, that can influence the nasal and skin microbiota. Endovascular infections are initiated by bacterial adherence to fibrinogen promoted by a homologue of Staphylococcus aureus clumping factor A and to von Willebrand factor on damaged endothelium by an uncharacterized mechanism. S. lugdunensis survives within mature phagolysosomes of macrophages without growing and is released only following apoptosis. This differs fundamentally from S. aureus, which actively grows and expresses bicomponent leukotoxins that cause membrane damage and could contribute to survival in the infected host. S. lugdunensis is being investigated as a probiotic to eradicate S. aureus from the nares of carriers. However, this is contraindicated by its innate virulence. Studies to obtain a deeper understanding of S. lugdunensis colonization, virulence, and microbiome interactions are therefore warranted.
Collapse
|
4
|
Chniba I, Boujemaa S, Mardassi BBA, Ben Abdelmoumen Mardassi B. Clonal dissemination of antibiotic resistance among Tunisian Mycoplasma gallisepticum isolates as revealed by gene-targeted sequencing analysis. Avian Dis 2020; 65:446278. [PMID: 33057595 DOI: 10.1637/aviandiseases-d-20-00080r1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 11/05/2022]
Abstract
SummaryTo date, very little is known about avian mycoplasma infections in Tunisia. Mycoplasma gallisepticum is one of the most economically significant pathogen for poultry in Tunisia and worldwide. Based on the paucity of data regarding the genetic profiles and antibacterial behavior of M. gallisepticum strains in Tunisia, the present study was conducted. Genetic typing and phylogenetic relationships of 40 M. gallisepticum strains (20 Tunisian isolates, 19 international strains collection, and S6 reference strain) were investigated by gene-targeted sequencing (GTS) using 4 loci ( pvpA , mgc2 , vlhA and the InterGenic Spacer Region (IGSR) between the 16S and the 23S rRNA genes). GTS reveals 12 STs that were found to spread over 2 clonal complexes (CC) and 5 singletons.Emergence of enrofloxacin and spiramycin resistance among M. gallisepticum local isolates have been revealed using the broth microdilution method. Causal mutations have been identified by sequencing the quinolone-resistance determining region (QRDR) and domain II and V of 23S rRNA as well as the rplD and rplV genes for enrofloxacine- and macrolide-resistant isolates, respectively. The emersion of antibiotic resistance to enrofloxacin and spiramycin has been identified as being related to a distinctive clonal complex formed by 4 different STs (ST2, ST3, ST4 and ST5) which would suggest that this phenotype was clonally disseminated.
Collapse
Affiliation(s)
- Imen Chniba
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13, Place Pasteur, BP 74, 1002, Tunis Belvédère, Tunisia
| | - Safa Boujemaa
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13, Place Pasteur, BP 74, 1002, Tunis Belvédère, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Group of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, 13, Place Pasteur, BP 74, 1002, Tunis Belvédère, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Institut Pasteur de Tunis Head of Mycoplasmas Unit Group of Mycoplasmas. Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development 13, Place Pasteur, B.P. 74.1002 Tunis, Belvédère TUNISIA Tunis 1002 00216 71844790
| |
Collapse
|
5
|
Lebeurre J, Dahyot S, Diene S, Paulay A, Aubourg M, Argemi X, Giard JC, Tournier I, François P, Pestel-Caron M. Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus. Front Microbiol 2019; 10:2479. [PMID: 31736914 PMCID: PMC6834553 DOI: 10.3389/fmicb.2019.02479] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus lugdunensis is a commensal bacterium of human skin that has emerged as a virulent Coagulase-Negative Staphylococcus in both community-acquired and healthcare associated infections. Genotyping methods have shown a clonal population structure of this pathogen but failed to identify hypervirulent lineages. Here, complete genomes of three pathogenic and three carriage S. lugdunensis strains were obtained by Single-Molecule sequencing (PacBio) and compared to 15 complete genomes available in GenBank database. The aim was to identify (i) genetic determinants specific to pathogenic or carriage strains or specific to clonal complexes (CCs) defined by MultiLocus Sequence Typing, and (ii) antibiotic resistance genes and new putative virulence factors encoded or not by mobile genetic elements (MGE). Comparative genomic analysis did not show a strict correlation between gene content and the ability of the six strains to cause infections in humans and in a Galleria mellonella infection model. However, this study identified new MGEs (five prophages, two genomic islands and one plasmid) and genetic variations of some putative virulence-associated loci, especially in CC3 strains. For a clonal population, high variability and eight CC-dependent genetic organizations were observed for the ess locus, which encodes a putative type VII secretion system (T7SS) homologous to that of S. aureus. Further phenotypic and functional studies are needed to characterize this particular CC3 and to evaluate the role of T7SS in the virulence of S. lugdunensis.
Collapse
Affiliation(s)
| | - Sandrine Dahyot
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Seydina Diene
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - Marion Aubourg
- EA4655 U2RM (Équipe Antibio-Résistance), Université de Caen Basse-Normandie, Caen, France
| | - Xavier Argemi
- CHRU de Strasbourg, VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Institut de Bactériologie, Université de Strasbourg, Strasbourg, France
| | - Jean-Christophe Giard
- EA4655 U2RM (Équipe Antibio-Résistance), Université de Caen Basse-Normandie, Caen, France
| | - Isabelle Tournier
- UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Martine Pestel-Caron
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| |
Collapse
|
6
|
Dahyot S, Lebeurre J, Laumay F, Argemi X, Dubos C, Lemée L, Prévost G, François P, Pestel-Caron M. fbl-Typing of Staphylococcus lugdunensis: A Frontline Tool for Epidemiological Studies, but Not Predictive of Fibrinogen Binding Ability. Front Microbiol 2019; 10:1109. [PMID: 31156610 PMCID: PMC6533592 DOI: 10.3389/fmicb.2019.01109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus lugdunensis is increasingly recognized as a potent pathogen, responsible for severe infections with an outcome resembling that of Staphylococcus aureus. Here, we developed and evaluated a tool for S. lugdunensis typing, using DNA sequence analysis of the repeat-encoding region (R-domain) in the gene encoding the fibrinogen (Fg)-binding protein Fbl (fbl-typing). We typed 240 S. lugdunensis isolates from various clinical and geographical origins. The length of the R-domain ranged from 9 to 52 repeats. fbl-typing identified 54 unique 18-bp repeat sequences and 92 distinct fbl-types. The discriminatory power of fbl-typing was higher than that of multilocus sequence typing (MLST) and equivalent to that of tandem repeat sequence typing. fbl-types could assign isolates to MLST clonal complexes with excellent predictive power. The ability to promote adherence to immobilized human Fg was evaluated for 55 isolates chosen to reflect the genetic diversity of the fbl gene. We observed no direct correlation between Fg binding ability and fbl-types. However, the lowest percentage of Fg binding was observed for isolates carrying a 5'-end frameshift mutation of the fbl gene and for those harboring fewer than 43 repeats in the R-domain. qRT-PCR assays for some isolates revealed no correlation between fbl gene expression and Fg binding capacity. In conclusion, this study shows that fbl-typing is a useful tool in S. lugdunensis epidemiology, especially because it is an easy, cost-effective, rapid and portable method (http://fbl-typing.univ-rouen.fr/). The impact of fbl polymorphism on the structure of the protein, its expression on the cell surface and in virulence remains to be determined.
Collapse
Affiliation(s)
- Sandrine Dahyot
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | | | - Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
| | - Xavier Argemi
- VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg, Institut de Bactériologie, Centre Hospitalier Régional Universitaire, Université de Strasbourg, Strasbourg, France.,Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Charline Dubos
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Ludovic Lemée
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Gilles Prévost
- VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg, Institut de Bactériologie, Centre Hospitalier Régional Universitaire, Université de Strasbourg, Strasbourg, France
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
| | - Martine Pestel-Caron
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| |
Collapse
|
7
|
Song M, Li Q, He Y, Lan L, Feng Z, Fan Y, Liu H, Qin F, Chen D, Yang M. A Comprehensive Multilocus Sequence Typing Scheme for Identification and Genotyping of Staphylococcus Strains. Foodborne Pathog Dis 2019; 16:331-338. [PMID: 30676080 DOI: 10.1089/fpd.2018.2565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Increasing clinical significance of coagulase-negative staphylococci requires effective methods for species identification and genotyping. In this study, six housekeeping genes (femA, ftsZ, gap, pyrH, rpoB, and tuf) with extensive allelic polymorphisms were identified and evaluated to develop a comprehensive multilocus sequence typing (MLST) scheme. Selected primers were capable of amplification of the six loci from all of the 180 Staphylococcus strains belonging to 18 different species. Sequence analysis of each locus (44-63 alleles) revealed higher nucleotide diversity than 16S rRNA (28 alleles). Phylogenetic analysis of the concatenated sequences (3054 bp) of the six loci provided accurate species identification and highly discriminatory typing for all the strains. Multilocus allelic analysis of the 180 Staphylococcus strains generated 103 different sequence profiles, suggesting high genetic diversity of the strains. For example, 30 S. aureus, 37 S. epidermidis, 32 S. haemolyticus, and 14 S. hominis strains were typed into 15, 21, 11, and 10 sequence profiles, respectively. Compared with published MLST schemes that restrict on a few particular species, this new scheme both achieved similar discrimination for typing S. aureus, S. epidermidis, S. haemolyticus, and S. hominis and provided sufficient discriminatory power for typing additional opportunistic species, such as S. cohnii, S. capitis, and S. warneri. Importantly, the comprehensive MLST scheme for Staphylococcus strains provides a better genotyping tool for understanding the phylogeny of coagulase-positive Staphylococcus aureus strains.
Collapse
Affiliation(s)
- Minghui Song
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Qiongqiong Li
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Yiping He
- 2 Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania
| | - Lefu Lan
- 3 Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Feng
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Yiling Fan
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hao Liu
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Feng Qin
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Dongying Chen
- 3 Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Meicheng Yang
- 1 Shanghai Institute for Food and Drug Control, Shanghai, China
| |
Collapse
|
8
|
Phylogenetics of Mycoplasma hominis clinical strains associated with gynecological infections or infertility as disclosed by an expanded multilocus sequence typing scheme. Sci Rep 2018; 8:14854. [PMID: 30291332 PMCID: PMC6173709 DOI: 10.1038/s41598-018-33260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022] Open
Abstract
To our knowledge, the phylodistribution of M. hominis clinical strains associated with various pathological conditions of the urogenital tract has not been explored hitherto. Here we analyzed the genetic diversity and phylogenetic relationships among 59 M. hominis Tunisian clinical isolates, categorized as gynecological infections- or infertility-associated pathotypes. For this purpose, we developed an expanded multilocus sequence typing (eMLST) scheme, combining the previously reported multilocus sequence typing (MLST) loci (gyrB, tuf, ftsY, uvrA, gap) with a new selected set of putative virulence genes (p120’, vaa, lmp1, lmp3, p60), referred herein to as multi-virulence-locus sequence typing (MVLST) loci. In doing so, M. hominis population was segregated into two distinct genetic lineages, which were differentially associated with each pathotype. Such a clear dichotomy was supported by several phylogenetic and population genetic analysis tools. Recombination was found to take place, but not sufficient enough to break down the overall clonal population structure of M. hominis, most likely as a result of purifying selection, which accommodated the most fit clones. In sum, and owing to the eMLST scheme described herein, we provide insightful data on the phylogenetics of M. hominis, arguing for the existence of genetically differentiable urogenital pathotypes.
Collapse
|
9
|
Argemi X, Matelska D, Ginalski K, Riegel P, Hansmann Y, Bloom J, Pestel-Caron M, Dahyot S, Lebeurre J, Prévost G. Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. BMC Genomics 2018; 19:621. [PMID: 30126366 PMCID: PMC6102843 DOI: 10.1186/s12864-018-4978-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci. Results We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system. Conclusion We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci. Electronic supplementary material The online version of this article (10.1186/s12864-018-4978-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xavier Argemi
- Service des Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Nouvel Hôpital Civil, 1 Place de l'Hôpital, 67000, Strasbourg, France. .,Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France.
| | - Dorota Matelska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Philippe Riegel
- Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| | - Yves Hansmann
- Service des Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Nouvel Hôpital Civil, 1 Place de l'Hôpital, 67000, Strasbourg, France.,Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| | - Jochen Bloom
- Bioinformatics & Systems Biology, Justus-Liebig-University Gießen, 35392, Gießen, Germany
| | - Martine Pestel-Caron
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Sandrine Dahyot
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Jérémie Lebeurre
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Gilles Prévost
- Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| |
Collapse
|
10
|
Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) and Tandem Repeat Sequence Typing (TRST), helpful tools for subtyping Staphylococcus lugdunensis. Sci Rep 2018; 8:11669. [PMID: 30076395 PMCID: PMC6076266 DOI: 10.1038/s41598-018-30144-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus lugdunensis is an emergent virulent coagulase-negative Staphylococcus that is increasingly responsible for severe infections. In an attempt to generate informative sequence data for subtyping S. lugdunensis, we selected and sequenced seven polymorphic variable number of tandem repeats (VNTRs) to develop two new methods: a classic length-based multiple-locus VNTR analysis (MLVA) method and a tandem repeat sequence typing (TRST) method. We assessed their performances compared to two existing methods, multilocus sequence typing (MLST) and multivirulence-locus sequence typing (MVLST) for 128 isolates from diverse clinical settings and geographical origins. The clustering achieved by the four methods was highly congruent, with MLVA discriminating within clonal complexes as defined by MLST. Indeed, MLVA was highly discriminant compared to MLST and MVLST in terms of number of genotypes as well as diversity indexes. Sequencing of the seven VNTRs showed that they were stable, and analysis of sequence polymorphisms provided superior discriminatory power. The typeability, reproducibility, and epidemiological concordance of these new methods were excellent. Of note, no link between clustering and clinical settings was identified. This study demonstrates that MLVA and TRST provide valuable information for molecular epidemiological study of S. lugdunensis, and represent promising tools to distinguish between strains of homogenous lineages in this clonal species.
Collapse
|
11
|
Pérez-Cataluña A, Tapiol J, Benavent C, Sarvisé C, Gómez F, Martínez B, Terron-Puig M, Recio G, Vilanova A, Pujol I, Ballester F, Rezusta A, Figueras MJ. Antimicrobial susceptibility, virulence potential and sequence types associated with Arcobacter strains recovered from human faeces. J Med Microbiol 2017; 66:1736-1743. [PMID: 29120301 DOI: 10.1099/jmm.0.000638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE The genus Arcobacter includes bacteria that are considered emergent pathogens because they can produce infections in humans and animals. The most common symptoms are bloody and non-bloody persistent diarrhea but cases with abdominal cramps without diarrhea or asymptomatic cases have also been described as well as cases with bacteremia. The objective was to characterize Arcobacter clinical strains isolated from the faeces of patients from three Spanish hospitals. METHODOLOGY We have characterized 28 clinical strains (27 of A. butzleri and one of A. cryaerophilus) isolated from faeces, analysing their epidemiological relationship using the multilocus sequence typing (MLST) approach and screening them for their antibiotic susceptibility and for the presence of virulence genes.Results/Key findings. Typing results showed that only one of the 28 identified sequence types (i.e. ST 2) was already present in the MLST database. The other 27 STs constituted new records because they included new alleles for five of the seven genes or new combinations of known alleles of the seven genes. All strains were positive for the ciaB virulence gene and sensitive to tetracycline. However, 7.4 % of the A. butzleri and A. cryaerophilus strains showed resistance to ciprofloxacin. CONCLUSION The fact that epidemiological unrelated strains show the same ST indicates that other techniques with higher resolution should be developed to effectively recognize the infection source. Resistance to ciprofloxacin, one of the antibiotics recommended for the treatment of Arcobacter intestinal infections, demonstrated in 10.7 % of the strains, indicates the importance of selecting the most appropriate effective treatment.
Collapse
Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiología, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Reus, Spain
| | | | | | | | | | | | | | - Gemma Recio
- Hospital Universitari Joan XXIII, Tarragona, Spain
| | | | | | | | | | - María Jose Figueras
- Unitat de Microbiología, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Reus, Spain
| |
Collapse
|
12
|
Mohamad M, Uçkay I, Hannouche D, Miozzari H. Particularities of Staphylococcus Lugdunensis in orthopaedic infections. Infect Dis (Lond) 2017; 50:223-225. [PMID: 28937308 DOI: 10.1080/23744235.2017.1374553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Morad Mohamad
- a Orthopaedic Surgery Service , Geneva University Hospitals , Geneva , Switzerland
| | - Ilker Uçkay
- a Orthopaedic Surgery Service , Geneva University Hospitals , Geneva , Switzerland.,b Faculty of Medicine, University of Geneva , Geneva , Switzerland
| | - Didier Hannouche
- a Orthopaedic Surgery Service , Geneva University Hospitals , Geneva , Switzerland
| | - Hermès Miozzari
- a Orthopaedic Surgery Service , Geneva University Hospitals , Geneva , Switzerland
| |
Collapse
|
13
|
Argemi X, Dahyot S, Lebeurre J, Hansmann Y, Ronde Oustau C, Prévost G. Staphylococcus lugdunensis small colony variant conversion resulting in chronic prosthetic joint infection. Med Mal Infect 2017; 47:498-501. [PMID: 28943172 DOI: 10.1016/j.medmal.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/16/2016] [Accepted: 05/23/2017] [Indexed: 11/19/2022]
Affiliation(s)
- X Argemi
- Maladies infectieuses et tropicales, hôpitaux universitaires, 67000 Strasbourg, France; EA7290 virulence bactérienne précoce, fédération de médecine translationnelle, université de Strasbourg, hôpitaux universitaires, Strasbourg, France.
| | - S Dahyot
- Laboratoire GRAM EA2656, UFR médecine pharmacie, université de Rouen, Rouen, France
| | - J Lebeurre
- Laboratoire GRAM EA2656, UFR médecine pharmacie, université de Rouen, Rouen, France
| | - Y Hansmann
- Maladies infectieuses et tropicales, hôpitaux universitaires, 67000 Strasbourg, France; EA7290 virulence bactérienne précoce, fédération de médecine translationnelle, université de Strasbourg, hôpitaux universitaires, Strasbourg, France
| | - C Ronde Oustau
- Service de chirurgie orthopédique, CCOM, hôpitaux universitaires, 67000 Strasbourg, France
| | - G Prévost
- EA7290 virulence bactérienne précoce, fédération de médecine translationnelle, université de Strasbourg, hôpitaux universitaires, Strasbourg, France
| |
Collapse
|