Complete genome sequence of a methicillin-resistant Staphylococcus lugdunensis strain and characteristics of its staphylococcal cassette chromosome mec.

Symptoms of Staphylococcus lugdunensis infection are often similar to those of Staphylococcus aureus infection, including skin and soft-tissue lesions, bacteremia and infective endocarditis. Despite the severity of these infections, S. lugdunensis is regarded as a less important pathogen than drug-resistant S. aureus. To investigate its ability to cause infectious diseases, a methicillin-resistant S. lugdunensis (MRSL) strain JICS135 was isolated from a patient with bacteremia and subjected to whole genome sequencing. Similar to most strains of methicillin-resistant S. aureus (MRSA), this MRSL strain possessed the staphylococcal cassette chromosome mec (SCCmec) located close to the origin of replication. However, the SCCmec in this MRSL strain, with three ccr complexes, was structurally unique and currently untypable. Moreover, the SCCmec of this MRSL strain was found to carry two genes encoding microbial surface components recognizing adhesive matrix molecules (MSCRAMM)-like proteins accompanied by glycosyl transferases, one of which may have been derived from S. aureus and the other from S. epidermidis, indicating that this MRSL evolved to carry virulence factors from other staphylococci. The emergence of this strain, the first MRSL strain whose genome has been sequenced completely, may be of public concern.

Evaluation of disc diffusion tests and agar screening for predicting mecA-mediated oxacillin resistance in Staphylococcus lugdunensis revealed a cefoxitin-susceptible, mecA-positive S. lugdunensis clonal complex 27 clone.

OBJECTIVES: This study evaluated disc diffusion tests and agar screening for detecting mecA-mediated oxacillin resistance in Staphylococcus lugdunensis (S. lugdunensis). METHODS: Staphylococcus lugdunensis isolates (n = 179) from diverse sources in Hong Kong during 1998-2018 were investigated by disc diffusion tests (cefoxitin and oxacillin) and inoculation onto oxacillin (1 µg/mL and 2 µg/mL) and chromID methicillin-resistant Staphylococcus aureus (MRSA) agars. The results were compared with mecA PCR as the reference. Isolates with discordant results were further tested by MIC and penicillin-binding protein 2a (PBP2a) assays. RESULTS: Cefoxitin and oxacillin zone diameters were not distributed in ways that allowed reliable division of the mecA-positive (n = 52) and mecA-negative (n = 127) isolates. On applying the 2019 Clinical Laboratory Standards Institute (CLSI) M100 breakpoints for cefoxitin disc results, there was 88% categorical agreement (CA) and 40% very major error (VME). Screening using 2 µg/mL oxacillin agar reliably differentiated mecA-positive and mecA-negative isolates (100% CA) without any major error (ME) or VME results. The performance of screening using 1 µg/mL oxacillin agar or ChromID MRSA agar was variable (74-89% CA, 0-38% ME and 0-37% VME). The mecA-positive isolates (n = 21) that could not be detected by the cefoxitin disc test were further characterised. The cefoxitin MIC for all 21 isolates was ≤4 µg/mL. Twenty isolates had an oxacillin MIC of 1-2 µg/mL and one had an oxacillin MIC of 4 µg/mL. All had positive PBP2a results and were typed as clonal cluster 27/SCCmec V. CONCLUSIONS: These findings highlight the need to evaluate phenotypic methods using mecA-positive S. lugdunensis with different oxacillin resistance phenotypes.

Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) and Tandem Repeat Sequence Typing (TRST), helpful tools for subtyping Staphylococcus lugdunensis.

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.

Specific clones of Staphylococcus lugdunensis may be associated with colon carcinoma.

Staphylococcus lugdunensis produces a tannase with activity that may be associated with the onset of colon carcinoma. To clarify this feature of colon carcinoma-associated S. lugdunensis, we obtained isolates from healthy subjects and patients with colon adenomas and carcinomas and analyzed their genetic backgrounds. In total, 40 S. lugdunensis isolates from 288 rectal swabs collected between 2002 and 2008 were used. These isolates were classified into four groups according to the diseases of the subjects: healthy (n=13), colon carcinoma (n=13), colon adenoma (n=9), and unknown (n=5). The isolates were also classified by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing. In addition, an antimicrobial susceptibility test and detection of resistance genes were performed for all isolates. According to the PFGE analysis, 40 isolates could be classified into five groups. Among the groups, carcinoma and colon adenoma patients were significantly more frequently (40.9%) classified into group D (p<0.05), whereas healthy subjects were more frequently (38.5%) classified into group A. All isolates in group D were typed as ST27, which was clearly different than isolates in the other groups. All isolates were susceptible to the antimicrobial agents tested, including ß-lactams, although seven strains produced ß-lactamase. Our data suggest that a specific clone of S. lugdunensis might be associated with colon carcinoma and colon adenoma. This clone showed high susceptibility to many antimicrobial agents. Therefore, eradication therapy may lead to a decreased risk of colon carcinoma.

Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements.

Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements. S. lugdunensis also bears various putative virulence genes but only one complete genome with extensive analysis has been published with one prophage sequence (φSL2) and a unique plasmid was previously described. In this study, we performed de novo sequencing, whole genome assembly and annotation of seven strains of S. lugdunensis from VISLISI clinical trial. We searched for the presence of virulence genes and mobile genetics elements using bioinformatics tools. We identified four new prophages, named φSL2 to φSL4, belonging to the Siphoviridae class and five plasmids, named pVISLISI_1 to pVISLISI_5. Three plasmids are homologous to known plasmids that include, amongst others, one S. aureus plasmid. The two other plasmids were not described previously. This study provides a new context for the study of S. lugdunensis virulence suggesting the occurrence of several genetic recombination' with other staphylococci.

Clinical Features, Outcomes, and Molecular Characteristics of Community- and Health Care-Associated Staphylococcus lugdunensis Infections.

Staphylococcus lugdunensis is a major cause of aggressive endocarditis, but it is also responsible for a broad spectrum of infections. The differences in clinical and molecular characteristics between community-associated (CA) and health care-associated (HA) S. lugdunensis infections have remained unclear. We performed a retrospective study of S. lugdunensis infections between 2003 and 2014 to compare the clinical and molecular characteristics of CA and HA isolates. We collected 129 S. lugdunensis isolates in total: 81 (62.8%) HA isolates and 48 (37.2%) CA isolates. HA infections were more frequent than CA infections in children (16.0% versus 4.2%, respectively; P = 0.041) and the elderly (38.3% versus 14.6%, respectively; P = 0.004). The CA isolates were more likely to cause skin and soft tissue infections (85.4% versus 19.8%, respectively; P < 0.001). HA isolates were more frequently responsible for bacteremia of unknown origin (34.6% versus 4.2%, respectively; P < 0.001) and for catheter-related bacteremia (12.3% versus 0%, respectively; P = 0.011) than CA isolates. Fourteen-day mortality was higher for HA infections than for CA infections (11.1% versus 0%, respectively). A higher proportion of the HA isolates than of the CA isolates were resistant to penicillin (76.5% versus 52.1%, respectively; P = 0.004) and oxacillin (32.1% versus 2.1%, respectively; P < 0.001). Two major clonal complexes (CC1 and CC3) were identified. Sequence type 41 (ST41) was the most common sequence type identified (29.5%). The proportion of ST38 isolates was higher for HA than for CA infections (33.3% versus 12.5%, respectively; P = 0.009). These isolates were of staphylococcal cassette chromosome mec element (SCCmec)type IV, V, or Vt. HA and CA S. lugdunensis infections differ in terms of their clinical features, outcome, antibiotic susceptibilities, and molecular characteristics.

Persistence of a major endemic clone of oxacillin-resistant Staphylococcus lugdunensis sequence type 6 at a tertiary medical centre in northern Taiwan.

OBJECTIVES: The aim of this study was to investigate the molecular epidemiology and clinical characteristics of a major clone of oxacillin-resistant Staphylococcus lugdunensis in a tertiary hospital. METHODS: All S. lugdunensis isolated from sterile sites between June 2003 and May 2013 were collected for analysis. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to study their genetic relationships. RESULTS: A total of 118 S. lugdunensis isolates were analysed by PFGE. Three major PFGE pulsotypes were found: A, H, and L. Most of the pulsotype A isolates were oxacillin-resistant, and SCCmec type V and type VT. Isolates from another major clonal group that consisted primarily of pulsotype L were oxacillin-resistant and SCCmec type II. These 14 SCCmec type II S. lugdunensis isolates demonstrated high PFGE similarity and were obtained in the study hospital over a period of 40 months. Three of these 14 patients had clinically significant bacteraemia, and all three cases were in the intensive care unit. Further MLST analysis of the isolates identified an endemic S. lugdunensis strain of sequence type 6, clonal complex 1. CONCLUSIONS: This study identified a major endemic clone of S. lugdunensis that is oxacillin-resistant, SCCmec type II, ST6, and capable of long-term persistence in the hospital. Continuous infection control surveillance and monitoring of S. lugdunensis should be considered in endemic areas.

Unbiased species-level identification of clinical isolates of coagulase-negative Staphylococci: does it change the perspective on Staphylococcus lugdunensis?

Unbiased species-level identification of coagulase-negative staphylococci (CoNS) using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identified Staphylococcus lugdunensis to be a more commonly isolated CoNS in our laboratory than previously observed. It has also highlighted the possibility of vertical transmission.

Genotypes and phenotypes of Staphylococcus lugdunensis isolates recovered from bacteremia.

BACKGROUND: Staphylococcus lugdunensis is a member of coagulase-negative staphylococci, which has the potential to cause serious infections, such as endocarditis, bone and joint infections, and septicemia. Differences in phenotypic/genotypic characterization may be linked to different diseases. METHODS: Genotypes of 11 S. lugdunensis isolates from bacteremia were determined by pulsed field gel electrophoresis and accessory gene regulator (agr) typing. The SCCmec elements in two oxacillin-resistant isolates were sequenced. Phenotypes were tested by antimicrobial susceptibility testing, biofilm formation assessments, and virulence factor analysis (hemolytic and protease activities). RESULTS: Among the 11 isolates, six pulsotypes were found, and seven isolates belonged to two major pulsotypes. Two agr types (agr-1sl or agr-2sl) were found. The 11 isolates were susceptible to most antimicrobial agents tested. The SCCmec elements in two oxacillin-resistant isolates belonged to the SCCmec type V, but with additional ccrAB2 genes. The agr-2sl isolates (n = 7) displayed higher hemolytic and protease activities than the agr-1sl isolates. All isolates contained the icaA gene but with variable biofilm activities. The results suggest that protein might play an important part in S. lugdunensis biofilms, possibly through an ica-independent pathway. Of the 11 patients with S. lugdunensis bacteremia, one patient had a community-onset infection, and others had a hospital-acquired infection, which were mostly central venous catheter-related infections. CONCLUSION: The 11 S. lugdunensis bacteremia isolates displayed various genotypes and phenotypes. Two oxacillin-resistant isolates contained SCCmec type V and carried additional ccrAB2 genes. Correlation of genotypes and phenotypes with infections needs further studies.

Carriage niches and molecular epidemiology of Staphylococcus lugdunensis and methicillin-resistant S. lugdunensis among patients undergoing long-term renal replacement therapy.

We collected nasal, axilla, and groin swabs from 252 adult patients from 2 nephrology centers in Hong Kong. Staphylococcus lugdunensis carriage was detected in 51.6% patients (groin, 39.3%; axilla, 19.8%; nose, 17.9%). The carriage rates of methicillin-sensitive S. lugdunensis and methicillin-resistant S. lugdunensis (MRSL) were 46.0% and 8.3%, respectively. Independent risk factors for S. lugdunensis carriage included male sex (odds ratio [OR], 4.4), hemodialysis (OR, 2.2), and aged 18-50years (OR, 2.4). The isolates belonged to 10 pulsotype clusters (n=129) and 8 singletons (n=8). All MRSL and most gentamicin- and tetracycline-resistant strains were found in a predominating sequence type 3 clone, designated HKU1, which accounted for 51.8% of all colonizing S. lugdunensis strains. The 21 MRSL isolates had SCCmec type V (n=18), type IV (n=2), and type I (n=1). The finding highlights the potential for dissemination of multidrug resistance through successful S. lugdunensis clones.

Virulence factors among Staphylococcus lugdunensis are associated with infection sites and clonal spread.

Staphylococcus lugdunensis has emerged as a significant human pathogen, with distinct clinical and microbiological characteristics. Our goal was to identify the virulence factors in S. lugdunensis recovered from infected patients of two Greek hospitals during a six-year period (2008-2013). A collection of 38 S. lugdunensis was tested for biofilm formation, antimicrobial susceptibility, clonal distribution, virulence factors (ica operon, fbl, atlL, vwbl, slush) and antibiotic resistance genes (mecA, ermC) carriage. Strains were classified into pulsotypes by pulsed-field gel electrophoresis (PFGE) of SmaI DNA digests. The majority (22) was isolated from skin and soft tissue infections (SSTIs), nine from deep-sited infections (DSIs), including three bacteraemias and seven from prosthetic device-associated infections (PDAIs). All isolates were oxacillin-susceptible, mecA-negative and fbl-positive. The highest resistance rate was detected for ampicillin (50%), followed by erythromycin and clindamycin (18.4%). Fourteen isolates (36.8%) produced biofilm, whereas 26/38 (68.4%) carried the ica operon. Biofilm formation was more frequent in isolates from PDAIs. Thirty-six strains (94.7%) carried atlL and 31 (81.6%) carried vwbl, whereas slush was detected in 15 (39.5%). PFGE revealed a low level of genetic diversity: strains were classified into seven pulsotypes, with two major clones (C: 22 and D: nine strains). Type C strains recovered from all infection sites prevailed in biofilm formation and ermC carriage, whereas type D strains associated with SSTIs and DSIs carried more frequently vwbl, slush or both genes. Despite susceptibility to antimicrobials, the clonal expansion and carriage of virulence factors, combined with biofilm-producing ability, render this species an important pathogen that should not be ignored.

Multi-virulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing.

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis.

Catalase-negative Staphylococcus lugdunensis strain with a novel point mutation in the catalase gene isolated from a patient with chronic suppurative otitis media.

This report describes the results of the sequence analysis of a methicillin-susceptible strain of catalase-negative Staphylococcus lugdunensis. Molecular characterization of the deduced sequence revealed a novel point mutation in the catalase gene. To our knowledge, this is the first report of a catalase-negative S. lugdunensis strain, although catalase-negative isolates of Staphylococcus aureus and Staphylococcus epidermidis have been previously reported.

Staphylococcus lugdunensis, an aggressive coagulase-negative pathogen not to be underestimated.

The new emerging coagulase-negative pathogen Staphylococcus lugdunensis is responsible for severe cardiac and joint infections. Since the biochemical phenotypic systems designed for the identification of CoNS do not appear to be species specific and are hardly reliable for the discrimination of S. lugdunensis from other staphylococci, its precise identification requires fine molecular methods. The pathogenic mechanisms by which S. lugdunensis causes severe infections are not yet completely elucidated and in this review its virulence and toxic determinants are surveyed as well as its adhesins and biofilm production.

Multilocus sequence typing analysis of Staphylococcus lugdunensis implies a clonal population structure.

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus.

Clinical and microbiological characteristics of community-acquired Staphylococcus lugdunensis infections in Southern Taiwan.

Most Staphylococcus lugdunensis strains (49/59, 83%) were related to clinical infections, were susceptible to most antimicrobial agents with an overall oxacillin-resistant rate of 5% (3/58), and carried relatively great genetic diversity. Community-acquired infections (41/49, 84%) were dominant, often developed in patients with comorbidity, and had rather benign clinical courses without mortality.