Molecular characterization of methicillin-resistant coagulase-negative staphylococci from a neonatal intensive care unit

Coagulase-Negative Staphylococci Clones Are Widely Distributed in the Hospital and Community

Coagulase-negative staphylococci (CoNS) may be considered contaminants when isolated from clinical specimens but may also be a cause of true infection. This study aimed to compare the clonality and SCCmec type of a collection of CoNS isolated from blood cultures of inpatients, nasal swabs of healthy individuals, and patients with chronic wounds, all from the same community, using SCCmec typing, pulsed-field gel electrophoresis (PFGE), and MLST. Staphylococcus epidermidis, exhibited high clonal diversity, but hospital and community clusters were observed. Nosocomial S. epidermidis clones belonged to sequence types ST2, ST6, and ST23. Some Staphylococcus haemolyticus clones were found to circulate in the hospital and community, while Staphylococcus saprophyticus exhibited very high clonal diversity. Staphylococcus lugdunensis, Staphylococcus warneri, and Staphylococcus capitis revealed several isolates belonging to the same clone in the hospital and community. The detection of different SCCmec types within the same cluster indicated high diversity. S. epidermidis was associated with SCCmec I and III, S. haemolyticus with I and II, S. capitis with type V, Staphylococcus hominis with mec complex type A and ccr1, and S. warneri and S. saprophyticus with SCCmec I. The generation of elements and new combinations of cassette genes were highly associated with CoNS isolates, suggesting that SCCmec may not be a good marker of clonality in these bacteria.

Multilocus variable number tandem repeat analysis and antimicrobial susceptibility pattern of Staphylococcus epidermidis isolates in Tehran, Iran

Objective:

Detection of sources of outbreaks caused by coagulase-negative Staphylococcus relies on molecular epidemiology methods. Little is known about the genetic diversity of the Staphylococcus epidermidis isolates isolated from various sources in Iran. We assessed the molecular epidemiology of S. epidermidis isolates collected from clinical and nonclinical sources from Tehran counties during 2014 to 2016 using MLVA (multilocus variable number tandem repeat analysis).

Methods:

One hundred and three clinical and nonclinical S. epidermidis isolates were collected from two hospitals in Tehran. Antibiotic susceptibility testing of isolates was evaluated for cefoxitin, tetracycline, erythromycin, clindamycin, mupirocin, vancomycin and linezolid according to Clinical and Laboratory Standards Institute, as well as prevalence of mecA gene was evaluated by PCR method. In addition, genetic relatedness of isolates was assessed by MLVA method.

Results:

Resistant rate to cefoxitin, tetracycline, erythromycin, clindamycin and mupirocin were 64, 36, 72, 44 and 23% in all isolates. All clinical and nonclinical isolates were susceptible to linezolid and vancomycin. In all, 49.5% of S. epidermidis isolates were multidrug resistant. Prevalence of mecA was 64%. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each variable number tandem repeat locus. The results of MLVA showed 64 types among all 103 isolates. There were 16 MLVA types that were common in two hospitals and 15 MLVA types were existed in various sources of S. epidermidis isolates. The diversity index obtained with MLVA was 0.989 (95% confidence interval [0.984–0.993]) for the 103 S. epidermidis isolates. A range of one to six alleles was identified at variable number tandem repeats loci with Simpson's diversity values between 0.526 and 0.781.

Conclusion:

Our study demonstrated presence of high molecular diversity among S. epidermidis isolates. In addition, the main conclusion was that some MLVA types can be disseminated over the wards and between the hospitals. In other hand, resistance to various antibiotics in S. epidermidis isolates and prevalence of methicillin-resistant S. epidermidis and multidrug resistant S. epidermidis isolates to be increasing.

Prevalence, clonality, and pathogenicity of Staphylococcus epidermidis isolates in newborn feces

Coagulase-negative staphylococci (CoNS) are the most prevalent pathogens causing late-onset sepsis in neonates. The question is whether neonates acquire endemic hospital-adapted clones or incidentally occurring CoNS strains after birth during their hospital stay. Therefore, a prospective study was performed on the prevalence of CoNS in the stool of babies (born vaginally or by cesarean section) during their first days of life. Their clonal relatedness and potential to induce invasive disease were characterized. CoNS were analyzed from the stool samples of newborns with a load of CoNS above 10³ colony-forming units (CFU)/mL. The identification of CoNS was performed phenotypically and genotypically. For typing, repetitive polymerase chain reaction (PCR), pulsed-field gel electrophoresis, and multilocus sequence typing were used. Resistance profiles, biofilm production, the presence of icaAD and of IS256 were determined as well. From a total of 207 stool samples (56 newborns), CoNS were detected in 41% of the newborns, mostly on day 3 for the first time (62.5%). Staphylococcus epidermidis was isolated in 85.7% of cases, harbored no IS256 element, and mostly expressed no biofilm. The isolates were separated into four main clusters by repetitive sequence-based PCR. 24% of the strains showed no antimicrobial resistance. 20% were resistant against four antibiotics of two different antibiotic classes. The remaining strains were resistant only against one antimicrobial substance class. Thus, it can be concluded that newborns do not acquire hospital-adapted endemic, multidrug-resistant S. epidermidis isolates during their first days of life. Yet, the results support the thesis that, during hospital stay, environmental parameters may convert sensible/noninvasive S. epidermidis strains into multidrug-resistant strains with characteristics of invasiveness.

Molecular Epidemiology of a Vancomycin-Intermediate Heteroresistant Staphylococcus epidermidis Outbreak in a Neonatal Intensive Care Unit

Coagulase-negative staphylococci (CoNS) have become the leading cause of bloodstream infections (BSIs) in intensive care units (ICUs), particularly in premature neonates. Vancomycin-intermediate heteroresistant CoNS (hVICoNS) have been identified as sources of BSIs worldwide, and their potential to emerge as significant pathogens in the neonatal ICU (NICU) remains uncertain. This study describes the molecular epidemiology of an outbreak of vancomycin-heteroresistant (hV) Staphylococcus epidermidis central-line-associated BSI (CLABSI) in a single tertiary care NICU and compares it to a second tertiary care NICU that had not been associated with an outbreak. Between November 2009 and April 2014, 119 S. epidermidis CLABSIs were identified in two tertiary care NICUs in Quebec, Canada. Decreased vancomycin susceptibility was identified in about 88% of all collected strains using Etest methods. However, discrepancies were found according to the Etest and population analysis profiling-area under the concentration-time curve (PAP-AUC) methods used. All strains were susceptible to linezolid, and a few isolates were nonsusceptible to daptomycin. Great genetic diversity was observed within the collection, with 31 pulsed-field gel electrophoresis (PFGE) patterns identified. The outbreak strains were all determined to be heteroresistant to vancomycin and were polyclonal. The study identified two major clones, PFGE patterns E and G, which were found in both NICUs across the 5-year study period. This suggests the persistence of highly successful clones that are well adapted to the hospital environment. hV S. epidermidis seems more common than currently realized in the NICU, and certain hV S. epidermidis clones can become endemic to the NICU. The reservoirs for these clones remain unknown at this time, and identification of the reservoirs is needed to better understand the impact of hV S. epidermidis in the NICU and to inform infection prevention strategies. In addition, there is a need to investigate and validate hV determination protocols for different species of CoNS.

Clinical characteristics of Staphylococcus epidermidis: a systematic review

Staphylococci are known as clustering Gram-positive cocci, nonmotile, non-spore forming facultatively anaerobic that classified in two main groups, coagulase-positive and coagulase-negative. Staphylococcus epidermidis with the highest percentage has the prominent role among coagulase-negative Staphylococci that is the most important reason of clinical infections. Due to various virulence factors and unique features, this microorganism is respected as a common cause of nosocomial infections. Because of potential ability in biofilm formation and colonization in different surfaces, also using of medical implant devices in immunocompromised and hospitalized patients the related infections have been increased. In recent decades the clinical importance and the emergence of methicillin-resistant Staphylococcus epidermidis strains have created many challenges in the treatment process.

The prevalence of aminoglycoside-modifying enzymes among coagulase negative staphylococci in Iranian pediatric patients

In spite of widespread emergence of aminoglycoside resistance, these drugs are still used in the treatment of staphylococcal infections. This study aimed to investigate the distribution of aminoglycoside resistance and genes encoding aminoglycoside - modifying enzymes (AMEs) as well as Staphylococcal Cassette Chromosome mec (SCCmec) type in coagulase negative staphylococci (CoNS) in pediatric patients. Totally, 93 CoNS isolates were examined for susceptibility to aminoglycosides using disk diffusion and/or E-test methods. AMEs genes and SCCmec types were detected using multiplex PCR. Strain typing was performed using repetitive extragenic palindromic (REP) - PCR assay. The non-susceptibility rates to kanamycin, tobramycin, gentamicin, amikacin and netilmicin were 73%, 59%, 49.5%, 16% and 7.5%, respectively. aac(6')-Ie-aph(2″)-Ia, ant(4')-Ia and aph(3')-IIIa were encountered in 56 (60.2%), 38 (40.8%) and 18 (19.3%) isolates, respectively. In aac(6')-Ie-aph(2″)-Ia- positive isolates, the non- susceptibility rates to kanamycin, gentamicin, tobramycin, amikacin and netilmicin were 83%, 74%, 73%, 49% and 43%, respectively. SCCmec types included type IV (n = 31), I (n = 17), II (n = 5), III (n = 4), and V (n = 2). Three isolates had two types; I + III (n = 2) and III + IV (n = 1) whereas 11 isolates were non-typeable. AMEs genes carriers were distributed frequently into type IV. We found diverse fingerprint patterns among our isolates. In conclusion, there was a strong correlation between alarming rate of aminoglycoside resistance and methicillin resistance. Discordances between phenotypic and genotypic detection of aminoglycoside resistance were discernible. AMEs genes might be related to SCCmec types.

Molecular analysis of Staphylococcus epidermidis strains isolated from community and hospital environments in China

Background

Staphylococcus epidermidis is a common cause of nosocomial infections worldwide. This study analyzed the differences in genetic endowment and clonal lineages with pathogenesis and resistance traits of S. epidermidis isolates collected from community and hospital environments (patients and healthcare staff) of the same ecological niche, time period, and geographical location in China.

Methodology/Principal Findings

Molecular epidemiology and population analysis showed that nasal colonization rates of S. epidermidis in the community of Shanghai area of China and in healthcare personnel were 44.8% (methicillin-resistant S. epidermidis, MRSE: 17.2%) and 61.3% (MRSE: 30.0%), respectively. 86.7% of clinical isolates were MRSE. Among the strains studied, 44 sequence types (STs) were identified with 91.7% belonging to clonal complex 2 (CC2). Only 40.8% isolates from patients were also found in healthy individuals. MRSE-ST2-SCCmecIII was the predominant clone in clinical isolates, almost resistant to all antibiotics tested. Biofilm-related genes IS256 and icaA were detected in majority of the predominant clinical MRSE-ST2 clone with a 40.5% biofilm-positive rate. No ST2 isolate was found in community setting. We found a high prevalence of arginine catabolic mobile element (ACME) (74.1%). The prevalence of ACME-arc and ACME-opp3 clusters was 71.6% and 32.4%, respectively. Methicillin-sensitive S. epidermidis (MSSE) isolates harbored more ACME (83.3%) than MRSE isolates (67.7%), and there was no association between ACME and SCCmec types. An association was found between low-level ACME presence and invasive infections.

Conclusions/Significance

We observed a high level of diversity within S. epidermidis in this study, with CC2 as the dominant clonal complex in both community and hospital settings. Only 40.8% of the isolates from patients were also found in healthy individuals. Contrary to that biofilm formation and multiple antibiotic resistance were associated closely with pathogenicity of S. epidermidis, ACME was more likely to be an indicator for colonization rather than a virulence factor.

Comparative epidemiology of Staphylococcus epidermidis isolates from patients with catheter-related bacteremia and from healthy volunteers

Staphylococcus epidermidis is a major cause of catheter-related bloodstream infections (CRBSIs). Recent studies suggested the existence of well-adapted, highly resistant, hospital-associated S. epidermidis clones. The molecular epidemiology of S. epidermidis in Belgian hospitals and the Belgian community has not been explored yet. We compared a set of 33 S. epidermidis isolates causing CRBSI in hospitalized patients with a set of 33 commensal S. epidermidis isolates. The factors analyzed included resistance to antibiotics and genetic diversity as determined by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and SCCmec typing. Additionally, the presence of virulence-associated mobile genetic elements, the ica operon and the arginine catabolic mobile element (ACME), was assessed and compared against clinical data. CRBSI S. epidermidis isolates were significantly resistant to more antibiotics than commensal S. epidermidis isolates. The two populations studied were very diverse and genetically distinct as only 23% of the 37 PFGE types observed were harbored by both CRBSI and commensal isolates. ACME was found in 76% of S. epidermidis strains, regardless of their origin, while the ica operon was significantly more prevalent in CRBSI isolates than in commensal isolates (P < 0.05). Nine patients presented a clinically severe CRBSI, eight cases of which were due to an ica-positive multiresistant isolate belonging to sequence type 2 (ST2) or ST54. S. epidermidis isolates causing CRBSI were more resistant and more often ica positive than commensal S. epidermidis isolates, which were genetically heterogeneous and susceptible to the majority of antibiotics tested. Clinically severe CRBSIs were due to isolates belonging to two closely related MLST types, ST2 and ST54.

Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: proposal for clone definition

In the present study we give some direction on the selection of the most appropriate typing method(s) to be used for the characterization of Staphylococcus epidermidis, in view of the most recent findings on the evolution, population structure, and epidemiology of this species. In order to achieve this aim, quantitative assessment of the correlation of the results of three typing methods--pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and staphylococcal chromosomal cassette mec (SCCmec) typing, which target different regions of the chromosome that evolve at different rates--was performed. In order to evaluate the discriminatory ability and the strength and direction of the correlation of the different typing methods, Simpson's index of diversity (SID), the adjusted Rand coefficient (AR), and the Wallace coefficient (W) were calculated. PFGE was the most discriminatory method (SID = 99%), followed by MLST (SID = 90%) and SCCmec typing (SID = 75%). The values of AR and W (0.10 < AR < 0.30; 0.50 < W < 0.75) indicated that the partition of the same isolate collection by PFGE, MLST, and SCCmec typing provided results that had only a poor correlation with each other. However, the information provided by the combination of PFGE and SCCmec enabled the prediction of the results obtained by MLST at the level of the clonal complex with a high degree of precision (W > 0.90). We propose that clones of S. epidermidis be defined by the combination of the PFGE type followed by the SCCmec type, which provides reliable information on the short-term epidemiology and the ability to predict with consistency long-term clonal evolution.

Inferring a population structure for Staphylococcus epidermidis from multilocus sequence typing data

Despite its importance as a human pathogen, information on population structure and global epidemiology of Staphylococcus epidermidis is scarce and the relative importance of the mechanisms contributing to clonal diversification is unknown. In this study, we addressed these issues by analyzing a representative collection of S. epidermidis isolates from diverse geographic and clinical origins using multilocus sequence typing (MLST). Additionally, we characterized the mobile element (SCCmec) carrying the genetic determinant of methicillin resistance. The 217 S. epidermidis isolates from our collection were split by MLST into 74 types, suggesting a high level of genetic diversity. Analysis of MLST data using the eBURST algorithm revealed the existence of nine epidemic clonal lineages that were disseminated worldwide. One single clonal lineage (clonal complex 2) comprised 74% of the isolates, whereas the remaining isolates were clustered into 8 minor clonal lineages and 13 singletons. According to our evolutionary model, SCCmec was acquired at least 56 times by S. epidermidis. Although geographic dissemination of S. epidermidis strains and the value of the index of association between the alleles, 0.2898 (P < 0.05), support the clonality of S. epidermidis species, examination of the sequence changes at MLST loci during clonal diversification showed that recombination gives rise to new alleles approximately twice as frequently as point mutations. We suggest that S. epidermidis has a population with an epidemic structure, in which nine clones have emerged upon a recombining background and evolved quickly through frequent transfer of genetic mobile elements, including SCCmec.

Genetic Diversity among Methicillin-ResistantStaphylococcus epidermidis(MRSE)

We selected 106 methicillin-resistant Staphylococcus epidermidis (MRSE) and 22 methicillin-susceptible S. epidermidis (MSSE) hospital isolates--each with a different PFGE pattern--for more detailed documentation of genetic diversity. The 106 MRSE isolates showed extensive variation in the SmaI DNA fragments hybridizing with the DNA probe for mecA, the molecular size of which varied from as low as 20 kb up to over 500 kb. Parallel variation was also observed in the size of DNA fragments hybridizing with the chromosomal genes orfX and gyrA, and this was also observed in MSSE isolates. In contrast, SmaI fragments associated with the housekeeping genes murE and aroE, both located distantly from orfX, showed little size variation. Typing for the mec complex and ccr identified 10 different SCCmec structures and a large number of strains (21 isolates) that were non-typeable. The majority of strains studied (36%) carried a SCCmec type IV-like structure, including strains with non-related PFGE profiles. On the other hand, closely related strains often carried different types of SCCmec. The findings indicate that the acquisition and/or loss of mobile genetic elements, including various structural types of SCCmec, may occur frequently in the vicinity of the orfX gene on the S. epidermidis chromosome.

Molecular epidemiology in the public health and hospital environments

The increasing speed and ease of genomic sequencing coupled with available funding to sequence multiple, unrelated strains of the same species will lead inevitably to the identification of candidate genes that can be used as molecular typing tools (MLST, SLST, microarray approach). However, it is important to note that even the most sophisticated typing tool should never replace a full epidemiologic investigation in which all available information is taken into account. Nevertheless, the typing methods discussed in this article and those yet to be developed have significantly improved the quality of health care worldwide.

Evaluation of a multilocus sequence typing system for Staphylococcus epidermidis

Staphylococcus epidermidis is a significant cause of nosocomial disease. However, the taxonomy of this pathogen, particularly at subspecies level, is unclear. A multilocus sequence typing (MLST) scheme has therefore been investigated as a tool to elucidate taxonomic relationships within this group, based on genetic relatedness. DNA sequences for internal fragments of seven housekeeping genes were compared in 47 geographically and temporally diverse S. epidermidis isolates that were obtained from clinical infections. Twenty-three different allelic profiles were detected; 17 of these were represented by single strains and the largest profile group contained 17 isolates. Diversity of the same collection of isolates was investigated by using PFGE of SmaI-digested genomic DNA to test the discrimination and validity of the MLST approach. Isolates within the largest profile group were resolved into four distinct PFGE clusters on the basis of their SmaI digest patterns. Isolates within other profile groups that contained multiple isolates had matching PFGE SmaI patterns within each group. It appears that MLST is an effective method for grouping S. epidermidis strains at the subspecies level; however, it is not as discriminatory as it has been for other species for which MLST schemes have been established and, used alone, would not be a useful method for epidemiological studies. In addition, it was demonstrated that this method was effective for confirming the identity of S. epidermidis CoNS (coagulase-negative) isolates.