Multiple-strain colonization in nasal carriers of Staphylococcus aureus

Nasopharyngeal carriage and antibiotic susceptibility patterns of streptococcus pneumoniae, haemophilus influenzae, moraxella catarrhalis and staphylococcus aureus among urban Ugandan children post-PCV10 introduction: a cross-sectional study

In 2013, Uganda introduced the PCV10 pneumococcal vaccine and it is given to children at 6, 10 and 14 weeks after birth. Carriage prevalence studies post PCV10-introduction are necessary for monitoring the impact of vaccination and trends in antibiotic resistance. Here, we studied carriage/antibiotic resistance of Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus isolated from 194 children at the Mulago Assessment Centre clinic in Kampala-Uganda, 5 years post-PCV10 introduction. Almost all the children were vaccinated with PCV10 (98.5%, 191/194). The overall carriage prevalence (any species) was 62% (120/194), and it was associated with a history of antibiotics use (p=0.0159) and having respiratory symptoms (p=0.0003). The pneumococcus, H. influenzae, M. catarrhalis, and S. aureus carriage prevalence was 46% (90/194), 21% (40/194), 7% (14/194), and 6% (12/194), respectively. Species co-carriage occurred in 32 children (17%, 32/194), predominantly multidrug resistant pneumococcus + H. influenzae (23 children). Furthermore, pneumococci were highly resistant to cotrimoxazole (100%), erythromycin (76%), and tetracycline (52%), 42% being multidrug-resistant. Overall, we note an increase in antibiotic resistance post-PCV10 introduction, and microbial shifts i.e., a decrease in pneumococcus, M. catarrhalis and S. aureus carriage and an increase in H. influenzae carriage suggesting vaccine-associated perturbation of the respiratory ecology.

The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.

Selection of Staphylococcus aureus in a murine nasopharyngeal colonization model

Staphylococcus aureus nasal colonization is a risk factor for infection. A large proportion of the population are identified as potential S. aureus carriers yet we only partially understand the repertoire of genetic factors that promote long-term nasal colonization. Here we present a murine model of nasopharyngeal colonization that requires a low S. aureus inoculum and is amenable to experimental evolution approaches. We used this model to experimentally evolve S. aureus using successive passages in the nasopharynx to identify those genetic loci under selection. After 3 cycles of colonization, mutations were identified in mannitol, sorbitol, arginine, nitrite and lactate metabolism genes promoting key pathways in nasal colonization. Stress responses were identified as being under selective pressure, with mutations in DNA repair genes including dnaJ and recF and key stress response genes clpL, rpoB and ahpF. Peptidoglycan synthesis pathway genes also revealed mutations indicating potential selection for alteration of the cell surface. The murine model used here is versatile to question colonization, persistence and evolution studies. We studied the human pathogen Staphylococcus aureus in our search to determine factors that contribute to its ability to live in the human nose and throat. The anterior nares and nasopharynx are considered primary habitats but we do not understand how the pathogen adapts as it moves from one person to the next. We first determined sustained survival of the pathogen over multiple days in the nasopharynx that might act as a good model for human persistence due to the low numbers of bacteria needed for it to establish. By using successive rounds of colonization of the nasopharynx across different mice we revealed that multiple genetic changes in the S. aureus occurred. These changes were found in genes associated with the cell surface and metabolism and might indicate adaptation to the niche. One gene showed an accumulation of multiple mutations supporting a key contribution in adaptation but the role of the protein it encodes is not yet known. The contribution of these genes and genetic changes are unclear but indicate an area for future research to better understand how this common human pathogen is so successful at human colonization and survival.

Right-sided endocarditis caused by polyclonal Staphylococcus aureus infection

We present a case of bacterial endocarditis with both methicillin-sensitive and methicillin-resistant Staphylococcus aureus, which based on typing, originated from two distinct clones. Such a case may be misinterpreted by microbiology lab automation to be a monoclonal multi-drug resistant Staphylococcus aureus, while simple microbiology techniques will instantly reveal distinct clonality.

A Comprehensive View on the Human Antibody Repertoire Against Staphylococcus aureus Antigens in the General Population

Our goal was to provide a comprehensive overview of the antibody response to Staphylococcus aureus antigens in the general population as a basis for defining disease-specific profiles and diagnostic signatures. We tested the specific IgG and IgA responses to 79 staphylococcal antigens in 996 individuals from the population-based Study of Health in Pomerania. Using a dilution-based multiplex suspension array, we extended the dynamic range of specific antibody detection to seven orders of magnitude, allowing the precise quantification of high and low abundant antibody specificities in the same sample. The observed IgG and IgA antibody responses were highly heterogeneous with differences between individuals as well as between bacterial antigens that spanned several orders of magnitude. Some antigens elicited significantly more IgG than IgA and vice versa. We confirmed a strong influence of colonization on the antibody response and quantified the influence of sex, smoking, age, body mass index, and serum glucose on anti-staphylococcal IgG and IgA. However, all host parameters tested explain only a small part of the extensive variability in individual response to the different antigens of S. aureus.

The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection

BACKGROUND

Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients' quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities.

RESULTS

Based on an assessment of > 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of < 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis.

CONCLUSIONS

The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.

Transmission and Long-Term Colonization Patterns of Staphylococcus aureus in a Nursing Home

Nursing homes might create an environment favorable for the transmission of Staphylococcus aureus because of the presence of hospitalized elderly, overcrowding and close contacts among people. We aimed at identifying risk factors for S. aureus colonization and determining the genetic relatedness of isolates demonstrating transmission among people. We investigated 736 swab samples from 92 residents and personnel for the presence of S. aureus. Swabs from anterior nares and throat were collected quarterly (2018) in a nursing home located in Poland. Genotyping was conducted using the multi-locus variable number of tandem repeats fingerprinting (MLVF) method. We observed high seasonal variation in the proportion of participants colonized with methicillin-resistant Staphylococcus aureus (MRSA) strains (0% to 13.5%). A multivariate analysis revealed that residents aged more than 85 years old are at risk for becoming intermittent S. aureus carriers (p = 0.013). The MLVF analysis revealed a high genetic diversity among methicillin-sensitive S. aureus (MSSA) strains and close genetic relatedness between MRSA strains. We proved the advanced aged were predisposed to intermittent S. aureus carriage. Genotyping revealed the transmission of S. aureus among the participants living in a closed environment. A high genetic relatedness among isolated MRSA suggests its clonal spread in the nursing home.

The first outbreak of methicillin-resistant Staphylococcus aureus in dairy cattle in Poland with evidence of on-farm and intrahousehold transmission

Staphylococcus aureus is a widely recognized pathogen responsible for many serious diseases in both humans and animals. It is also one of the major causative agents of bovine mastitis. Methicillin-resistant S. aureus (MRSA), although relatively rare in this pathology, has been increasingly reported in livestock animals, mainly in pigs, but also cattle, sheep, and poultry. The recent emergence of livestock-associated (LA-)MRSA is cause for an immediate public health concern due to the risk of zoonotic transmission to humans, and is of particular concern for people who work in animal husbandry or have prolonged contact with livestock animals. This study reports on the first LA-MRSA outbreak in dairy cattle and the first probable case of MRSA transmission between humans and cows in Poland. A single dairy farm located in Eastern Poland was monitored on a regular basis for the occurrence of mastitis. Over a 1-yr study period, 717 quarter-milk samples from 583 cows were collected and examined microbiologically. A total of 5 MRSA isolates from as many cows with subclinical mastitis were cultured. They all belonged to the same outbreak, given a 2-mo time window in which they were identified. During the outbreak, 24 oral and nasal swabs were voluntarily taken from 6 people: a milker, a veterinarian, and 4 members of the veterinarian's family. Eight swabs from a milker, veterinarian, and 2 family members yielded positive MRSA cultures. All MRSA isolates were genotyped with a combination of multiple-locus variable number tandem repeat analysis, multilocus sequence typing, and staphylococcal protein A gene (spa) typing. Eleven bovine (n = 5; 5 cases) and human (n = 6; 4 cases) isolates showed an identical drug-susceptibility profile and were indistinguishable upon multiple-locus variable number tandem repeat analysis (pattern A), multilocus sequence typing (ST398) and spa (t034) typing. The results of this study provide the evidence of transmission of MRSA between humans and cows, and between humans in the family setting. This work, despite being a preliminary investigation, underscores the risk of intra- and interspecies transmission of LA-MRSA and urges enhancement of the existing biosecurity measures aimed at preventing MRSA (and other milk pathogens) spread at both the farm- and household levels.

Outpatient decolonization after recurrent skin infection with Panton-Valentine leukocidin (PVL)-producing S. aureus-The importance of treatment repetition

BACKGROUND

Recurrent skin abscesses are often associated with Panton-Valentine leukocidin-producing strains of S. aureus (PVL-SA). Decolonization measures are required along with treatment of active infections to prevent re-infection and spreading. Even though most PVL-SA patients are treated as outpatients, there are few studies that assess the effectiveness of outpatient topical decolonization in PVL-SA patients.

METHODS

We assessed the results of topical decolonization of PVL-SA in a retrospective review of patient files and personal interviews. Successful decolonization was defined as the absence of any skin abscesses for at least 6 months after completion of the final decolonization treatment. Clinical and demographic data was assessed. An intention-to-treat protocol was used.

RESULTS

Our cohort consisted of 115 symptomatic patients, 66% from PVL-positive MSSA and 19% from PVL-positive MRSA. The remaining 16% consisted of symptomatic patients with close contact to PVL-SA positive index patients but without detection of PVL-SA. The majority of patients were female (66%). The median age was 29.87% of the patients lived in multiple person households. Our results showed a 48% reduction in symptomatic PVL-SA cases after the first decolonization treatment. The results also showed that the decrease continued with each repeated decolonization treatment and reached 89% following the 5th treatment. A built multivariable Cox proportional-hazards model showed that the absence of PVL-SA detection (OR 2.0) and living in single person households (OR 2.4) were associated with an independently increased chance of successful decolonization.

CONCLUSION

In our cohort, topical decolonization was a successful preventive measure for reducing the risk of PVL-SA skin abscesses in the outpatient setting. Special attention should be given to patients living in multiple person households because these settings could confer a risk that decolonization will not be successful.

Efficacy and acceptability of treatment to eradicate nasal Staphylococcus aureus carriage among haemodialysis patients

AIM

For patients requiring haemodialysis, the risk of Staphylococcus aureus disease is higher in those colonized and persists while the person requires haemodialysis, necessitating frequent decolonization. However, the duration of successful decolonization is not known. This study aimed to determine the duration of efficacy of decolonization in intermittent and persistent S. aureus carriers requiring haemodialysis using two decolonization strategies.

METHODS

We screened 100 outpatients requiring haemodialysis for S. aureus carriage and then decolonized 14 intermittent carriers and 18 persistent carriers. Participants were invited to undertake two decolonization attempts, using systemic or topical antibiotics 12 weeks apart. Nasal swabs were taken weekly to determine the duration of successful decolonization.

RESULTS

Decolonization was successful in 24/32 (75%) participants and the median duration of decolonization was 35 days (95% confidence interval (CI) 11-59). The median duration of S. aureus decolonization was significantly shorter for persistent carriers (19 days, 95% CI 13-25 days) in comparison with intermittent carriers (70 days, 95% CI 61-79 days; P < 0.01). 28/52 (54%) post-decolonization surveys indicated that they would use the treatment again, 14/52 (27%) surveys indicated that they would not use the treatment again, and 10/52 (19%) were undecided. 16/53 (30%) decolonization attempts resulted in an adverse drug reaction.

CONCLUSION

Staphylococcus aureus decolonization using topical or systemic treatments was successful for many haemodialysis patients, and provided a month free of S. aureus colonization. Although decolonization treatment provided a shorter duration of success for persistent carriers in comparison with intermittent carriers, persistent carriers are likely to gain the most from effective decolonization strategies.

Co-occurrence of carbapenemase encoding genes in Acinetobacter baumannii, a dream or reality?

BACKGROUND

Acinetobacter baumannii is an important opportunistic pathogen that is rapidly evolving towards multidrug resistance and is responsible for life-threatening infections. Carbapenems are commonly used to treat A. baumannii infections but the emergence of carbapenemase encoding genes, such as blaOXA-23-like, blaOXA-24-like, blaOXA-58-like, and blaNDM has been reported. Moreover, several studies have reported the co-occurrence of two distinct carbapenemases in some isolates. The aim of the present study is to demonstrate whether the phenomenon of co-occurrence of two distinct carbapenemase encoding genes in a single isolate still exists.

RESULTS

We studied six strains of A. baumannii including one harboring blaOXA-23-like and blaOXA-24-like genes and five with blaOXA-23-like and blaNDM genes. One colony of each strain was inoculated in sterile water and diluted ten-fold. Each dilution was cultivated on trypticase soy agar plates for 24 h at 37 °C and the isolated bacteria were analyzed. For two of the six tested strains, we identified two different populations of A. baumannii, each with a different carbapenemase, genes encoding aminoglycoside modifying enzymes, resistance phenotype, and clonal type. In addition, the two different populations had the same aspect on the agar plate.

CONCLUSIONS

Here, we demonstrate that A. baumannii infections could be linked to multiple clones harboring different carbapenemase encoding genes in the same sample. In addition, we describe an easy method of verifying the presence of co-occurrence of carbapenemase in one isolate.

Challenges in Estimating Characteristics of Staphylococcus aureus Nasal Carriage Among Humans Enrolled in Surveillance Studies

Evaluating carriage of Staphylococcus aureus, an opportunistic pathogen of humans and animals capable of causing antibiotic-resistant infections, is epidemiologically important. However, clinical and epidemiological surveillance studies of S. aureus typically rely on characterizing one isolate per individual, which may not represent the actual population diversity in a carrier. The objective of this study was to determine if one isolate is sufficient for determining carrier status of particular strains or characteristics of S. aureus in a healthy (non-hospitalized) human population. We compared spa types, genetic markers (mecA, scn), and antibiotic resistance profiles of 10 S. aureus isolates recovered from a single nasal swab for each of 19 participants (190 isolates total) selected from a cohort of industrial hog operation workers and their household members. Participants included both persistent (n = 10) and intermediate (n = 9) carriers of S. aureus. Among the participants, 17 (89%) carried a single S. aureus spa type intranasally and the other two carried dominant spa types. Less similarity was observed for genes encoded on mobile genetic elements (mecA, scn) and antibiotic resistance profiles. Statistical modeling, based on receiving operating characteristic curves, suggests that three to five isolates may be necessary to accurately assign nasal carriage status for these more variable characteristics. Variability was observed for both persistent and intermediate carriers of S. aureus. These results suggest that surveillance studies that rely on testing one S. aureus isolate are likely to identify predominant spa types but may not fully capture more variable characteristics of S. aureus, including antibiotic resistance. Surveillance studies that rely on testing one isolate may underestimate prevalence of nasal carriage of S. aureus with these more variable characteristics.

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia

Background

Nasal colonization by Staphylococcus aureus is a key risk factor for bacteremia. The objective of this study is to identify genomic modifications occurring in nasal carriage strains of S. aureus as they progress to bacteremia in a cohort of hospitalized patients.

Methods

Eight patients with S. aureus bacteremia were identified. Genomic sequences of the bloodstream isolates were compared with 57 nasal isolates collected longitudinally prior to the occurrence of bacteremia, which covered a timespan of up to 326 days before bacteremia.

Results

Within each subject, nasal colonizing strains were closely related to bacteremia strains. Within a subject, the number of single nucleotide polymorphisms (SNPs) observed between time points was greater than within a single time point. Co-colonization and strain replacement were observed in one case. In all cases colonization progressed to bacteremia without addition of new virulence genes. In one case, a mutation in the accessory gene regulator gene caused abrogation of agr function.

Conclusion

S. aureus evolves in the human nares at a variable rate. Progression of S. aureus nasal colonization to nosocomial infection is seldom associated with acquisition of new virulence determinants. Mutation in the agr gene with abrogation of function was associated with progression to bacteremia in one case.

Staphylococcus aureus in Some Brazilian Dairy Industries: Changes of Contamination and Diversity

Staphylococcus aureus, a major food-poisoning pathogen, is a common contaminant in dairy industries worldwide, including in Brazil. We determined the occurrence of S. aureus in five dairies in Brazil over 8 months. Of 421 samples, 31 (7.4%) were positive for S. aureus and prevalence varied from 0 to 63.3% between dairies. Sixty-six isolates from the 31 samples were typed by Multi-Locus Sequence Typing to determine if these isolates were persistent or continuously reintroduced. Seven known sequence types (STs), ST1, ST5, ST30, ST97, ST126, ST188 and ST398, and four new ST were identified, ST3531, ST3540, ST3562 and ST3534. Clonal complex (CC) 1 (including the four new ST), known as an epidemic clone, was the dominant CC. However, there were no indications of persistence of particular ST. The resistance toward 11 antibiotic compounds was assessed. Twelve profiles were generated with 75.8% of strains being sensitive to all antibiotic classes and no Methicillin-resistant S. aureus (MRSA) strains were found. The enterotoxin-encoding genes involved in food-poisoning, e.g., sea, sed, see, and seg were targeted by PCR. The two toxin-encoding genes, sed and see, were not detected. Only three strains (4.5%) harbored seg and two of these also harbored sea. Despite the isolates being Methicillin-sensitive S. aureus (MSSA), the presence of CC1 clones in the processing environment, including some harboring enterotoxin encoding genes, is of concern and hygiene must have high priority to reduce contamination.

Longitudinal study of Staphylococcus aureus colonization and infection in a cohort of swine veterinarians in the United States

Background

People working with pigs are at elevated risk of harboring methicillin resistant S. aureus (MRSA) in their nose, which is attributable to occupational exposure to animals harboring livestock adapted S. aureus. To obtain insight into the biological nature of occupationally related nasal culture positivity, we conducted a longitudinal study of 66 swine veterinarians in the USA.

Methods

The study cohort resided in 15 US states and worked predominantly with swine. Monthly for 18 months, participants self-collected nasal swabs and completed a survey to report recent exposure to pigs and other animals; the occurrence of work related injuries; and any relevant health events such as skin and soft tissue infections or confirmed staphylococcal infections. Nasal swabs were cultured using selective methods to determine the presence of MRSA and methicillin susceptible S. aureus (MSSA), and isolates were characterized by spa typing and MLST.

Results

Prevalences of S. aureus (64%, monthly range from 58 to 82%) and MRSA (9.5%; monthly range from 6 to15%) were higher than reported for the US population (30% and 1.5% respectively). Predominant spa types were t034 (ST398, 37%), t002 (ST5, 17%) and t337 (ST9/ST398 13%), a distribution similar to that found in a concurrent study in pigs in the USA. Veterinarians were classified into three groups: Persistent carriers (PC, 52%), Intermittent carriers (IC, 47%) and Non-carriers (NC, 1%). Persistent carriage of a single spa type was observed in 14 (21%) of participants, and paired (first and last) isolates from PC subjects had minor genetic differences. Swabs from PC veterinarians carried higher numbers of S. aureus. Among IC veterinarians, culture positivity was significantly associated with recent contact with pigs.

Conclusions

Exposure to pigs did not lead to prolonged colonization in most subjects, and the higher numbers of S. aureus in PC subjects suggests that unknown host factors may determine the likelihood of prolonged colonization by S. aureus of livestock origin. Exposure to S. aureus and persistent colonization of swine veterinarians was common but rarely associated with S. aureus disease.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2802-1) contains supplementary material, which is available to authorized users.

The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare

Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. A characteristic of atopic eczema (AE) is colonization by S. aureus, with exacerbations associated with an increased bacterial burden of the organism. Despite this, the origins and genetic diversity of S. aureus colonizing individual patients during AE disease flares is poorly understood. To examine the microevolution of S. aureus colonization, we deep sequenced S. aureus populations from nine children with moderate to severe AE and 18 non-atopic children asymptomatically carrying S. aureus nasally. Colonization by clonal S. aureus populations was observed in both AE patients and control participants, with all but one of the individuals carrying colonies belonging to a single sequence type. Phylogenetic analysis showed that disease flares were associated with the clonal expansion of the S. aureus population, occurring over a period of weeks to months. There was a significant difference in the genetic backgrounds of S. aureus colonizing AE cases versus controls (Fisher exact test, P = 0.03). Examination of intra-host genetic heterogeneity of the colonizing S. aureus populations identified evidence of within-host selection in the AE patients, with AE variants being potentially selectively advantageous for intracellular persistence and treatment resistance.

Healthy Bovines as Reservoirs of Major Pathogenic Lineages of Staphylococcus aureus in Portugal

The nosocomial prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Portugal is close to 50% and remains one of the highest in Europe. MRSA reservoirs in the animal setting in Portugal have been very poorly investigated, namely among animal husbandry. A total of 52 samples (nasal, inguinal region, and milk) were obtained from bovine animals and analyzed for the presence of S. aureus. The isolates were characterized by pulsed-field gel electrophoresis (PFGE), spa typing, SCCmec typing, and multilocus sequence typing and tested for antimicrobial susceptibility, presence of mecA and mecC genes, and virulence determinants. Overall, 54% of the screened animals were colonized with S. aureus in at least one body site. Notably, S. aureus nasal carriage followed an increasing trend with animal age (p = 0.0006). None of the isolates harbored the mecA or mecC genes. Resistance to penicillin, rifampicin, and tetracycline was observed in 24%, 18%, and 6% of the isolates, respectively. The isolates were distributed into three clonal lineages: PFGE type A, spa type t1166, ST1247-CC133 (43%), PFGE B-t267-ST352-CC97 (30%), and PFGE C-t091-ST7-CC7 (27%). CC133 was associated to older animals (p = 0.0025), whereas CC97 was isolated from calves (p = 0.0016). Virulence determinants commonly found in mastitis were widely detected in carriage isolates: lukDE and hlgv (100%), hlb (76%), and lukM (35%). Although healthy bovines do not represent a MRSA reservoir in Portugal, they are mainly colonized with S. aureus pathogenic lineages associated to mastitis in cattle (CC97 and CC133).

Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation

Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for Staphylococcus aureus, the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this study, we hypothesized the converse, namely, that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analyzed WGS data from 20 historical outbreaks and applied phylogenetic methods to assess genetic relatedness and to estimate the time to most recent common ancestor (TMRCA). The findings were compared with the routine investigation results and epidemiological evidence. Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% highest posterior density interval [HPD], 143 to 343 days) compared with 55 days (95% HPD, 28 to 81 days) for outbreaks lacking epidemiological evidence for an LTC (P = 0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1. We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles; however, these had only modestly increased pairwise diversity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) compared with isolates with identical antibiograms (12.7 SNVs [95% CI, 12.5 to 12.8]) (P < 0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates that were genetically distinct despite having the outbreak pulsed-field gel electrophoresis (PFGE) pulsotype. The duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g., in health care workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.

Skin infection caused by a novel strain of Staphylococcus pseudintermedius in a Siberian husky dog owner

Introduction.Staphylococcus pseudintermedius, an opportunistic pathogen of dogs and cats, is rarely reported to cause infection in humans. Here, we describe a case of severe skin infection caused by S. pseudintermedius, in a 47-year-old male, a dog owner; to the best of our knowledge, this is the first such case reported from Scotland.

Case presentation. The patient presented with a short history of a severe ecthyma-like lesion on his forehead, with smaller lesions on his abdomen and legs. Bacterial culture revealed Clostridium perfringens, thought to be colonizing the wound, and a Staphylococcus species, identified as S. pseudintermedius by matrix-assisted laser desorption/ionization-time of flight MS and confirmed by molecular methods using a PCR-RFLP approach. The patient was treated with flucloxacillin, penicillin V and Fucibet cream, and recovered fully. Zoonotic infection was considered likely; however, screening swabs from his dogs grew S. pseudintermedius of a different clonal type. Both patient and dog strains carried Staphylococcus intermedius exfoliative toxin and leucocidin I, closely related to Panton–Valentine leucocidin, possibly contributing to the severity of the infection. S pseudintermedius, although coagulase positive, is normally negative by rapid slide clumping and latex agglutination tests routinely used to identify Staphylococcus aureus. Hence, S. pseudintermedius may easily be misidentified as a coagulase-negative staphylococcus and considered insignificant.

Conclusion. This is, to the best of our knowledge, the first reported case of a human S. pseudintermedius infection in Scotland. Zoonotic transmission of S. pseudintermedius between pets and owners has been shown. However, in this case zoonosis could not be confirmed.

Multi-site and nasal swabbing for carriage of Staphylococcus aureus: what does a single nose swab predict?

Background

Carriage of Staphylococcus aureus is a risk for infections. Targeted decolonization reduces postoperative infections but depends on accurate screening.

Aim

To compare detection of S. aureus carriage in healthy individuals between anatomical sites and nurse- versus self-swabbing; also to determine whether a single nasal swab predicted carriage over four weeks.

Methods

Healthy individuals were recruited via general practices. After consent, nurses performed multi-site swabbing (nose, throat, and axilla). Participants performed nasal swabbing twice-weekly for four weeks. Swabs were returned by mail and cultured for S. aureus. All S. aureus isolates underwent spa typing. Persistent carriage in individuals returning more than three self-swabs was defined as culture of S. aureus from all or all but one self-swabs.

Findings

In all, 102 individuals underwent multi-site swabbing; S. aureus carriage was detected from at least one site from 40 individuals (39%). There was no difference between nose (29/102, 28%) and throat (28/102, 27%) isolation rates: the combination increased total detection rate by 10%. Ninety-nine patients returned any self-swab, and 96 returned more than three. Nasal carriage detection was not significantly different on nurse or self-swab [28/99 (74%) vs 26/99 (72%); χ²: P = 0.75]. Twenty-two out of 25 participants with first self-swab positive were persistent carriers and 69/71 with first self-swab negative were not, giving high positive predictive value (88%), and very high negative predictive value (97%).

Conclusion

Nasal swabs detected the majority of carriage; throat swabs increased detection by 10%. Self-taken nasal swabs were equivalent to nurse-taken swabs and predicted persistent nasal carriage over four weeks.

Staphylococcus aureus from the German general population is highly diverse

OBJECTIVES

This prospective cohort study evaluates colonization dynamics and molecular characteristics of methicillin-susceptible and - resistant Staphylococcus aureus (MSSA/MRSA) in a German general population.

METHODS

Nasal swabs of 1878 non-hospitalized adults were screened for S. aureus. Participants were screened thrice in intervals of 6-8 months. Isolates were characterized by spa and agr typing, mecA and mecC possession, respectively, and PCRs targeting virulence factors.

RESULTS

40.9% of all participants carried S. aureus at least once while 0.7% of the participants carried MRSA (mainly spa t011). MSSA isolates (n=1359) were associated with 331 different spa types; t084 (7.7%), t091 (6.1%) and t012 (71, 5.2%) were predominant. Of 206 participants carrying S. aureus at all three sampling time points, 14.1% carried the same spa type continuously; 5.3% carried different spa types with similar repeat patterns, but 80.6% carried S. aureus with unrelated spa types. MSSA isolates frequently harboured genes encoding enterotoxins (sec: 16.6%, seg: 63.1%, sei: 64.5%) and toxic shock syndrome toxin (tst: 17.5%), but rarely Panton-Valentine leukocidin (lukS-PV/lukF-PV: 0.2%).

CONCLUSIONS

MSSA colonizing human nares in the community are clonally highly diverse. Among those constantly carrying S. aureus, clonal lineages changed over time. The proportion of persistent S. aureus carriers was lower than reported elsewhere.

Validation of self-administered nasal swabs and postage for the isolation of Staphylococcus aureus

Staphylococcus aureus carriers are at higher risk of S. aureus infection and are a reservoir for transmission to others. Detection of nasal S. aureus carriage is important for both targeted decolonization and epidemiological studies. Self-administered nasal swabbing has been reported previously, but the effects of posting swabs prior to culture on S. aureus yield have not been investigated. A longitudinal cohort study was performed in which healthy volunteers were recruited, trained in the swabbing procedure and asked to take weekly nasal swabs for 6 weeks (median: 3 weeks, range 1–6 weeks). Two swabs were taken at each sampling episode and randomly assigned for immediate processing on arrival to the laboratory (Swab A) or second class postage prior to processing (Swab B). S. aureus was isolated using standard methods. A total of 95 participants were recruited, who took 944 swabs (472 pairs) over a median of 5 weeks. Of these, 459 swabs were positive for S. aureus. We found no significant difference (P=0.25) between 472 pairs of nasal self-swabs processed immediately or following standard postage from 95 study participants (51.4 % vs. 48.6 %, respectively). We also provide further evidence that persistent carriers can be detected by two weekly swabs with high degrees of sensitivity [92.3 % (95 % CI 74.8–98.8 %)] and specificity [95.6 % (95 % CI 84.8–99.3 %)] compared with a gold standard of five weekly swabs. Self-swabbing and postage of nasal swabs prior to processing has no effect on yield of S. aureus, and could facilitate large community-based carriage studies.

Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks

Background

Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF.

Methods

Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners).

Results

We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission.

Conclusions

These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0353-5) contains supplementary material, which is available to authorized users.

Persistence, Discordance and Diversity of Staphylococcus aureus Nasal and Oropharyngeal Colonization in School-aged Children

BACKGROUND

The anterior nares are regarded as the primary site for Staphylococcus aureus colonization, although studies have highlighted the potential importance of colonization at extra-nasal sites, including the oropharynx. Accordingly, the aims of this study were to assess the prevalence, persistence and molecular epidemiology of S. aureus colonization in the nares and oropharynx of Māori and Pacific children, a population with strikingly high rates of S. aureus infection.

METHODS

A cross-sectional study of predominantly Māori and Pacific school-aged children in Auckland, New Zealand was performed in October 2013, and swabs were taken from the nares and oropharynx. Sampling was repeated from the same schools in October 2014. All S. aureus isolates underwent antimicrobial susceptibility testing and spa typing.

RESULTS

Overall, 506/893 (56.7%) children were colonized with S. aureus, and the colonization prevalence was significantly higher in the oropharynx than nares (41.1% vs. 31.5%; P < 0.001). Longitudinal colonization was significantly higher in the oropharynx than the nares, and children with longitudinal oropharyngeal colonization were more likely to be colonized with the same spa type than those colonized in the nares (67.6% vs. 37.0%; P = 0.01). Approximately 40% of children had discordant spa types at the nares and oropharynx.

CONCLUSIONS

Oropharyngeal S. aureus colonization represents a significant reservoir of S. aureus and it is possible that the oropharynx may represent a protected anatomical niche, enabling persistent colonization with the same S. aureus strain. Future study should attempt to better understand the determinants of oropharyngeal carriage.

Intermittent nasal carriage with Staphylococcus aureus within a menstrual cycle: Results from a prospective cohort of healthy carriers

Female sex hormones have been related to nasal Staphylococcus aureus carriage in healthy individuals; however, whether nasal staphylococcal carriage varies by menstrual cycle phase remains unknown.We sampled anterior nares of female healthcare workers twice per week for 6 consecutive menstrual cycles. We used mixed-effects Poisson regression models to determine whether intermittent carriage was associated with cycle phases in a given individual. We also performed recurrent event survival analysis to identify host factors linked to incident carriage status.Overall, we collected 754 nasal swabs over 89 consecutive person-cycles from 14 intermittent carriers. In 84 ovulation-defined menstrual cycles (715 swabs), the period prevalence of staphylococcal carriage was 58.7%, 63.1%, and 64.9% in the follicular, periovulatory, and luteal phases, respectively; these differences were not statistically significant after multivariable adjustment and correction for within-person correlation (adjusted relative risk [RR]-periovulatory 0.92, P: 0.30; luteal 1.00, P: 0.98).Using survival analysis, we identified several host factors that were associated with incident loss, gain of colonization, or both. For example, as compared to women aged 20 to 30 years, those aged 30 to 40 years were less likely to losing carriage (hazard ratio [HR]: 0.26, 95% confidence interval [CI]: 0.09, 0.80) but were as likely to regaining carriage (HR: 0.53, 95% CI: 0.21, 1.34). In comparison, being underweight (body mass index [BMI] <18.5) was significantly associated with a higher risk for regaining (HR: 1.95, 95% CI: 1.34, 1.51) and losing (HR: 1.57, 95% CI: 1.16, 2.12) colonization, indicating the alternating tendency for status changes. Personal hygiene behaviors, such as nostril cleansing habit and methods, differentially affected carriers' risk for losing or regaining staphylococcal colonization.Using an intensive sampling scheme, we found that nasal staphylococcal carriage could vary substantially over time in healthy carriers. Yet, such dynamic intraperson changes in carriage status did not depend on menstrual cycle phases but were associated with host age, BMI, and personal hygiene behavior.

Within-host evolution of bacterial pathogens

Whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in an infected host--in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens--has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatability of evolution. In this Review, we describe how these studies have advanced our understanding of the mechanisms and principles of within-host genome evolution, and we consider the consequences of findings such as a potent adaptive potential for pathogenicity. Finally, we discuss the possibility that genomics may be used in the future to predict the clinical progression of bacterial infections and to suggest the best option for treatment.

Co-colonization and clonal diversity of methicillin-sensitive and methicillin-resistant Staphylococcus aureus in sows

Methicillin-susceptible Staphylococcus (S.) aureus (MSSA) and methicillin-resistant S. aureus (MRSA) are colonizers of skin and mucosa. In humans, MSSA and MRSA compete for colonization space in the anterior nares of pig farmers; however, it was also shown that MSSA/MRSA co-colonization is common and one clone can be found rather than differing types of MSSA and MRSA. We investigated the colonization and clonality of both, MSSA and MRSA in pigs over a longer time. Eighteen sows were nasally sampled three times every ten weeks. Additionally, environmental samples were taken. Samples were investigated for MSSA and MRSA, respectively. The spa type was defined from up to five MRSA and MSSA isolates found per sample and sampling time; selected isolates were further investigated by microarray. Three sows (16.7%) were completely negative for MSSA and MRSA. Twelve pigs (66.7%) were irregularly positive for both, MSSA and MRSA over the time, whereas seven out of them (38.9%) were simultaneously colonized. CC398 (t034, t011) MRSA and CC9 (t337, t1430, and t13816) MSSA associated spa types were exclusively found. In 44.4% (n=8) of sows up to two different types of MSSA were present at the same time and sample. Strains of the same clonal lineage showed a high genetic identity despite their origin. Highly identic clones were present in sows and their environment. As conclusion, MSSA/MRSA may not exclude each other in the anterior nares of pigs. Pigs may also carry different clones at the same time.

Epidemiology of Staphylococcus aureus Nasal Carriage Patterns in the Community

Staphylococcus aureus (S. aureus) is a Gram-positive opportunistic pathogen that colonizes frequently and asymptomatically the anterior nares of humans and animals. It can cause different kinds of infections and is considered to be an important nosocomial pathogen. Nasal carriage of S. aureus can be permanent or intermittent and may build the reservoir for autogenous infections and cross-transmission to other individuals. Most of the studies on the epidemiology of S. aureus performed in the past were focused on the emergence and dissemination of methicillin-resistant Staphylococcus aureus (MRSA) in healthcare settings. There are, however, a number of more recent epidemiological studies have aimed at analysing carriage patterns over time in the community settings providing new insights on risk factors for colonization and important data for the development of strategies to prevent infections. This chapter aims to give a review of current epidemiological studies on S. aureus carriage patterns in the general community and put them into perspective with recent, yet unpublished, investigations on the S. aureus epidemiology in the general population in northern Germany.

The turnover of strains in intermittent and persistent nasal carriers of Staphylococcus aureus

OBJECTIVES

We aimed to examine the dynamics of Staphylococcus aureus nasal carriage in healthy adults.

METHOD

Selected S. aureus strains isolated from weekly nasal swabs obtained from 122 healthy young adults over a 13 week period were spa typed.

RESULTS

The median duration of intermittent carriage was 4 weeks (IQR 2-6) and the median interval between episodes of carriage of different spa types was 3.5 weeks (IQR 2.25-4). 6/19 (32%) Persistent carriers were colonised with more than one spa type during the study, and in two persistent carriers a brief period of mixed colonisation with two spa types was observed. Even when the carriage strain changed, it was very rare for persistent carriers to have a period during which they were culture-negative (only 6/188 (3%) swabs submitted by persistent carriers failed to culture S. aureus).

CONCLUSIONS

Our results imply that at least every eight weeks a healthy young adult is exposed to S. aureus sufficient to cause a new episode of carriage among intermittent carriers. Persistent carriers are almost always colonised with S. aureus and over the course of a year there will be at least one replacement of the dominant strain.

Within-host diversity of MRSA antimicrobial resistances

OBJECTIVES

MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and potential mechanisms of resistance gene transfer in vivo.

METHODS

Nasal swabs from 38 MRSA carriers admitted to hospital were plated and 20 individual colonies from each patient tested for phenotypic antibiotic susceptibility and genetically for lineage, carriage of four prophages and three plasmid families. Free bacteriophages were detected in swabs as well as their capacity for transducing resistance genes.

RESULTS

Nine (24%) patients carried phenotypic AMR variants and 24 (63%) carried prophage and plasmid variants. If a single colony was selected for testing, the probability of detecting all AMR in that patient was 87%. Sixty-four different AMR and mobile genetic element (MGE) profiles were detected, mostly in the MRSA CC22 background (where CC stands for clonal complex), with up to 8 profiles per patient. Nearly half of the patients carried detectable free bacteriophages and phages successfully transduced resistance genes between laboratory and patient isolates in vitro. WGS showed MRSA core genomes were stable, while AMR and MGEs varied.

CONCLUSIONS

'Clouds' of MRSA variants that have acquired or lost AMR and MGEs are common in nasal colonizing populations and bacteriophages may play an important role in gene transfer. Accurate estimation of AMR and genetic variability has implications for diagnostics, epidemiology, antimicrobial stewardship and understanding the evolutionary selection of AMR in colonizing populations.

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

Genome sequencing is revolutionizing clinical microbiology and our understanding of infectious diseases. Previous studies have largely relied on the sequencing of a single isolate from each individual. However, it is not clear what degree of bacterial diversity exists within, and is transmitted between individuals. Understanding this ‘cloud of diversity’ is key to accurate identification of transmission pathways. Here, we report the deep sequencing of methicillin-resistant Staphylococcus aureus among staff and animal patients involved in a transmission network at a veterinary hospital. We demonstrate considerable within-host diversity and that within-host diversity may rise and fall over time. Isolates from invasive disease contained multiple mutations in the same genes, including inactivation of a global regulator of virulence and changes in phage copy number. This study highlights the need for sequencing of multiple isolates from individuals to gain an accurate picture of transmission networks and to further understand the basis of pathogenesis.

Populations of bacterial pathogens can be diverse within colonized individuals. Here, the authors sequence the genomes of methicillin-resistant Staphylococcus aureus isolated from staff and animal patients at a veterinary hospital and show considerable within-host diversity that can rise and fall over time.

Improved protocol for rapid identification of certain spa types using high resolution melting curve analysis

Methicillin-resistant Staphylococcus aureus is one of the most significant pathogens associated with health care. For efficient surveillance, control and outbreak investigation, S. aureus typing is essential. A high resolution melting curve analysis was developed and evaluated for rapid identification of the most frequent spa types found in an Austrian hospital consortium covering 2,435 beds. Among 557 methicillin-resistant Staphylococcus aureus isolates 38 different spa types were identified by sequence analysis of the hypervariable region X of the protein A gene (spa). Identification of spa types through their characteristic high resolution melting curve profiles was considerably improved by double spiking with genomic DNA from spa type t030 and spa type t003 and allowed unambiguous and fast identification of the ten most frequent spa types t001 (58%), t003 (12%), t190 (9%), t041 (5%), t022 (2%), t032 (2%), t008 (2%), t002 (1%), t5712 (1%) and t2203 (1%), representing 93% of all isolates within this hospital consortium. The performance of the assay was evaluated by testing samples with unknown spa types from the daily routine and by testing three different high resolution melting curve analysis real-time PCR instruments. The ten most frequent spa types were identified from all samples and on all instruments with 100% specificity and 100% sensitivity. Compared to classical spa typing by sequence analysis, this gene scanning assay is faster, cheaper and can be performed in a single closed tube assay format. Therefore it is an optimal screening tool to detect the most frequent endemic spa types and to exclude non-endemic spa types within a hospital.

Bacterial Strain Diversity Within Wounds

Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.

Ensuring backwards compatibility: traditional genotyping efforts in the era of whole genome sequencing

When using next-generation whole genome sequencing (WGS), extraction of spa types from WGS data is essential for backwards compatibility with Sanger sequencing-based spa typing of methicillin-resistant Staphylococcus aureus (MRSA). We evaluated WGS-based spa typing with a 2×250 bp protocol in a diverse collection of 423 MRSA isolates using two pipelines that executed sequence quality-trimming and de novo assembly before spa typing. The SeqSphere(+) pipeline correctly typed 419 isolates (99.1%) whereas the CLCbio pipeline succeeded in 249 isolates (58.9%). In summary, WGS combined with an optimized de novo assembly enables nearly full compatibility with Sanger sequencing-based spa typing data.

Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition

Antibiotic resistance is a key medical concern, with antibiotic use likely being an important cause. However, here we describe an alternative route to clinically relevant antibiotic resistance that occurs solely due to competitive interactions among bacterial cells. We consistently observe that isolates of Methicillin-resistant Staphylococcus aureus diversify spontaneously into two distinct, sequentially arising strains. The first evolved strain outgrows the parent strain via secretion of surfactants and a toxic bacteriocin. The second is resistant to the bacteriocin. Importantly, this second strain is also resistant to intermediate levels of vancomycin. This so-called VISA (vancomycin-intermediate S. aureus) phenotype is seen in many hard-to-treat clinical isolates. This strain diversification also occurs during in vivo infection in a mouse model, which is consistent with the fact that both coevolved phenotypes resemble strains commonly found in clinic. Our study shows how competition between coevolving bacterial strains can generate antibiotic resistance and recapitulate key clinical phenotypes.

Prevalence of Staphylococcus aureus protein A (spa) mutants in the community and hospitals in Oxfordshire

Background

Staphylococcal protein A (spa) is an important virulence factor which enables Staphylococcus aureus to evade host immune responses. Genotypes known as “spa-types”, based on highly variable Xr region sequences of the spa-gene, are frequently used to classify strains. A weakness of current spa-typing primers is that rearrangements in the IgG-binding region of the gene cause 1-2% of strains to be designated as “non-typeable”.

Results

We developed an improved primer which enabled sequencing of all strains, containing any type of genetic rearrangement, in a large study among community carriers and hospital inpatients in Oxfordshire, UK (6110 isolates). We identified eight novel spa-gene variants, plus one previously described. Three of these rearrangements would be designated “non-typeable” using current spa-typing methods; they occurred in 1.8% (72/3905) asymptomatically carried and 0.6% (14/2205) inpatient S. aureus strains. Some individuals were simultaneously colonized by both formerly non-typeable and typeable strains; previously such patients would have been identified as carrying only currently typeable strains, underestimating mixed carriage prevalence and diversity. Formerly non-typeable strains were found in more spa-types associated with multilocus sequence type ST398 (35%), common among livestock, compared to other groups with any non-typeable strains (1-4%), suggesting particular spa-types may have been under-represented in previous human studies.

Conclusions

This improved method allows us to spa-type previously non-typeable strains with rearrangements in the spa-gene and to resolve cases of mixed colonization with deletions in one or more strains, thus accounting for hidden diversity of S. aureus in both community and hospital environments.