Improved Genomic Prediction of Staphylococcus epidermidis Isolation Sources with a Novel Polygenic Score.

Staphylococcus epidermidis infections can be challenging to diagnose due to the species frequent contamination of clinical specimens and indolent course of infection. Nevertheless, S. epidermidis is the major cause of late-onset sepsis among premature infants and of intravascular infection in all age groups. Prior work has shown that bacterial virulence factors, antimicrobial resistances, and strains have up to 80% in-sample accuracy to distinguish hospital from community sources, but are unable to distinguish true bacteremia from blood culture contamination. Here, a phylogeny-informed genome-wide association study of 88 isolates was used to estimate effect sizes of particular genomic variants for isolation sources. A "polygenic score" was calculated for each isolate as the summed effect sizes of its repertoire of genomic variants. Predictive models of isolation sources based on polygenic scores were tested with in-samples and out-samples from prior studies of different patient populations. Polygenic scores from accessory genes (AGs) distinguished hospital from community sources with the highest accuracy to date, up to 98% for in-samples and 65% to 91% for various out-samples, whereas scores from single nucleotide polymorphisms (SNPs) had lower accuracy. Scores from AGs and SNPs achieved the highest in-sample accuracy to date, up to 76%, in distinguishing infection from contaminant sources within a hospital. Model training and testing data sets with more similar population structures resulted in more accurate predictions. This study reports the first use of a polygenic score for predicting a complex bacterial phenotype and shows the potential of this approach for enhancing S. epidermidis diagnosis.

Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources?

Staphylococcus epidermidis is a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure of S. epidermidis distinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected between fdh-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (icaA, IS256, sesD [bhp], mecA, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital.

Multilocus sequence typing and further genetic characterization of the enigmatic pathogen, Staphylococcus hominis.

Staphylococcus hominis is a commensal resident of human skin and an opportunistic pathogen. The species is subdivided into two subspecies, S. hominis subsp. hominis and S. hominis subsp. novobiosepticus, which are difficult to distinguish. To investigate the evolution and epidemiology of S. hominis, a total of 108 isolates collected from 10 countries over 40 years were characterized by classical phenotypic methods and genetic methods. One nonsynonymous mutation in gyrB, scored with a novel SNP typing assay, had a perfect association with the novobiocin-resistant phenotype. A multilocus sequence typing (MLST) scheme was developed from six housekeeping gene fragments, and revealed relatively high levels of genetic diversity and a significant impact of recombination on S. hominis population structure. Among the 40 sequence types (STs) identified by MLST, three STs (ST2, ST16 and ST23) were S. hominis subsp. novobiosepticus, and they distinguished between isolates from different outbreaks, whereas 37 other STs were S. hominis subsp. hominis, one of which was widely disseminated (ST1). A modified PCR assay was developed to detect the presence of ccrAB4 from the SCCmec genetic element. S. hominis subsp. novobiosepticus isolates were oxacillin-resistant and carriers of specific components of SCCmec (mecA class A, ccrAB3, ccrAB4, ccrC), whereas S. hominis subsp. hominis included both oxacillin-sensitive and -resistant isolates and a more diverse array of SCCmec components. Surprisingly, phylogenetic analyses indicated that S. hominis subsp. novobiosepticus may be a polyphyletic and, hence, artificial taxon. In summary, these results revealed the genetic diversity of S. hominis, the identities of outbreak-causing clones, and the evolutionary relationships between subspecies and clones. The pathogenic lifestyle attributed to S. hominis subsp. novobiosepticus may have originated on more than one occasion.

Thoracic vertebral osteomyelitis with paraspinous mass and intraspinal extension: an atypical presentation of cat-scratch disease.

Children with cat-scratch disease (CSD) commonly present with fever and tender lymphadenopathy. The disease is mild and manifestations of infection resolve spontaneously within several weeks. However, some children with CSD have unusual features that present diagnostic challenges. Children with atypical CSD may present with prolonged fever, hepatosplenic disease or ocular disease. We performed an MRI on a child who presented with persistent back pain. The MRI demonstrated a paravertebral mass with intraspinous extension and the collapse of T7 vertebral body. A biopsy was reported to show a small round blue cell tumor. An evaluation for malignancy was negative, but Bartonella henselae DNA was detected by polymerase chain reaction on the biopsy specimen. We present this case because it is a rare but important radiological presentation of CSD.

Simultaneous carriage of multiple genotypes of Staphylococcus aureus in children.

The co-existence of multiple genotypes in colonization by Staphylococcus aureus has not been fully investigated. The aim of this study was to evaluate the heterogeneity of S. aureus carriage in children. We evaluated 125 nasal and perianal swab samples that were positive for S. aureus from 76 children scheduled for elective surgery. For each sample, at least four colonies with the same or different morphotypes were selected for analysis. Multiple-locus variable-number tandem-repeat fingerprinting was used to determine the genetic relatedness and to characterize the clonality of the S. aureus strains. Of the 125 swabs, 91 (73 %) contained meticillin-sensitive S. aureus (MSSA), 8 (6 %) contained meticillin-resistant S. aureus (MRSA), and 26 (21 %) contained MSSA and MRSA simultaneously. A total of 738 S. aureus strains were evaluated with a mean of 6 colonies (range 4-15) picked from each culture. Of the 125 swabs, 32 (26 %) samples contained two genetically distinct S. aureus strains and 6 (5 %) contained three different genotypes. Multiple S. aureus strains simultaneously carried by individual children were genetically unrelated to each other. We concluded that the co-existence of multiple genotypes of S. aureus was common. The significance of multiple carriage is yet to be determined, but this intraspecies interplay could be important to pathogenicity and virulence in S. aureus.

Molecular surveillance of Staphylococcus aureus colonization in a neonatal intensive care unit.

In a survey of staphylococcal colonization, Staphylococcus aureus was detected in 7 of 67 infants (10%). Two of the infants (3%) carried methicillin-resistant S aureus (MRSA), revealing an unsuspected transmission of MRSA within the neonatal intensive care unit. Molecular surveillance of S aureus provided useful information to improve infection control practices.

Acquisition of high-level mupirocin resistance and its fitness cost among methicillin-resistant Staphylococcus aureus strains with low-level mupirocin resistance.

We investigated whether methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) isolates with low-level mupirocin resistance can serve as recipients of a pSK41-like plasmid conferring high-level mupirocin resistance without substantial fitness cost. Our results suggest that acquisition of the plasmid conferring high-level mupirocin resistance was not necessarily associated with fitness cost in some MRSA recipients with low-level mupirocin resistance.

Epidemiology of community-onset Staphylococcus aureus infections in pediatric patients: an experience at a Children's Hospital in central Illinois.

BACKGROUND: The nation-wide concern over methicillin-resistant Staphylococcus aureus (MRSA) has prompted many clinicians to use vancomycin when approaching patients with suspected staphylococcal infections. We sought to characterize the epidemiology of community-onset S. aureus infections in hospitalized children to assist local clinicians in providing appropriate empiric antimicrobial therapy. METHODS: From January 2005-June 2008, children (0-18 years old) admitted to the Children's Hospital of Illinois with community-onset S. aureus infections were identified by a computer-assisted laboratory-based surveillance and medical record review. RESULTS: Of 199 patients, 67 (34%) had invasive infections, and 132 (66%) had skin and soft tissue infections (SSTIs). Among patients with invasive infections, S. aureus isolates were more likely to be susceptible to methicillin (MSSA 63% vs. MRSA 37%), whereas patients with SSTIs, S. aureus isolates were more likely to be resistant to methicillin (MRSA 64% vs. MSSA 36%). Bacteremia and musculoskeletal infections were the most common invasive infections in both groups of S. aureus. Pneumonia with empyema was more likely to be caused by MRSA (P = 0.02). The majority (approximately 90%) of MRSA isolates were non-multidrug resistant, even in the presence of healthcare-associated risk factors. CONCLUSION: Epidemiological data at the local level is important for antimicrobial decision-making. MSSA remains an important pathogen causing invasive community-onset S. aureus infections among hospitalized children. In our hospital, nafcillin in combination with vancomycin is recommended empiric therapy in critically ill patients with suspected invasive staphylococcal infections. Because up to 25% of MSSA circulating in our area are clindamycin-resistant, clindamycin should be used cautiously as empiric monotherapy in patients with suspected invasive staphylococcal infections.

Level of maternal IgG anti-group B streptococcus type III antibody correlated with protection of neonates against early-onset disease caused by this pathogen.

The present study estimates the level of maternal immunoglobulin (Ig) G anti-group B streptococcus (GBS) type III required to protect neonates against early-onset disease (EOD) caused by this pathogen. Levels of maternal serum IgG anti-GBS type III, measured by enzyme-linked immunosorbent assay, in 26 case patients (neonates with EOD caused by GBS type III) and 143 matched control subjects (neonates colonized by GBS type III who did not develop EOD) of > or = 34 weeks gestation were compared. The probability of EOD decreased with increasing levels of maternal IgG anti-GBS type III (P = .01). Neonates whose mothers had > or = 10 microg/mL IgG anti-GBS type III had a 91% lower risk for EOD, compared with those whose mothers had levels of < 2 microg/mL. A vaccine that induces IgG anti-GBS type III levels of > or = 10 microg/mL in mothers can be predicted to offer a significant degree of protection against EOD caused by this pathogen.

Aortitis in a child with Abiotrophia defectiva endocarditis.

Abiotrophia defectiva, one of several nutritionally variant Streptococcus species, is an uncommon but important cause of endocarditis in children. We describe an unusual case complicated by extensive aortitis with pits in the ascending aorta and the proximal aortic arch.