Kathleen G. Beavis

Community-Associated Methicillin-Resistant Staphylococcus aureus Colonization Burden in HIV-Infected Patients

BACKGROUND The epidemic of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has had a disproportionate impact on patients with human immunodeficiency virus (HIV). METHODS We evaluated CA-MRSA colonization burden (number of colonized sites per total number sampled) among HIV-infected and HIV-negative inpatients within 72 hours of hospitalization. From March 2011 through April 2012, we obtained cultures from nasal and extranasal sites (throat, axilla, inguinal, perirectal, and chronic wound if present) and collected risk factor data. RESULTS Of 745 patients (374 HIV-infected, 371 HIV-negative), 15.7% were colonized with CA-MRSA at any site: 20% of HIV and 11% of HIV-negative patients (relative prevalence=1.8, P=.002). HIV-infected patients had a higher prevalence of nasal, extranasal, and exclusive extranasal colonization as well as higher colonization burden. Perirectal and inguinal areas were the extranasal sites most frequently colonized, and 38.5% of colonized patients had exclusive extranasal colonization. Seventy-three percent of isolates were identified as USA300. Among HIV-infected patients, male sex, younger age, and recent incarceration were positively associated whereas Hispanic ethnicity was negatively associated with higher colonization burden. Among HIV-negative patients, temporary housing (homeless, shelter, or substance abuse center) was the only factor associated with higher colonization burden. Predictors of USA300 included HIV, younger age, illicit drug use, and male sex; all but 1 colonized individual with current or recent incarceration carried USA300. CONCLUSIONS HIV-infected patients were more likely to have a higher CA-MRSA colonization burden and carry USA300. In certain populations, enhanced community and outpatient-based infection control strategies may be needed to prevent CA-MRSA cross-transmission and infection.

Evaluation of FilmArray and Verigene Systems for Rapid Identification of Positive Blood Cultures

ABSTRACT The Verigene tests for Gram-positive and Gram-negative organisms in blood culture and the FilmArray blood culture identification panel were assessed for their ability to identify pathogens from positive blood cultures. Both platforms correctly identified bacteria in 92% of monomicrobial cultures analyzed, with times to identification that were significantly shorter than those for identification from subcultures.

Community-Associated Methicillin-Resistant Staphylococcus aureus Colonization in High-Risk Groups of HIV-Infected Patients

BACKGROUND We examined the epidemiology of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) nasal colonization among 3 groups of human immunodeficiency virus (HIV)-infected and 1 group of HIV-negative outpatients. METHODS We determined prevalence and risk factors associated with MRSA colonization among women, recently incarcerated, and Hispanic HIV-infected patients and HIV-negative patients; isolates were typed by pulsed-field gel electrophoresis. Relative prevalence was calculated using Poisson regression, and logistic regression was used for multivariate analysis. RESULTS Of 601 patients, 9.3% were colonized with MRSA; 11% of HIV-infected and 4.2% of HIV-negative patients were colonized (relative prevalence, 2.6; 95% confidence interval [CI], 1.12-6.07; P = .03). Among HIV-infected patients, recently incarcerated patients had the highest colonization prevalence (15.6%) followed by women (12%); Hispanic patients had the lowest (2.8%). Eighty percent of confirmed MRSA isolates were identified as USA300. On multivariate analysis, history of incarceration or residence in alternative housing (odds ratio [OR], 2.3; 95% CI, 1.1-4.7; P = .03) was associated with MRSA colonization; Hispanic ethnicity was negatively associated (OR, 0.3; 95% CI, .11-.98; P = .045). There was a trend (OR, 1.6; 95% CI, .9-3.0; P = .097) toward geographic location of residence being associated with colonization. After controlling for incarceration, residence, and geography, HIV status was no longer significantly associated with colonization. CONCLUSIONS The CA-MRSA and HIV epidemics have intersected. Examination of networks of individuals released from incarceration, both HIV positive and negative, is needed to assess the role of social networks in spread of CA-MRSA and inform prevention strategies.

Influenza Among Afebrile and Vaccinated Healthcare Workers

Among healthcare workers with influenza, half were afebrile. There was no significant difference in the rate of fever among individuals with influenza who had been previously vaccinated compared with those who had not been vaccinated (55% vs 39%; P = .33).

Rapid Identification of Positive Blood Cultures by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using Prewarmed Agar Plates

ABSTRACT This study describes an inexpensive and straightforward method for identifying bacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) directly from positive blood cultures using prewarmed agar plates. Different inoculation methods and incubation times were evaluated to determine the optimal conditions. The two methods using pelleted material from positive culture bottles performed best. In particular, the pellet streak method correctly identified 94% of the Gram negatives following 4 h of incubation and 98% of the Gram positives following 6 h of incubation.

Comparison of Cepheid Xpert® Flu/RSV XC and BioFire FilmArray® for detection of influenza A, influenza B, and respiratory syncytial virus

ABSTRACT The Xpert Flu/RSV XC was compared to the FilmArray respiratory panel for detection of influenza (Flu) A, Flu B, and respiratory syncytial virus (RSV), using 128 nasopharyngeal swabs. Positive agreements were 100% for Flu A and RSV and 92.3% for Flu B. The Xpert may be useful in clinical situations when extensive testing is not required and may serve an important role in laboratories already performing broader respiratory panel testing.

Use of the Accelerate Pheno System for Identification and Antimicrobial Susceptibility Testing of Pathogens in Positive Blood Cultures and Impact on Time to Results and Workflow

ABSTRACT The Accelerate Pheno system uses automated fluorescence in situ hybridization technology with morphokinetic cellular analysis to provide rapid species identification (ID) and antimicrobial susceptibility testing (AST) results for the most commonly identified organisms in bloodstream infections. The objective was to evaluate the accuracy and workflow of bacterial and yeast ID and bacterial AST using the Accelerate Pheno system in the clinical microbiology laboratory. The consecutive fresh blood cultures received in the laboratory were analyzed by the Accelerate Pheno system within 0 to 8 h of growth detection. ID/AST performance, the average times to results, and workflow were compared to those of the routine standard of care. Of the 232 blood cultures evaluated (223 monomicrobial and 9 polymicrobial) comprising 241 organisms, the overall sensitivity and specificity for the identification of organisms were 95.6% and 99.5%, respectively. For antimicrobial susceptibility, the overall essential agreement was 95.1% and categorical agreement was 95.5% compared to routine methods. There was one very major error and 3 major errors. The time to identification and the time to susceptibility using the Accelerate Pheno system were decreased by 23.47 and 41.86 h, respectively, compared to those for the standard of care. The reduction in hands on time was 25.5 min per culture. The Accelerate Pheno system provides rapid and accurate ID/AST results for most of the organisms found routinely in blood cultures. It is easy to use, reduces hands on time for ID/AST of common blood pathogens, and enables clinically actionable results to be released much earlier than with the current standard of care.

Pseudo-outbreak of Mycobacterium gordonae Following the Opening of a Newly Constructed Hospital at a Chicago Medical Center

OBJECTIVE To identify the source of a pseudo-outbreak of Mycobacterium gordonae DESIGN Outbreak investigation. SETTING University Hospital in Chicago, Ilinois. PATIENTS Hospital patients with M. gordonae-positive clinical cultures. METHODS An increase in isolation of M. gordonae from clinical cultures was noted immediately following the opening of a newly constructed hospital in January 2012. We reviewed medical records of patients with M. gordonae-positive cultures collected between January and December 2012 and cultured potable water specimens in new and old hospitals quantitatively for mycobacteria. RESULTS Of 30 patients with M. gordonae-positive clinical cultures, 25 (83.3%) were housed in the new hospital; of 35 positive specimens (sputum, bronchoalveolar lavage, gastric aspirate), 32 (91.4%) had potential for water contamination. M. gordonae was more common in water collected from the new vs. the old hospital [147 of 157 (93.6%) vs. 91 of 113 (80.5%), P=.001]. Median concentration of M. gordonae was higher in the samples from the new vs. the old hospital (208 vs. 48 colony-forming units (CFU)/mL; P<.001). Prevalence and concentration of M. gordonae were lower in water samples from ice and water dispensers [13 of 28 (46.4%) and 0 CFU/mL] compared with water samples from patient rooms and common areas [225 of 242 (93%) and 146 CFU/mL, P<.001]. CONCLUSIONS M. gordonae was common in potable water. The pseudo-outbreak of M. gordonae was likely due to increased concentrations of M. gordonae in the potable water supply of the new hospital. A silver ion-impregnated 0.5-μm filter may have been responsible for lower concentrations of M. gordonae identified in ice/water dispenser samples. Hospitals should anticipate that construction activities may amplify the presence of waterborne nontuberculous mycobacterial contaminants.

Anatomic sites of colonization with community-associated methicillin-resistant Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) has emerged over the past 20 years as a cause of infections in community populations, so-called community-associated MRSA (CA-MRSA). By pulsed-field gel electrophoresis (PFGE) subtyping, USA300 is the most common CA-MRSA strain in the US. It has been suggested that the colonization dynamics for CA-MRSA may be different than those for traditional MRSA strains1, with extra-nasal colonization potentially playing a role in CA-MRSA transmission and infection1. Another distinguishing characteristic of USA300 MRSA strains is greater susceptibility to non-β-lactam antibiotics compared to healthcare-associated MRSA strains. However, multi-drug resistant (MDR) USA300 strains have been described, largely among HIV-infected patients and men who have sex with men (MSM)2. Also of concern, resistance to common decolonizing agents such as mupirocin2 and chlorhexidine gluconate (CHG)3 has been reported in CA-MRSA. The objectives of this study were to examine the phenotype of USA300 MRSA strains, the prevalence of the qacA/B gene in this population, and the anatomic sites of colonization by PFGE pattern. We previously reported on the prevalence of nasal and extra-nasal CA-MRSA colonization among inpatients (374 HIV-infected and 371 HIV-negative) at Stroger Hospital of Cook County (CCH), the major safety-net hospital in Chicago, IL4. As described elsewhere, nasal and extra-nasal (throat, axilla, inguinal, peri-rectal, and chronic wound if present) surveillance swab specimens were collected from patients within 72 hours of admission from March 2011-April 2012; cultures were processed with broth enrichment4. Gender was recorded and enrolled men were asked if they identified themselves as MSM. Genotypic analysis with PFGE was performed on all identified MRSA isolates. Results were interpreted as described by McDougal, et al5. Confirmed MRSA isolates had antibiotic susceptibility determined (MicroScan Walkaway System, Siemens Healthcare Diagnostics, West Sacramento, CA). For USA300 MRSA strains, MDR was defined as resistance to four or more non-β lactam antibiotic classes. High-level mupirocin resistance was assessed using disk diffusion6. Carriage of qacA and qacB genes, which code for efflux pumps associated with increased minimum inhibitory concentrations (MICs) of CHG7, was assessed using real-time PCR as described previously8. Chi-square analysis was used to examine the association of PFGE patterns and colonization sites, with Fisher’s exact test used for small samples. SAS software version 9.2 (SAS Institute, Cary, NC) was used for statistical analysis. The study was approved by the Institutional Review Board of CCH and Rush University Medical Center. We observed that following the nares, the peri-rectal area was the second most common site of colonization (58% of colonized individuals). Prevalence of extra-nasal and exclusive extra-nasal colonization was not significantly different between patients colonized with USA300 or non-USA300 strains (Table 1). However, the average number of sites colonized was significantly higher for USA300 versus non-USA300 strains [2.8 (SD 1.51) and 2.2 (1.48), respectively, p=0.049]. Inguinal, peri-rectal, and concomitant inguinal and peri-rectal colonization were all significantly associated with colonization with the USA300 strain type in comparison to non-USA300 MRSA strains (Table 1). Inguinal or peri-rectal MRSA colonization was found more often in men (63/480; 13%)—MSM (OR=2.2; 95% CI, 1.1, 4.2; p=0.02) and heterosexual men (OR=1.8; 95% CI, 1.02, 3.2; p=.04)—than in women (20/265; 8%), OR=1.9 (95% CI, 1.1, 3.1), p=0.02. Table 1 Association of Pattern of Anatomic Site of Colonization and Pulsed-Field Gel Electrophoresis Profile among Individuals Colonized with Community-Associated Methicillin-Resistant Staphylococcus aureus There were 5 individuals who had a MRSA infection at the time of enrollment and they were all found to have colonization with MRSA. Four of these individuals had SSTIs and were colonized with the USA300 strain type and one individual had a bloodstream infection and was colonized with a non-USA300 strain type. Excluding chronic wound cultures, each of these individuals had 3–5 sites of MRSA colonization, suggesting a significant level of extra-nasal colonization and colonization burden for individuals infected with MRSA. 3.4% of colonized individuals carried high-level mupirocin-resistant strains (1 USA100, 2 USA500, 1 USA300). Of the individuals colonized with USA300 MRSA strains, 4 (5%) carried MDR strains. There were 117 MRSA isolates evaluated for the presence of the qacA/B genes; all were negative. We examined colonization and molecular characteristics of CA-MRSA isolates collected from patients seeking care at the major safety-net hospital in Chicago. We found that inguinal and peri-rectal colonization was more common with the USA300 strain type than with non-USA300 MRSA strains. In addition, highly antibiotic resistant USA300 MRSA strains were rare and none of the MRSA isolates collected over a 14 month study period was found to harbor the qacA/B genes. We observed that males—both heterosexual males and MSM—had a higher prevalence of inguinal and peri-rectal MRSA colonization in comparison to females. Similarities observed in colonization patterns between MSM and heterosexual males suggest that perhaps social, hormonal, skin biology, or genetic differences between genders play a role in colonization dynamics rather than sexual orientation9. The absence of qacA/B genes among MRSA isolates in the population we studied is consistent with other reports in the US10. In contrast to reports in San Francisco2, MDR USA300 strains were relatively rare in our population, which comprised a diverse group of HIV-infected and HIV-negative individuals. However, continued surveillance of antibiotic resistance patterns is needed to understand the evolving epidemiology of USA300 strains as well as to inform empiric therapeutic decisions. Our study is limited in that we did not assess frequency of mupirocin or CHG use in our population, although CCH does not have mupirocin on its antibiotic formulary and CHG bathing use has been limited to ICU and pre-operative patients. In addition, we relied on self-report of MSM status which could lead to recall bias. Finally, we performed PFGE on one MRSA colony morphotype per body site and therefore may have failed to detect coexistent minority subpopulations. In summary, our study highlights that inguinal and peri-rectal colonization appears to be more frequent with the USA300 strain type and that gender may play a role in location of extra-nasal CA-MRSA colonization. Patients with clinical MRSA infections appeared to be those with more sites of MRSA colonization. Although mupirocin resistance and presence of qacA/B were uncommon, continued monitoring of MRSA prevalence and resistance is warranted.

BioFire FilmArray Respiratory Panel for Detection of Enterovirus D68

ABSTRACT During the enterovirus D68 (EV-D68) outbreak of 2014, the BioFire FilmArray (FA) respiratory panel was used to detect rhinovirus/enterovirus in respiratory specimens; suspected EV-D68-positive specimens were sent to CDC for confirmation. Positive rhinovirus/enterovirus FA targets revealed patterns loosely associated with EV-D68 that may be useful for confirmation triaging.