Annual estimates of the influenza disease burden provide information to evaluate programs and allocate resources. We used a multiplier method with routine population-based surveillance data on influenza hospitalization in the United States to correct for under-reporting and estimate the burden of influenza for seasons after the 2009 pandemic. Five sites of the Influenza Hospitalization Surveillance Network (FluSurv-NET) collected data on the frequency and sensitivity of influenza testing during two seasons to estimate under-detection. Population-based rates of influenza-associated hospitalization and Intensive Care Unit admission from 2010–2013 were extrapolated to the U.S. population from FluSurv-NET and corrected for under-detection. Influenza deaths were calculated using a ratio of deaths to hospitalizations. We estimated that influenza-related hospitalizations were under-detected during 2010-11 by a factor of 2.1 (95%CI 1.7–2.9) for age < 18 years, 3.1 (2.4–4.5) for ages 18-64 years, and 5.2 (95%CI 3.8–8.3) for age 65+. Results were similar in 2011-12. Extrapolated estimates for 3 seasons from 2010–2013 included: 114,192–624,435 hospitalizations, 18,491–95,390 ICU admissions, and 4,915–27,174 deaths per year; 54–70% of hospitalizations and 71–85% of deaths occurred among adults aged 65+. Influenza causes a substantial disease burden in the U.S. that varies by age and season. Periodic estimation of multipliers across multiple sites and age groups improves our understanding of influenza detection in sentinel surveillance systems. Adjusting surveillance data using a multiplier method is a relatively simple means to estimate the impact of influenza and the subsequent value of interventions to prevent influenza.

Estimating the US burden of methicillin-resistant Staphylococcus aureus (MRSA) infections is important for planning and tracking success of prevention strategies. OBJECTIVE To describe updated national estimates and characteristics of health care-and community-associated invasive methicillin-resistant Staphylococcus aureus (MRSA) infections in 2011. DESIGN, SETTING, AND PARTICIPANTS Active laboratory-based case finding identified MRSA cultures in 9 US metropolitan areas from 2005 through 2011. Invasive infections (MRSA cultured from normally sterile body sites) were classified as health care-associated community-onset (HACO) infections (cultured Յ3 days after admission and/or prior year dialysis, hospitalization, surgery, long-term care residence, or central vascular catheter presence Յ2 days before culture); hospital-onset infections (cultured >3 days after admission); or community-associated infections if no other criteria were met. National estimates were adjusted using US census and US Renal Data System data. MAIN OUTCOMES AND MEASURES National estimates of invasive HACO, hospital-onset, and community-associated MRSA infections using US census and US Renal Data System data as the denominator. RESULTS An estimated 80 461 (95% CI, 69 515-93 914) invasive MRSA infections occurred nationally in 2011. Of these, 48 353 (95% CI, 40 195-58 642) were HACO infections; 14 156 (95% CI, 10 096-20 440) were hospital-onset infections; and 16 560 (95% CI, 12 806-21 811) were community-associated infections. Since 2005, adjusted national estimated incidence rates decreased among HACO infections by 27.7% and hospital-onset infections decreased by 54.2%; community-associated infections decreased by only 5.0%. Among recently hospitalized community-onset (nondialysis) infections, 64% occurred 3 months or less after discharge, and 32% of these were admitted from long-term care facilities. CONCLUSIONS AND RELEVANCE An estimated 30 800 fewer invasive MRSA infections occurred in the United States in 2011 compared with 2005; in 2011 fewer infections occurred among patients during hospitalization than among persons in the community without recent health care exposures. Effective strategies for preventing infections outside acute care settings will have the greatest impact on further reducing invasive MRSA infections nationally.

Background Invasive group A Streptococcus (GAS) infections are associated with significant morbidity and mortality rates. We report the epidemiology and trends of invasive GAS over 8 years of surveillance. Methods From January 2005 through December 2012, we collected data from the Centers for Disease Control and Prevention’s Active Bacterial Core surveillance, a population-based network of 10 geographically diverse US sites (2012 population, 32.8 million). We defined invasive GAS as isolation of GAS from a normally sterile site or from a wound in a patient with necrotizing fasciitis (NF) or streptococcal toxic shock syndrome (STSS). Available isolates were emm typed. We calculated rates and made age- and race-adjusted national projections using census data. Results We identified 9557 cases (3.8 cases per 100 000 persons per year) with 1116 deaths (case-fatality rate, 11.7%). The case-fatality rates for septic shock, STSS, and NF were 45%, 38%, and 29%, respectively. The annual incidence was highest among persons aged ≥65 years (9.4/100 000) or <1 year (5.3) and among blacks (4.7/100 000). National rates remained steady over 8 years of surveillance. Factors independently associated with death included increasing age, residence in a nursing home, recent surgery, septic shock, NF, meningitis, isolated bacteremia, pneumonia, emm type 1 or 3, and underlying chronic illness or immunosuppression. An estimated 10 649–13 434 cases of invasive GAS infections occur in the United States annually, resulting in 1136–1607 deaths. In a 30-valent M-protein vaccine, emm types accounted for 91% of isolates. Conclusions The burden of invasive GAS infection in the United States remains substantial. Vaccines under development could have a considerable public health impact.

The WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.

Our whole genome sequence (WGS) pipeline was assessed for accurate prediction of antimicrobial phenotypes. For 2316 invasive pneumococcal isolates recovered during 2015 we compared WGS pipeline data to broth dilution testing (BDT) for 18 antimicrobials. For 11 antimicrobials categorical discrepancies were assigned when WGS-predicted MICs and BDT MICs predicted different categorizations for susceptibility, intermediate resistance or resistance, ranging from 0.9% (tetracycline) to 2.9% (amoxicillin). For β-lactam antibiotics, the occurrence of at least four-fold differences in MIC ranged from 0.2% (meropenem) to 1.0% (penicillin), although phenotypic retesting resolved 25%-78% of these discrepancies. Non-susceptibility to penicillin, predicted by penicillin-binding protein types, was 2.7% (non-meningitis criteria) and 23.8% (meningitis criteria). Other common resistance determinants included mef (475 isolates), ermB (191 isolates), ermB + mef (48 isolates), tetM (261 isolates) and cat (51 isolates). Additional accessory resistance genes (tetS, tet32, aphA-3, sat4) were rarely detected (one to three isolates). Rare core genome mutations conferring erythromycin-resistance included a two-codon rplD insertion (rplD69-KG-70) and the 23S rRNA A2061G substitution (six isolates). Intermediate cotrimoxazole-resistance was associated with one or two codon insertions within folP (238 isolates) or the folA I100L substitution (38 isolates), whereas full cotrimoxazole-resistance was attributed to alterations in both genes (172 isolates). The two levofloxacin-resistant isolates contained parC and/or gyrA mutations. Of 11 remaining isolates with moderately elevated MICs to both ciprofloxacin and levofloxacin, seven contained parC or gyrA mutations. The two rifampin-resistant isolates contained rpoB mutations. WGS-based antimicrobial phenotype prediction was an informative alternative to BDT for invasive pneumococci.