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.

Introduction of PCV13 for universal infant use was associated with significant reductions in nasopharyngeal carriage of PCV13 serotypes and resistant strains. Carriage of non-PCV13 serotypes increased modestly, particularly serotype 35B. Further investigation is warranted to determine whether nonvaccine pneumococcal serotypes carried in the nasopharynx are associated with significant replacement disease.

Introduction Invasive community-associated methicillin-resistant Staphylococcus aureus (MRSA) incidence in the United States is higher among black persons than white persons. We explored the extent to which socioeconomic factors might explain this racial disparity. Methods A retrospective cohort was based on CDC’s Emerging Infections Program surveillance data for invasive community-associated MRSA cases (isolated from a normally sterile site of an outpatient or on hospital admission day ≤3 in a patient without specified major healthcare exposures) from 2009–2011 in 33 counties of 9 states. We used generalized estimating equations to determine census tract-level factors associated with differences in MRSA incidence and inverse odds ratio weighted mediation analysis to determine the proportion of racial disparity mediated by socioeconomic factors. Results Annual invasive community-associated MRSA incidence was 4.59/100,000 among whites and 7.60/100,000 among blacks (rate ratio: 1.66, 95% CI, 1.52–1.80). In the mediation analysis, after accounting for census tract-level measures of federally-designated medically underserved areas, education, income, housing value, and rural status, 91% of the original racial disparity was explained; no significant association of black race with community-associated MRSA remained (rate ratio: 1.05, 95% CI, 0.92–1.20). Conclusions The racial disparity in invasive community-associated MRSA rates was almost entirely mediated by socioeconomic factors. The specific factors that underlie the association between tract-level socioeconomic measures and MRSA incidence, which may include modifiable social (e.g., poverty, crowding) and biological factors (not explored in this analysis), should be elucidated to define strategies for reducing racial disparities in community-associated MRSA rates.

Background Disseminated gonococcal infections (DGI) are thought to be uncommon; surveillance is limited and case reports are analyzed retrospectively or in case clusters. We describe the population-level burden of culture-confirmed DGI through the Active Bacterial Core surveillance (ABCs) system. Methods During 2015–2016, retrospective surveillance was conducted among residents in two ABCs areas and prospectively in three ABCs areas during 2017–2019. A DGI case was defined as isolation of Neisseria gonorrhoeae (Ng) from a normally sterile site. A case report form was completed for each case and antimicrobial susceptibility testing (AST) was performed on available isolates. Results During 2015–2019, 77 DGI cases were identified (~a rate of 0.13 cases per 100,000 population) and accounted for 0.06% of all reported gonorrhea cases in the three surveillance areas. Most DGI cases were male (64%), non-Hispanic Black (68%), and ranged from 16–67 years; blood (55%) and joint (40%) were the most common sterile sites. Among 29 isolates with AST results during 2017–2019, all were susceptible to ceftriaxone. Conclusions DGI is an infrequent complication of Ng; since Ng can quickly develop antimicrobial resistance, continued DGI surveillance, including monitoring trends in antimicrobial susceptibility, could help inform DGI treatment recommendations.