Spatial, Ecologic, and Clinical Epidemiology of Community-onset, Ceftriaxone-resistant Enterobacteriaceae, Cook County, Illinois, USA

Vanessa Sardá; William E. Trick; Huiyuan Zhang; David N. Schwartz


Emerging Infectious Diseases. 2021;27(8):2127-2134. 

In This Article


Cook County Health (CCH) is a large safety-net healthcare system in Chicago and suburban Cook County, Illinois. It consists of a 450-bed teaching hospital near downtown Chicago, a small community hospital in the South Side of Chicago, a small hospital and clinic for the treatment of detainees in the Cook County jail, and 13 community clinics distributed throughout Cook County. In 2018, CCH cared for 205,322 persons, most of whom self-identified as non-Hispanic Black (49.1%) or Hispanic (32.7%). Through electronic queries, we identified all culture isolates of the commonest Enterobacteriaceae species collected at CCH: E. coli, K. pneumoniae, Enterobacter cloacae, Proteus mirabilis, Enterobacter aerogenes, and Klebsiella oxytoca collected from Cook County residents during January 1, 2016–December 31, 2018. We determined antimicrobial susceptibilities by using the MicroScan Gram-negative panel (Beckman Coulter, and interpreted results by using Clinical and Laboratory Standards Institute breakpoints.[18] We obtained antimicrobial susceptibilities retrospectively and did not retain any isolates for further analysis. We excluded isolates collected from persons <18 years of age, surveillance isolates, isolates with intermediate susceptibility to ceftriaxone or intermediate susceptibility or resistance to carbapenems, and duplicate isolates (defined as isolates from the same persons, of the same species, and collected within 30 days). To select for community-onset isolates, we included only isolates collected in the ambulatory clinic or emergency department (ED) setting and those collected during the first 2 days of hospitalization.

Demographic characteristics, collected from the electronic medical record (EMR), were patient sex and age and self-identified race and ethnicity, categorized as non-Hispanic Black, non-Hispanic White, Hispanic, or other. We classified encounter types as outpatient (ambulatory clinic), ED, or inpatient. Census-tract variables for Cook County were obtained from the 2017 US Census Bureau American Community Survey 5-year estimates.[19] We extracted census tract data on race and ethnicity, immigration status (US-born or foreign-born), deprivation (households below poverty level and uninsured status), and overcrowding (>1.5 occupants per room).

Spatial Analysis

Cook County, which includes the city of Chicago, contains 1,319 land census tracts and has an estimated population of 5,149,580 residents.[19] We used ArcGIS version 10.4.1 (ESRI, to geocode isolates to their census tract of provenance by using residential addresses available in the EMR. We calculated and mapped the percentage of CTX-R isolates in each census tract (i.e., the number of CTX-R isolates divided by the number of all isolates multiplied by 100). To minimize imprecision of CTX-R percentages in census tracts with low number of isolates, we excluded from the spatial analysis census tracts that had <3 isolates collected during the study period. We used spatial autocorrelation analysis (Moran I) to identify whether Enterobacteriaceae CTX-R percentages were distributed at random or clustered in census tracts across Cook County. Similarly, we conducted spatial autocorrelation analysis on CTX-R percentage distribution of E. coli isolates alone.

Ecologic Analysis

After excluding census tracts with <3 isolates, we categorized the remaining census tracts on the basis of the presence or absence of a CTX-R isolate. We evaluated the relationship between each population-level variable and the presence of >1 CTX-R isolates in a census tract by using bivariate logistic regression, summarized by odds ratios (ORs) and corresponding 95% CIs. We conducted a similar analysis for E. coli isolates alone.

Individual Risk Analysis

We categorized individual Enterobacteriaceae isolates on the basis of the identification of ceftriaxone resistance in the susceptibility panel. We included all isolates in the analysis of individual risk. The variables of interest were the individual demographic variables collected from the EMR and the type of clinical encounter. In addition, we included an ecologic variable, the percentage of foreign-born population in the census tract of residency. We evaluated the relationship between each variable and identification of ceftriaxone resistance in an individual isolate by using bivariate logistic regression, summarized by ORs and corresponding 95% CIs. We conducted all statistical analyses by using Stata version 14.2 (StataCorp,