We assessed laboratory practices using data from the NHSN Patient Safety Component Annual Hospital Survey (OMB No. 0920–0666),¹ which collects information about hospital characteristics and practices, including clinical microbiology testing. The respondent, typically the hospital’s infection preventionist,² is instructed to consult the hospital’s laboratory lead for applicable questions.¹

The analysis was limited to clinical microbiology laboratory practices for Enterobacteriaceae. All ACHs that reported for calendar years 2015 and 2016 by July 1, 2017, were included; more than 90% of US ACHs completed this survey each year. Psychiatric hospitals were excluded. Data were analyzed using SAS version 9.4 software (SAS Institute, Cary, NC). The Pearson χ² test with minimum significance of P < .05 was used to assess differences between survey years. Results are presented for 2016; 2015 results were reviewed to evaluate changes over time and are presented where they differed significantly from 2016 results.

This is the first national assessment of laboratory practices for Enterobacteriaceae among ACHs. A small but significant increase in the use of offsite laboratories was observed in 2016. Capacity to detect carbapenemase-producing organisms and to identify colistin resistance in hospital laboratories was limited, impairing efforts to prevent the spread of highly drug-resistant Enterobacteriaceae.

Although most hospitals used onsite laboratories, this proportion decreased in 2016. Among facilities that completed the same survey for 2014, more facilities using onsite laboratories reported receiving MDRO results rapidly than facilities using offsite laboratories.² Increased reporting times can delay infection control interventions, such as contact precautions. Regardless of laboratory location, facilities should implement procedures to ensure that identification of targeted MDROs is rapidly communicated to the appropriate clinical and infection control staff.

In 2010, the CLSI lowered Enterobacteriaceae carbapenem MIC breakpoints,^3,4 which increased sensitivity for carbapenemase-producing isolates. However, 6 years later, nearly 25% of laboratories reported using pre-2010 breakpoints. Delays may be linked to the overwhelming popularity of ATIs for primary AST of major pathogens; it can take years for ATI manufacturers to develop and the US Food and Drug Administration (FDA) to clear updated ATI panels.⁴ Once they are commercially available, laboratories may not promptly acquire and implement them. The CLSI recommends that laboratories using the pre-2010 break-points test for and interpret carbapenemase-producing isolates as carbapenem resistant. Overall, 11% of hospital laboratories were not following this guidance, which likely resulted in underdetection of CRE and missed infection control opportunities. Further work, potentially led by public health agencies, is needed to update and improve susceptibility testing in local clinical laboratories.

Half of facilities reported that their laboratories did not test for carbapenemases. Those that used newer carbapenem breakpoints were less likely to test for carbapenemases, which although consistent with clinical testing recommendations,³ indicates that fewer facilities used testing for infection control purposes. In 2016, the Centers for Disease Control and Prevention (CDC) launched the Antibiotic Resistance Laboratory Network (ARLN) to expand mechanism testing of carbapenem-resistant Enterobacteriaceae and Pseudomonas aeruginosa to 50 state public health laboratories, 5 local public health laboratories, and Puerto Rico.⁵ Initiatives like ARLN aim to ensure that testing for carbapenemases is widely available, even if clinical laboratory testing capacities shrink. These public health laboratories and their associated health departments’ healthcare-associated infection programs may also serve as a resource to improve testing practices at laboratories in their jurisdictions.

The recent identification of the plasmid-mediated colistin resistance gene mcr has increased the importance of identifying colistin-nonsusceptible isolates⁶; however, only 1% of hospitals indicated that their laboratories used reference broth microdilution, which is the currently recommended method.⁷ The most commonly reported methods included Etest and disk diffusion, both of which are discouraged due to inaccurate results obtained with polymyxins.⁷ Notably, 24% of facilities reported using an ATI for colistin susceptibility, despite the absence of an FDA-cleared automated test.⁷ This lack of availability of polymyxin AST hampers detection of mcr-carrying isolates; undetected dissemination of mcr could increase the prevalence of colistin resistance among Enterobacteriaceae. Further work is needed to identify risk factors to better target colistin AST to identify isolates for mcr screening. Colistin susceptibility testing is available through the ARLN, and results from this work will be useful to better define this issue.

This analysis has several limitations. Data are self-reported to NHSN and are not validated by the CDC. Although respondents are instructed to confer with their laboratory’s lead, limited laboratory expertise or communication could result in incomplete or incorrect responses, particularly among hospitals that used offsite laboratories.

Nearly all US ACHs completed the survey for 2015 and 2016; therefore, these data are the most complete representation of clinical microbiology laboratory practices for Enterobacteriaceae currently available. Clinical microbiology laboratories should prioritize implementation of current CLSI breakpoints. Laboratories should also develop a strategy for routine carbapenemase testing, either in-house or through the ARLN. Hospital epidemiologists, infection control staff, and clinicians should be aware of the limitations of their laboratories’ practices when interpreting results. Additionally, public health surveillance and prevention programs should consider current clinical laboratory practices when developing programs and interpreting data.