Volume 21, Number 9—September 2015
Emerging Infections Program
Effect of Culture-Independent Diagnostic Tests on Future Emerging Infections Program Surveillance
|Program, pathogen (year surveillance started)||Case definition criteria||Cases identified by culture, %||FDA-approved CIDTs related to EIP case definitions, by test type/% laboratories offering test (year data collected)†||Laboratories offering laboratory-developed NATs (year data collected), %†||Additional cases, %‡|
|Active Bacterial Core surveillance|
|Streptococcus pneumoniae (1995)||Isolation from sterile site||100||ABT on sterile site specimens/13 (2012)||1% (2014)||Not available|
|Haemophilus influenzae (1995)||Isolation from sterile site||100||ABT on sterile site specimens/7 (2012)||<1 (2014)||Not available|
|Neisseria meningitidis (1995)||Isolation from sterile site||100||ABT on sterile sites specimens/8 (2012)||1 (2014)||9§|
|Group A Streptococcus (1995)||Isolation from sterile site||100||None on direct specimen from sterile site||1 (2014)||Not available|
|Group B Streptococcus(1995)||Isolation from sterile site||100||None on direct specimen from sterile site||1 (2014)||Not available|
|Methicillin-resistant Staphylococcus aureus (2005)||Isolation from sterile site||100||None on direct specimen from sterile site||1 (2014)||Not available|
|Pertussis (2011)||Clinical criteria plus isolation from clinical specimen or PCR positive||<1||None||Not available||Not available|
||Isolation, positive urine antigen or rise in serologic titers¶
||Urine antigen test/92 (2010–2011)#
|Campylobacter||Isolation from clinical specimen||100||ABT/14 (2014) NAT multiplex/1 (2014)||1 (2014)||13|
|Salmonella||Isolation from clinical specimen||100||NAT multiplex/1 (2014)||1 (2014)||1.3|
|Shigella||Isolation from clinical specimen||100||NAT multiplex/0.5 (2014)||0.5 (2014)||5|
|Vibrio||Isolation from clinical specimen||100||NAT multiplex/0 (2014)||0.6 (2014)||2|
|Yersinia||Isolation from clinical specimen||100||NAT multiplex/0 (2014)||0.5 (2014)||2|
|Listeria||Isolation from sterile site||100||NAT-based multiplex/0 (2014)||0 (2014)||0|
|Cryptosporidium||Detection of organism, antigen, or nucleic acid||0||ABT/88 (2014); NAT multiplex/1 (2014)||2 (2014)||Not applicable|
|Cyclospora||Detection of organism or nucleic acid||0||NAT multiplex/0 (2014)||0||Not applicable|
|Shiga toxin–producing Escherichia coli
||Isolation of E. coli O157:H7; or, isolation of E. coli with detection of Shiga toxin or genes that encode the toxins
||ABT/57 (2014); NAT multiplex/1 (2014)
|Health care–associated infections|
|Gram-negative bacilli E. coli, Klebsiella pneumoniae, K. oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Acinetobacter baumannii||Isolation from a sterile site or urine determined to be not susceptible to certain antimicrobial organisms**||100||None on direct specimen from sterile site||Not available||Not available|
|Candida spp.||Isolation from blood||100||Magnetic resonance test for multiple species/offering unknown||Not available||Not available|
||Positive toxin or molecular assay from stool specimen
||NAT for C. difficile/58 (2013)
NAT multiplex/1 (2013)
toxin-based ABT/37 (2013)
|Influenza virus||Isolation or detection from fluorescent antibody staining, antigen test or RT-PCR||<2††||ABTs NAT (singleplex or multiplex)/24 (2013)‡‡||2||Not applicable|
*Data from EIP laboratory surveys. ABT, antigen-based test; CIDT, culture-independent diagnostic test; EIP, Emerging Infections Program; FDA, Food and Drug Administration; NAT, nucleic acid test; RT-PCR, reverse transcription PCR.
†Laboratory tests may be offered either onsite or offsite.
‡Estimated additional cases that could be captured by CIDTs in use. These infections are not counted in EIP surveillance because they represent a positive CIDT result that is not part of current case definitions.
§Data from http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6117a3.htm.
¶Includes confirmed cases only.
#Data from http://journals.cambridge.org/abstract_S0195941700093735.
**E. coli, K. pneumoniae, K. oxytoca, E. cloacae, and E. aerogenes nnot susceptible to doripenem, meropenem or imipenem and resistant to all third-generation cephalosporins; A. baumannii not susceptible to doripenem, meropenem, or imipenem.
††In 2003, 12% of influenza cases were identified by culture; whereas in 2013, <2% were identified by culture.
‡‡Most samples tested by ABTs at clinical laboratories are sent to public health laboratories for results confirmation by PCR.