CDC Releases Genome Sequencing Data on Antibiotic-Resistant Salmonella


For the first time, the National Antimicrobial Resistance Monitoring System includes whole genome sequencing data of bacteria from individuals with antibiotic-resistant Salmonella infections.

The National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) tracks changes in the antimicrobial susceptibility of certain enteric bacteria found in ill people, retail meats, and food animals in the United States. This is possible through collaboration among state and local public health departments, including the Centers for Disease Control and Prevention (CDC), the US Food and Drug Administration (FDA), and the US Department of Agriculture (USDA).

For the first time in its annual reporting, NARMS has included whole genome sequencing (WGS) data for bacteria from individuals with antibiotic-resistant Salmonella infections. WGS enables CDC officials to track antibiotic resistance patterns and trends more effectively.

The NARMS 2014 Human Isolates Report provides the most recent data on antimicrobial resistance in bacteria such as: Salmonella, Shigella, Campylobacter, E. coli O157, and Vibrio species other than Vibrio cholerae.

All 50 states and the District of Columbia participated, representing the entire United States population of approximately 319 million persons. The report highlighted some encouraging trends:

Multidrug resistance in Salmonella was similar to the previous year and has remained stable, between 9% and 11% over the past 10 years. Resistance to ceftriaxone in Salmonella remained rare, and resistance to certain groups of antibiotics in Salmonella Typhimurium (ACSSuT) and Salmonella Newport (ACSSuTAuCx) remained lower in 2014 compared with the years 2004 through 2008.

No Salmonella isolates had decreased susceptibility to both azithromycin and ciprofloxacin, and none had both decreased susceptibility to azithromycin and resistance to ceftriaxone, which are important drugs for the treatment of severe Salmonella infections.

There were some concerning trends as well, including, multidrug resistance in a common Salmonella serotype greater than 40%. Resistance more than doubled since 2011 (18% in 2011 vs 43% in 2014) and has been linked to animal exposure and eating pork or beef, including meat purchased from live animal markets.

Six of the 51 ceftriaxone-resistant Salmonella in 2014 had an extended-spectrum β-lactamase (ESBL) gene identified by WGS. ESBLs are rare among Salmonella in the United States; many of these infections are acquired during international travel.

Among Salmonella serotypes Dublin, Heidelberg, Newport, and Typhimurium, nearly two-thirds of the isolates were resistant to ceftriaxone. Decreased susceptibility to ciprofloxacin in Salmonella was found to be higher in 2014 (4%) than in the baseline period between the years 2004 and 2008 (2%) and between the years 2009 and 2013 (3%). Healthcare and public health officials are encouraged to review the data for themselves. To aid others in viewing all of the data, an interactive web tool has been developed.

According to a media statement released by the CDC, “With WGS, health officials can rapidly detect genes that make bacteria resistant to some antibiotics which are critically important to treat infections.”

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