Emergence of Salmonella enterica serotype Enteritidis with decreased susceptibility to ciprofloxacin in humans and poultry in the United States

Abstract Salmonella enterica serotype Enteritidis is the most common cause of salmonellosis in the United States, resulting in significant morbidity. In 2024, the National Antimicrobial Resistance Monitoring System (NARMS) reported a concerning increase in the number of Enteritidis isolates with decreased susceptibility to ciprofloxacin (DSC) in ill persons and chicken products. We analyzed Enteritidis isolates in humans and poultry in the United States (2013–2024); 31% (20,298/65,052) had a GyrA(D87Y) mutation and 96% (19,447/20,298) of these isolates fell into NCBI SNP cluster PDS000065758 (strain SE65758-D87Y). The emergence of SE65758-D87Y has resulted in an increase in DSC Enteritidis infections in humans and has replaced previously circulating Enteritidis strains in poultry. Trends of SE65758-D87Y in poultry were co-occurring with trends in human clinical illnesses. Leading sources of SE65758-D87Y outbreaks included consuming chicken or shell eggs and backyard poultry contact. Human and poultry isolates were genetically indistinguishable. Overall, this suggests poultry is an important reservoir for human SE65758-D87Y infections. Ecological drivers are likely not linked directly to antimicrobial use because fluoroquinolones have been banned for use in poultry in the United States since 2005. Given the importance of serotype Enteritidis and pathogenic strain SE65758-D87Y, focused prevention strategies to contain further spread should be considered.