The ongoing pandemic: contaminated chicken produce is the primary source of antimicrobial resistant campylobacteriosis in the United States

Background Campylobacter species are the primary cause of bacterial gastroenteritis and are a significant burden on health care systems worldwide. Campylobacteriosis typically causes sporadic, zoonotic disease in patients, and clinical isolates can be attributed to putative reservoir sources using probabilistic models. <br> Methods As part of routine national surveillance, genomes were sequenced for 8,889 isolates from campylobacteriosis cases in the US from 2009 through 2019; and 18,405 Campylobacter isolates from contemporaneous samples of potential human infection sources. We used a random forest approach to identify markers for probabilistic attribution of clinical isolates to potential reservoir sources. <br> Findings Campylobacteriosis incidence has doubled since 2009, with the greatest surge in cases coming after becoming a notionally notifiable pathogen in 2015. Probabilistic attribution of sequenced isolates identifies chicken as the primary source of infections (72% and 67% of Campylobacter jejuni and Campylobacter coli isolates, respectively), with increasing contribution to the disease burden over time. Most of the remaining isolates were attributed to ruminant sources, with relatively few isolates attributed to wild bird, environment, pork, and turkey sources. However, increasing rates of fluoroquinolone and aminoglycoside resistance in these populations (sources?) remain a public health concern. <br> Interpretation National-scale surveillance and quantification of the putative burden of each source reservoir on clinical cases can guide policy and set improved performance standards for food production in the US. Taken in context with global studies, our results support the view that the largest reductions in human campylobacteriosis in industrialized countries will come from interventions that focus on the poultry industry.