Molecular typing ofin industrial and backyard poultry: a 14-year study in Italy.

Abstract

UNLABELLED: The incidence of() in poultry farms is closely tied to intensive production systems, where high-density flocks and shared operational networks amplify transmission risks. Northern Italy is a densely populated poultry area (DPPA) of industrial and backyard poultry farms providing a unique setting to studydynamics, particularly given the integrated production model-where companies manage geographically dispersed farms with shared logistics. Using multi-locus sequence typing (MLST), we analyzed 227Italian samples (181 industrial, 46 backyard) collected over 14 years (2010-2024) to assess transmission patterns and genetic diversity. Our results revealed high genetic diversity (99 sequence types, 95 novel). Transmission was linked to company networks, as identical strains circulated across farms under shared ownership, while backyard and industrial sectors showed minimal overlap. Phylogenetic analysis confirmed country-specific clustering. Moreover, population genetic analyses showed that Italy's diversity was intermediate between the highly diverse USA and the more homogenized Chinese populations, with variability measures further suggesting distinct evolutionary pressures across genes and countries. Finally, this study challenges assumptions about backyard farms as reservoirs and shows thatspread in Italy is primarily driven by industrial logistics. Our findings also highlight the value of MLST in tracing outbreaks at the company level, supporting its adoption for poultry pathogen surveillance. By providing the first long-term, system-wide perspective onepidemiology in a DPPA, this work offers critical insights for managing pathogen spread in integrated production networks worldwide. IMPORTANCE: This study provides valuable insights into the genetic diversity, spread, and evolutionary dynamics ofin Italy. By analyzing genetic differences across isolates, we discovered two critical patterns: first, these bacteria tend to stay within national poultry production systems, forming country-specific genetic groups; second, within Italy, identical strains circulate within the same companies rather than by region. This suggests the pathogen spreads through poultry trade or shared farming practices rather than local environmental transmission. Surprisingly, we found no evidence of the bacteria moving between small backyard farms and large industrial operations despite concerns about such cross-transmission. The persistence of certain strains over time demonstrates the bacterium's ability to survive even with strict biosecurity measures in industrial settings. Future studies should focus on the mechanisms that drive the persistence and spread ofstrains, as well as on the potential role of new transmission vectors and potential reservoirs.