Co-circulation of genetically diverse population of vaccine related and unrelated respiratory mycoplasmas and viruses in UK poultry flocks with health or production problems

•Co-circulation of vaccine and field strains of IBV, Mg and Ms in poultry flocks.•Additional Mg gene analysis needed for differentiation of field versus vaccine Mg strains.•Field strains of Mg detected in flocks previously vaccinated against Mg.•MLST analysis showed the co-presence of field and vaccine-like Ms sequence types.•IBV 793B, Arkansas and D274 vaccine-like or field strains detected in flocks. Respiratory diseases continue to have a major impact on poultry health, welfare and productivity. However, little information is available on their current status in UK poultry flocks. We investigated the presence of four economically important respiratory pathogens in healthy or problematic flocks; infectious bronchitis virus (IBV), avian metapneumovirus (aMPV), Mycoplasma gallisepticum (Mg) and Mycoplasma synoviae (Ms). Samples from 131 UK poultry flocks were received during the 12 month study period. Oropharyngeal (OP) swabs were taken from eight birds per flock and accompanied with flock health information. The study included 118 chicken, 6 pheasant and 5 turkey flocks, and 1 quail and 1 partridge flock. Chicken flocks were of layers (n = 98), broilers (n = 15), breeders (n = 3) and undisclosed (n = 2). Flock ages ranged from 3 to 72 weeks old, and the average flock size was 17,633 birds. PCR detected 65 (49.6%), 59 (45%) and 8 (6.1%) flocks as positive for IBV, Mg/Ms and aMPV respectively. Analysis of the mgc2 gene of the Mg isolates revealed high similarities to Mg TS-11 and Mg 6/85. Further gene analysis found that the TS-11-like isolates were unrelated to the TS-11 vaccine. Multi-locus sequence typing (MLST) analysis identified the majority of positive Ms as ST21, along with ST2 (MS-H-like), ST6 and ST43. IBV S1 gene sequencing identified strains as 793B (66.7%), Arkansas (23.8%) and Massachusetts (9.5%). All aMPV positive samples belonged to subtype B. Findings indicate that over half of the flocks sampled were positive for at least one of the four vaccine or field strains of mycoplasmas or viruses.