Introduction: The genomes of nine H5 subtypes of low pathogenic avian influenza virus (LPAIV) strains identified in wild birds in Poland between 2010 and 2015 were sequenced, and their phylogenetic relationship was determined. Material and Methods: AIV genome segments were amplified by RT-PCR and the PCR products were sequenced using Sanger method. Phylogenetic trees were generated in MEGA6 software and digital genotyping approach was used to visualise the relationship between analysed strains and other AIVs. Results: High genetic diversity was found in the analysed strains as multiple subgroups were identified in phylogenetic trees. In the HA tree, Polish strains clustered in two distinct subclades. High diversity was found for PB2, PB1, PA and NP, since 5-8 sublineages could be distinguished. Each strain had a different gene constellation, although relationship of as much as six out of eight gene segments was observed between two isolates. A relationship with poultry isolates was found for at least one segment of each Polish strain. Conclusion: The genome configuration of tested strains indicates extensive reassortment, although the preference for specific gene constellation could be noticed. A significant relationship with isolates of poultry origin underlines the need for constant monitoring of the AIV gene pool circulating in the natural reservoir.

Escherichia coli isolates from chickens with colibacillosis were assigned to phylogenetic groups based on multiplex polymerase chain reaction (PCR) and antibacterial resistance of E. coli belonging to these groups was examined. Furthermore, the gyrA gene of isolates was sequenced and a phylogenetic tree was generated. A total of 84 E. coli isolates were grouped using multiplex PCR of TSPE4.C2, chuA, yjaA, and gadA molecular markers. Four phylogenetic groups were identified with strains divided as follows: 16 in group A (19.05%), 17 in group B1 (20.24%), 23 in group B2 (27.38%), and 28 in group D (33.33%). Escherichia coli isolates belonging to phylogenetic groups B2 and D were resistant to Soltrim and Flumequine unlike the majority of E. coli isolates that belonged to groups A and B1, and which were susceptible to these antibiotics. The phylogenetic results based on gyrA gene sequences from multiplex PCR revealed that E. coli phylogenetic grouping was in accordance with the clusters obtained in the phylogenetic tree. In conclusion, the comparative sequence analysis of gyrA sequences provides a firm framework for an accurate classification of E. coli and related taxa and may constitute a pertinent phylogenetic marker for E. coli.

Genus Iotatorquevirus consists of 2 species, Torque teno sus virus 1a and Torque teno sus virus 1b, which are ubiquitous in swine populations, and are widely reported in association with porcine circovirus associated disease (PCVAD). To evaluate the relationship with PCVAD, 100 formalin-fixed paraffin-embedded tissue samples were used to detect both Iotatorquevirus species by nested PCR and sequencing. Sixty-eight PCVAD cases were selected as well as 32 porcine circovirus type 2 (PCV2) non-affected cases. Overall, 33 of the 100 cases were positive for Torque teno sus virus 1a and 8 of 100 were positive for Torque teno sus virus 1b. Only 24 of 68 (35%) PCVAD cases were positive for Torque teno sus virus 1a; 39% (9/23) of post-weaning multisystemic wasting syndrome, and 33% (15/45) of PCV2-associated reproductive failure cases. Among PCV2 non-affected cases, 28% were positive for Torque teno sus virus 1a and 6% were positive for Torque teno sus virus 1b. Torque teno sus virus 1b was not detected in PCV2-associated reproductive failure cases. Regardless of the PCV2-status, a lower frequency of both Iotatorquevirus species was found than depicted in other reports and there was no statistical relationship with PCVAD (χ 2 < 0.01). Given the worldwide genomic variability of Iotatorquevirus species, it is feasible that species prevalent in Mexico share a lower nucleotide sequence identity, leading to different pathogenic potential.