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Background <p>Granuloma lesions in poultry are a frequent pathological finding, representing a chronic inflammatory response to persistent infectious agents, most commonly bacteria or fungi. Accurate differentiation of the underlying cause requires additional diagnostic tests, such as acid-fast staining, fungal culture, or bacterial isolation and genetic identification. However, the pathogens often remain undetermined when conventional detection methods fail. The present case aimed to investigated granulomatous disease in multiple organs of layer chickens by applying metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing.</p> Case presentation <p>A total of 35 deaths occurred in a flock of layer chickens, accompanied by a decrease in daily feed intake from 144 g to 104 g. Six carcasses from 38-weeks-old layer chickens were submitted for disease diagnosis. During necropsy, granuloma/neoplastic lesions were observed in the liver, ovary, proventriculus, pancreas and kidney. Histopathological examination revealed compartmentalized infiltration of lymphocytes and multinucleated giant cells in liver, ovary, proventriculus, pancreas and renal parenchyma. While <i>Escherichia coli</i> was isolated from the oviduct, no viral agents (IBV, CIAV, MDV, ALV, REV, or HEV) were detected by RT-PCR. Notably, some of the initial metagenomic shotgun results were recognized as different taxa due to the misclassification of certain reads. Following a re-analysis of these shotgun reads against the nucleotide database, both metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing identified <i>E. coli</i> as the dominant species in liver samples.</p> Conclusion <p>The present case indicates that <i>E. coli</i> may contribute to granuloma lesions in layer chickens. While 16S rRNA amplicon sequencing provided more reliable bacterial identification for diagnostic purposes, metagenomic shotgun sequencing offers complementary insight by detecting broader microbial communities. Therefore, integrating both approaches alongside conventional diagnosis may improve the accuracy of diagnosis for granulomatous diseases in poultry.</p>

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Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月20日

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  • Chi Sun Yun,
  • Jae-Kyeom Kim,
  • Hyojung Kwon,
  • Moon Her,
  • Jin San Moon

摘要

Background

Granuloma lesions in poultry are a frequent pathological finding, representing a chronic inflammatory response to persistent infectious agents, most commonly bacteria or fungi. Accurate differentiation of the underlying cause requires additional diagnostic tests, such as acid-fast staining, fungal culture, or bacterial isolation and genetic identification. However, the pathogens often remain undetermined when conventional detection methods fail. The present case aimed to investigated granulomatous disease in multiple organs of layer chickens by applying metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing.

Case presentation

A total of 35 deaths occurred in a flock of layer chickens, accompanied by a decrease in daily feed intake from 144 g to 104 g. Six carcasses from 38-weeks-old layer chickens were submitted for disease diagnosis. During necropsy, granuloma/neoplastic lesions were observed in the liver, ovary, proventriculus, pancreas and kidney. Histopathological examination revealed compartmentalized infiltration of lymphocytes and multinucleated giant cells in liver, ovary, proventriculus, pancreas and renal parenchyma. While Escherichia coli was isolated from the oviduct, no viral agents (IBV, CIAV, MDV, ALV, REV, or HEV) were detected by RT-PCR. Notably, some of the initial metagenomic shotgun results were recognized as different taxa due to the misclassification of certain reads. Following a re-analysis of these shotgun reads against the nucleotide database, both metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing identified E. coli as the dominant species in liver samples.

Conclusion

The present case indicates that E. coli may contribute to granuloma lesions in layer chickens. While 16S rRNA amplicon sequencing provided more reliable bacterial identification for diagnostic purposes, metagenomic shotgun sequencing offers complementary insight by detecting broader microbial communities. Therefore, integrating both approaches alongside conventional diagnosis may improve the accuracy of diagnosis for granulomatous diseases in poultry.