Pathogenic diagnosis and phylogenetic analysis of Giardia lamblia from an infected case

doi:10.12140/j.issn.1000-7423.2026.03.020

Abstract

Abstract:

To clarify the infection source and genetic characteristics of Giardia lamblia isolated from a diarrheal patient, fresh fecal sample of the patient was collected. Microscopy, real-time fluorescent quantitative PCR and nested PCR were comprehensively applied for pathogen detection. Metagenomic sequencing and analysis were performed targeting the small subunit ribosomal RNA (SSU rRNA), triosephosphate isomerase (tpi), glutamate dehydrogenase (gdh), β-giardin (bg) and translation elongation factor 1α (ef1α). Multilocus genotyping and genetic evolution analysis were carried out via sequence alignment and phylogenetic tree construction. Both microscopy and real-time fluorescent quantitative PCR confirmed Giardia infection. Only the gdh and ef1α genes were successfully amplified by nested PCR, and the SSU rRNA gene sequence was successfully detected by metagenomic sequencing. Multilocus genotyping showed that the isolate DXH001 obtained in this study belonged to assemblage B, and no mixed infection was detected. Phylogenetic analysis indicated that the gdh gene of isolate DXH001 shared 100% sequence identity with the human-derived strain EU847734 from Belgium, belonging to subtype BⅣ; the ef1α gene shared 98.43% sequence identity with the human-derived isolate HQ179598 from Australia, and the SSU rRNA gene shared 90.45% sequence identity with the human-derived strain U09491 from the United States, both clustered into the assemblage B branch. Compared with the human-derived reference sequence U09491, the SSU rRNA gene had 35 base substitutions and 5 deletions, and the sequence difference was mainly related to the insufficient sequencing data volume caused by the low abundance of the target sequence in the sample; the variations of gdh and ef1α genes were relatively conservative, which did not cause significant functional changes. In this study, the isolate DXH001 was identified as G. lamblia assemblage BⅣ via multilocus genetic analysis, suggesting the trans-regional transmission risk of this subtype. Metagenomic sequencing shows high sensitivity in low-abundance target detection, which can serve as an effective supplement for conventional molecular genotyping.

Key words: Giardia lamblia, Diarrheal infection, Molecular aetiology, Phylogenetic tree, Variable loci

CLC Number:

R531.73

YU Shukun, LIU Lang, CUI Ziyan, TAN Yaxin, HUANG Shunkai, TAO Zhiyang. Pathogenic diagnosis and phylogenetic analysis of Giardia lamblia from an infected case[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2026, 44(3): 448-453.

Figures/Tables 5

References 16

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基因名称	引物序列（5'→3'）	片段大小/bp
SSU rRNA	F1：CATCCGGTCGATCCTGCC	292
	R1：AGTCGAACCCTGATTCTCCGCCCAGG	292
	F2：GACGCTCTCCCCAAGGAC	174
	R2：CTGCGTCACGCTGCTCG	174
gdh	F1：TTCCGTRTYCAGTACAACTC	829
	R1：ACCTCGTTCTGRGTGGCGCA3	829
	F2：ATGACYGAGCTYCAGAGGCACGT	432
	R2：GTGGCGCARGGCATGATGCA	432
tpi	F1：AAATIATGCCTGCTCGTCG	605
	R1：CAAACCTTITCCGCAAACC	605
	F2：CCCTTCATCGGIGGTAACTT	530
	R2：GTGGCCACCACICCCGTGCC	530
bg	F1：AAGCCCGACGACCTCACCCGCAGTGC	753
	R1：GAGGCCGCCCTGGATCTTCGAGACGAC	753
	F2：CATAACGACGCCATCGCGGCTCTCAGGAA	384
	R2：GAGGCCGCCCTGGATCTTCGAGACGAC	384
ef1α	F：GCCGAGGAGTTCGACTACATC	191
ef1α	R：GACGCCSGAGATCTTGTAGAC	191