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已发表论文
一种罕见引起菌血症的氟喹诺酮类药物中间耐药菌株 Herbaspirillum sp. HhutSZ1 的基因组特征分析
Authors Luo Y , Li T , Zhang S , Gu D, Fan B
Received 20 May 2025
Accepted for publication 29 October 2025
Published 11 November 2025 Volume 2025:18 Pages 5887—5894
DOI https://doi.org/10.2147/IDR.S541348
Checked for plagiarism Yes
Review by Single anonymous peer review
Peer reviewer comments 3
Editor who approved publication: Dr Hazrat Bilal
Yi Luo,1 Taihan Li,1 Suo Zhang,2 Dayong Gu,1 Bing Fan1
1Department of Laboratory, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China; 2Department of Rheumatology and Immunology, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China
Correspondence: Bing Fan, Department of Laboratory, Shenzhen Second People’s Hospital, No. 3002, Sungang West Road, Futian District, Shenzhen, Guangdong, People’s Republic of China, Email 13631587960@qq.com
Purpose: This study aims to conduct a whole-genome analysis of the isolated strain HhutSZ1, providing more reliable clinical experience for the treatment of patients infected with such bacteria.
Patients and Methods: A patient with IgA nephropathy failed to respond to treatment with ciprofloxacin for an infection. A rare strain of Herbaspirillum was isolated from the patient’s blood. The VITEK MS Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) System and VITEK 2 Automated Microbial Identification System were used to conduct a preliminary identification and antibiotic susceptibility tests. Then we performed whole-genome sequencing of this strain along with comparative genomic analysis.
Results: VITEK 2 System identified HhutSZ1 as Burkholderia cepacia, while the VITEK MS System identified it as Herbaspirillum huttiense with a high confidence coefficient. The phylogenetic tree based on the 16S rRNA gene showed that HhutSZ1 belonged to the genus Herbaspirillum. Average Nucleotide Identity (ANI) analysis showed that the scores of this strain compared with other Herbaspirillum huttiense strains were all lower than 95, confirming that this strain did not belong to Herbaspirillum huttiense. The patient’s infection failed to resolve despite ciprofloxacin treatment. Subsequent antimicrobial susceptibility testing revealed that HhutSZ1 exhibited intermediate resistance to ciprofloxacin, which is consistent with the clinical treatment failure. Six genes were detected in the Comprehensive Antibiotic Resistance Database (CARD). And among them, five RND family efflux pump genes resistant to fluoroquinolone were all located on chromosomes.
Conclusion: For the genus Herbaspirillum, mass spectrometry identification cannot accurately identify the species. The analysis based on 16s rRNA combined with ANI can be more accurate. Some Herbaspirillum spp may have inherent resistance to fluoroquinolone antibiotics. In conclusion, our findings suggest that the low detection rate and low drug resistance of this strain cannot be overlooked, and the study provides valuable clinical insight for managing infections in immunocompromised patients.
Keywords: Herbaspirillum hutitense, bloodstream infection, whole genome sequence, antibiotic resistance
1Department of Laboratory, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China; 2Department of Rheumatology and Immunology, Shenzhen Second People’s Hospital, Shenzhen, People’s Republic of China
Correspondence: Bing Fan, Department of Laboratory, Shenzhen Second People’s Hospital, No. 3002, Sungang West Road, Futian District, Shenzhen, Guangdong, People’s Republic of China, Email 13631587960@qq.com
Purpose: This study aims to conduct a whole-genome analysis of the isolated strain HhutSZ1, providing more reliable clinical experience for the treatment of patients infected with such bacteria.
Patients and Methods: A patient with IgA nephropathy failed to respond to treatment with ciprofloxacin for an infection. A rare strain of Herbaspirillum was isolated from the patient’s blood. The VITEK MS Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) System and VITEK 2 Automated Microbial Identification System were used to conduct a preliminary identification and antibiotic susceptibility tests. Then we performed whole-genome sequencing of this strain along with comparative genomic analysis.
Results: VITEK 2 System identified HhutSZ1 as Burkholderia cepacia, while the VITEK MS System identified it as Herbaspirillum huttiense with a high confidence coefficient. The phylogenetic tree based on the 16S rRNA gene showed that HhutSZ1 belonged to the genus Herbaspirillum. Average Nucleotide Identity (ANI) analysis showed that the scores of this strain compared with other Herbaspirillum huttiense strains were all lower than 95, confirming that this strain did not belong to Herbaspirillum huttiense. The patient’s infection failed to resolve despite ciprofloxacin treatment. Subsequent antimicrobial susceptibility testing revealed that HhutSZ1 exhibited intermediate resistance to ciprofloxacin, which is consistent with the clinical treatment failure. Six genes were detected in the Comprehensive Antibiotic Resistance Database (CARD). And among them, five RND family efflux pump genes resistant to fluoroquinolone were all located on chromosomes.
Conclusion: For the genus Herbaspirillum, mass spectrometry identification cannot accurately identify the species. The analysis based on 16s rRNA combined with ANI can be more accurate. Some Herbaspirillum spp may have inherent resistance to fluoroquinolone antibiotics. In conclusion, our findings suggest that the low detection rate and low drug resistance of this strain cannot be overlooked, and the study provides valuable clinical insight for managing infections in immunocompromised patients.
Keywords: Herbaspirillum hutitense, bloodstream infection, whole genome sequence, antibiotic resistance