Oita University Faculty of Medicine, Department of Infectious Disease Control, Yufu, Oita, Japan.
Faculty of Medicine, Department of Anatomy, Histology and Pharmacology, Universitas Airlangga, Surabaya, Indonesia.
PLoS One. 2023 May 18;18(5):e0284958. doi: 10.1371/journal.pone.0284958. eCollection 2023.
Inadequate antimicrobial treatment has led to multidrug-resistant (MDR) bacteria, including Helicobacter pylori (H. pylori), which one of the notable pathogens in the stomach. Antibiotic-induced changes in the microbiota can negatively affect the host. This study aimed to determine the influence of H. pylori resistance on the diversity and abundance of the stomach microbiome.
Bacterial DNA was extracted from biopsy samples of patients presenting dyspepsia symptoms with H. pylori positive from cultures and histology. DNA was amplified from the V3-V4 regions of the 16S rRNA gene. In-vitro E-test was used to detect antibiotic resistance. Microbiome community analysis was conducted through α-diversity, β-diversity, and relative abundance.
Sixty-nine H. pylori positive samples were eligible after quality filtering. Following resistance status to five antibiotics, samples were classified into 24 sensitive, 24 single resistance, 16 double resistance, 5 triple resistance. Samples were mostly resistant to metronidazole (73.33%; 33/45). Comparation of four groups displayed significantly elevated α-diversity parameters under the multidrug resistance condition (all P <0.05). A notable change was observed in triple-resistant compared to sensitive (P <0.05) and double-resistant (P <0.05) groups. Differences in β-diversity by UniFrac and Jaccard were not significant in terms of the resistance (P = 0.113 and P = 0.275, respectively). In the triple-resistant group, the relative abundance of Helicobacter genera was lower, whereas that of Streptococcus increased. Moreover, the linear discriminant analysis effect size (LEfSe) was associated with the presence of Corynebacterium and Saccharimonadales in the single-resistant group and Pseudomonas and Cloacibacterium in the triple-resistant group.
Our results suggest that the resistant samples showed a higher trend of diversity and evenness than the sensitive samples. The abundance of H. pylori in the triple-resistant samples decreased with increasing cohabitation of pathogenic bacteria, which may support antimicrobial resistance. However, antibiotic susceptibility determined by the E-test may not completely represent the resistance status.
抗菌治疗不充分导致了包括幽门螺杆菌（H. pylori）在内的多种耐药菌的出现，H. pylori 是胃中一种重要的病原体。抗生素诱导的微生物群变化可能会对宿主产生负面影响。本研究旨在确定 H. pylori 耐药性对胃微生物组多样性和丰度的影响。
从培养和组织学中呈 H. pylori 阳性的消化不良症状患者的活检样本中提取细菌 DNA。从 16S rRNA 基因的 V3-V4 区扩增 DNA。使用体外 E 试验检测抗生素耐药性。通过 α 多样性、β 多样性和相对丰度进行微生物组群落分析。
经过质量过滤后，共有 69 个 H. pylori 阳性样本符合条件。根据对五种抗生素的耐药情况，将样本分为 24 个敏感组、24 个单耐药组、16 个双耐药组和 5 个三耐药组。样本对甲硝唑的耐药率最高（73.33%；33/45）。在多药耐药条件下，四个组的 α 多样性参数显著升高（均 P <0.05）。与敏感组（P <0.05）和双耐药组（P <0.05）相比，三耐药组的变化更为显著。基于 UniFrac 和 Jaccard 的 β 多样性差异在耐药性方面没有统计学意义（分别为 P = 0.113 和 P = 0.275）。在三耐药组中，Helicobacter 属的相对丰度较低，而链球菌属的相对丰度增加。此外，线性判别分析效应量（LEfSe）与单耐药组中 Corynebacterium 和 Saccharimonadales 的存在以及三耐药组中 Pseudomonas 和 Cloacibacterium 的存在相关。
我们的结果表明，耐药样本的多样性和均匀度呈上升趋势，高于敏感样本。三耐药样本中 H. pylori 的丰度随着共生致病菌的增加而降低，这可能支持抗生素耐药性。然而，E 试验确定的抗生素药敏性可能并不能完全代表耐药状态。
