Machado Maxsueli Aparecida Moura, Panzenhagen Pedro, Lázaro Cesar, Rojas Miguel, Figueiredo Eduardo Eustáquio de Souza, Conte-Junior Carlos Adam
Food Science Program (PPGCAL), Chemistry Institute (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, Brazil.
Antibiotics (Basel). 2024 Aug 6;13(8):737. doi: 10.3390/antibiotics13080737.
In this pioneering in silico study in Peru, we aimed to analyze () genomes for antimicrobial resistance genes (ARGs) diversity and virulence and for its mobilome. For this purpose, 469 assemblies from human, domestic, and wild animal hosts were investigated. Of these genomes, three were strains (pv05, pv06, and sf25) isolated from chickens in our previous study, characterized for antimicrobial susceptibility profile, and sequenced in this study. Three other genomes were included in our repertoire for having rare cgMLSTs. The phenotypic analysis for antimicrobial resistance revealed that pv05, pv06, and sf25 strains presented multidrug resistance to antibiotics belonging to at least three classes. Our in silico analysis indicated that many Peruvian genomes included resistance genes, mainly to the aminoglycoside class, ESBL-producing , sulfonamides, and tetracyclines. In addition, through Multi-locus Sequence Typing, we found more than 180 different STs, with ST10 being the most prevalent among the genomes. Pan-genome mapping revealed that, with new lineages, the repertoire of accessory genes in increased, especially genes related to resistance and persistence, which may be carried by plasmids. The results also demonstrated several genes related to adhesion, virulence, and pathogenesis, especially genes belonging to the high pathogenicity island (HPI) from , with a prevalence of 42.2% among the genomes. The complexity of the genetic profiles of resistance and virulence in our study highlights the adaptability of the pathogen to different environments and hosts. Therefore, our in silico analysis through genome sequencing enables tracking the epidemiology of from Peru and the future development of strategies to mitigate its survival.
在秘鲁开展的这项开创性的计算机模拟研究中，我们旨在分析（）基因组中的抗微生物耐药基因（ARG）多样性、毒力及其可移动基因组。为此，我们研究了来自人类、家畜和野生动物宿主的469个基因组组装体。在这些基因组中，有三个是我们之前研究中从鸡身上分离出的菌株（pv05、pv06和sf25），已对其抗微生物药敏谱进行了表征，并在本研究中进行了测序。另外三个基因组因其具有罕见的核心基因组多位点序列分型（cgMLST）而被纳入我们的研究范围。抗微生物耐药性的表型分析表明，pv05、pv06和sf25菌株对至少三类抗生素呈现多重耐药性。我们的计算机模拟分析表明，许多秘鲁基因组含有耐药基因，主要对氨基糖苷类、产超广谱β-内酰胺酶（ESBL）的（菌）、磺胺类和四环素类耐药。此外，通过多位点序列分型，我们发现了180多种不同的序列型（ST），其中ST10在这些基因组中最为常见。泛基因组图谱显示，随着新谱系的出现，（某种菌）的辅助基因库增加，尤其是与耐药性和持续性相关的基因，这些基因可能由质粒携带。结果还显示了几个与黏附、毒力和致病机制相关的基因，特别是来自（某种菌）的高致病性岛屿（HPI）的基因，在这些基因组中的流行率为42.2%。我们研究中耐药性和毒力基因谱的复杂性突出了病原体对不同环境和宿主的适应性。因此，我们通过基因组测序进行的计算机模拟分析能够追踪来自秘鲁的（某种菌）的流行病学情况以及制定减轻其生存的策略的未来发展。
