Whole genome sequencing (WGS) fails to detect antimicrobial resistance (AMR) from heteroresistant subpopulation of Salmonella enterica

Ye Htut Zwe; Seow Fong Chin; Gurjeet Singh Kohli; Kyaw Thu Aung; Liang Yang; Hyun-Gyun Yuk

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Whole genome sequencing (WGS) fails to detect antimicrobial resistance (AMR) from heteroresistant subpopulation of Salmonella enterica

机译：全基因组测序（WGS）未能检测来自沙门氏菌肠的杂硼亚群的抗微生物抗性（AMR）

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Due to rapidly falling costs, whole genome sequencing (WGS) is becoming an essential tool in the surveillance of antimicrobial resistance (AMR) in Salmonella enterica. Although there have been many recent works evaluating the accuracy of WGS in predicting AMR from a large number of Salmonella isolates, little attention has been devoted to deciphering the underlying causes of disagreement between the WGS genotype and experimentally determined AMR phenotype. This study analyzed the genomes of six S. enterica isolates previously obtained from raw chicken which exhibited disagreements between WGS genotype and AMR phenotype. A total of five WGS false negative predictions toward ampicillin, amoxicillin/clavulanate, colistin, and fosfomycin resistance were presented in conjunction with their corresponding empirical phenotypic and/or genetic evidence of hetero-resistance. A further case study highlighting the inherent limitations of WGS to detect the underlying genetic mechanisms of colistin heteroresistance was presented. These findings implicate heteroresistance as an underlying cause for false negative WGS-based AMR predictions in S. enterica and suggest that widespread use of WGS in the surveillance of AMR in food isolates might severely underestimate true resistance rates.

机译：由于成本迅速下降，全基因组测序（WGS）正成为沙门氏菌肠道抗菌抗性（AMR）的重要工具。虽然最近有许多作品评估WG在从大量沙门氏菌的预测AMR预测AMR的准确性，但是致力于解读WGS基因型和实验确定的AMR表型之间分歧的潜在原因的重视。该研究分析了先前从生鸡肉获得的六次肠道分离物的基因组，其在WGS基因型和AMR表型之间表现出分类。对于氨苄青霉素，阿莫西林/克拉维亚酸酯，乳蛋白和福染霉素抗性总共五个WGS假阴性预测结果与其相应的经验表型和/或异质抗性的遗传证据一起呈现。介绍了一种进一步的案例研究，突出了WG的固有局限性，以检测Colistin杂化率的基本遗传机制。这些发现将杂收呈现为S.Nexica中基于假阴性WGS的AMR预测的潜在原因，并表明WG在食品分离株中AMR监测中的广泛使用可能严重低估了真正的阻力率。

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来源
《Food microbiology》 |2020年第10期|103530.1-103530.7|共7页
作者
Ye Htut Zwe; Seow Fong Chin; Gurjeet Singh Kohli; Kyaw Thu Aung; Liang Yang; Hyun-Gyun Yuk;
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作者单位

Department of Food Science and Technology National University of Singapore Singapore;

Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore;

Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore Alfred Wegener-Institut Helmholtz-Zentrum fuer Polarund Meeresforschung Bremerhaven Germany;

National Centre for Food Science Singapore Food Agency Singapore School of Chemical and Biomedical Engineering Nanyang Technological University Singapore School of Biological Sciences Nanyang Technological University Singapore;

Singapore Centre for Environmental Life Sciences Engineering Nanyang Technological University Singapore School of Biological Sciences Nanyang Technological University Singapore School of Medicine Southern University of Science and Technology Shenzhen China;

Department of Food Science and Technology Korea National University of Transportation Jeungpyeong-gun Chungbuk Republic of Korea;

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收录信息美国《科学引文索引》(SCI);美国《化学文摘》(CA);
原文格式 PDF
正文语种 eng
中图分类
关键词
Salmonella enterica; Whole genome sequencing; Heteroresistance; Antimicrobial resistance prediction; False negative errors;

机译：沙门氏菌肠道;全基因组测序;杂项;抗微生物抗性预测;假阴性错误;

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1. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain [J] . Elena A. Oniciuc, Eleni Likotrafiti, Adrián Alvarez-Molina, Genes . 2018,第5期

机译：全基因组测序（WGS）和全基因组测序（WMS）在整个食物链中的耐药菌和耐药基因监测的现状和未来
2. Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhimurium Strain WG49 and Escherichia coli Strain WG5 Used in South Africa for Phage Detection in Water Samples [J] . L. Bothma, D. Gonzalez-Ibeas, C. Mienie, Genome Announcements . 2018,第26期

机译：肠道沙门氏菌亚种的全基因组序列。南非使用Enterero血清型鼠伤寒菌株WG49和大肠杆菌WG5进行噬菌体检测
3. Hospital transmission of carbapenemase-producing Enterobacterales (CPE) and Salmonella enterica – two outbreaks linked by using whole genome sequencing (WGS) [J] . Andie S. Lee, Elizabeth White, Jacquelyn Petty, Infection, Disease & Health . 2019,第3期

机译：产生碳青霉烯酶的肠杆菌（CPE）和肠炎沙门氏菌的医院传播–使用全基因组测序（WGS）关联的两次暴发
4. Antimicrobial photodynamic therapy applied to inactivation of Salmonella enterica and Staphylococcus aureus [C] . Ranniele L. V. Silva, Ialy A. Moura, Juliana O. Moraes, Optical Interactions with Tissue and Cells XXX . 2019

机译：抗菌光动力疗法用于灭活肠炎沙门氏菌和金黄色葡萄球菌
5. Role of Incompatibility Group 1 (IncI1) Plasmid-encoded Factors on Salmonella enterica Antimicrobial Resistance and Virulence [D] . Kaldhone, Pravin Raghunath. 2017

机译：不相容性组1（IncI1）质粒编码因子对肠炎沙门氏菌的耐药性和毒力的作用
6. Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife [O] . Milton Thomas, Gavin John Fenske, Linto Antony, 2017

机译：基于全基因组测序的野生型非伤寒沙门氏菌中抗菌素耐药性和毒力的检测
7. Correction: Oniciuc, E. A.; et al. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes 2018, 9, 268. [O] . Elena Oniciuc, Eleni Likotrafiti, Adrián Alvarez-Molina, 2018

机译：纠正：oniciuc，E. a .;等等。整个基因组测序（WGS）和全部偏心组测序（WMS）的现状和未来，用于在食物链上监测抗微生物抗性微生物和抗微生物抗性基因。 2018,9,268基因。

Whole genome sequencing (WGS) fails to detect antimicrobial resistance (AMR) from heteroresistant subpopulation of Salmonella enterica

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