摘要
      非伤寒沙门氏菌（NTS）是全球细菌性小肠结肠炎的主要原因，但也会引起侵入性血液感染。抗微生物耐药性（AMR）阻碍了这些感染的治疗，了解AMR如何在NTS之间传播可能有助于制定有效的策略。我们调查了越南动物和人类中与侵袭性疾病、腹泻病和无症状携带相关的NTS分离株。分离物包括多个血清型和常见和罕见的表型AMR谱；使用长读和短读测序来研究与表型AMR谱相关的遗传机制和基因组背景。我们证明了大多数AMR基因型和表型之间的一致性，但在临床相关表型中发现了巨大的基因型多样性，以及在这种情况下AMR基因（ARG）的高迁移潜力。我们发现84 % 鉴定的ARGs位于质粒上，最常见的是含有IncHI1A_1和IncHI1B（R27）_1_R27复制子的质粒（33%），以及含有IncHI2_1和IncHI2A_1复制子的（31%）。绝大多数（95%）的ARGS是在10kbp的IS6/IS26元件内发现的，这为质粒提供了在质粒和基因组其他部分之间交换ARGS的机制。在One Health环境中应用的全基因组测序和靶向长读测序确定了与AMR相关的插入序列和质粒复制子的数量相对有限。因此，在来自越南的NTS的背景下，以及可能在其他环境中，ARGs移动的机制比特定的ARGs有助于更成功的AMR图谱，促进细菌适应不同的环境或选择压力。
ABSTRACT
 
Non-typhoidal Salmonella (NTS) is a major cause of bacterial enterocolitis globally but also causes invasive bloodstream infections. Antimicrobial resistance (AMR) hampers the treatment of these infections and understanding how AMR spreads between NTS may help in developing effective strategies. We investigated NTS isolates associated with invasive disease, diarrhoeal disease and asymptomatic carriage in animals and humans from Vietnam. Isolates included multiple serovars and both common and rare phenotypic AMR profiles; long- and short-read sequencing was used to investigate the genetic mechanisms and genomic backgrounds associated with phenotypic AMR profiles. We demonstrate concordance between most AMR genotypes and phenotypes but identified large genotypic diversity in clinically relevant phenotypes and the high mobility potential of AMR genes (ARGs) in this setting. We found that 84 % of ARGs identified were located on plasmids, most commonly those containing IncHI1A_1 and IncHI1B(R27)_1_R27 replicons (33%), and those containing IncHI2_1 and IncHI2A_1 replicons (31%). The vast majority (95%) of ARGS were found within 10 kbp of IS6/IS26 elements, which provide plasmids with a mechanism to exchange ARGs between plasmids and other parts of the genome. Whole genome sequencing with targeted long-read sequencing applied in a One Health context identified a comparatively limited number of insertion sequences and plasmid replicons associated with AMR. Therefore, in the context of NTS from Vietnam and likely for other settings as well, the mechanisms by which ARGs move contribute to a more successful AMR profile than the specific ARGs, facilitating the adaptation of bacteria to different environments or selection pressures.

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000798