Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates.

I-Chen Li,Gine-Ye Yu,Chung-Hsi Chou,Jing-Fang Huang,Zeng-Weng Chen

doi:10.3390/microorganisms10020227

I-Chen Li, Gine-Ye Yu + Show 3 more

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https://doi.org/10.3390/microorganisms10020227

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Abstract

It is well established that plasmids carrying multiple antimicrobial resistance (AMR) genes can be easily transferred among bacterial isolates by horizontal gene transfer. Previous studies have shown that a combination of short- and long-read approaches is effective in reconstructing accurate plasmids. However, high-quality Illumina short reads mapped onto the long reads in the context of an AMR hybrid monitoring strategy have not yet been explored. Hence, this study aimed to improve the reconstruction of plasmids, including the localization of AMR genes, using the above-described parameters on whole-genome sequencing (WGS) results. To the best of our knowledge, this study is the first to use S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) to confirm the number and sizes of plasmids detected by in silico-based predictions in Salmonella strains. Our results showed that de novo assembly did not detect the number of bacterial plasmids more accurately than reference-based assembly did. As this new hybrid mapping strategy surpassed de novo assembly in bacterial reconstruction, it was further used to identify the presence and genomic location of AMR genes among three Salmonella enterica serovar Schwarzengrund isolates. The AMR genes identified in the bacterial chromosome among the three Salmonella enterica serovar Schwarzengrund isolates included: AAC(3)-IV, AAC(6′)-Iy, aadA2, APH(4)-Ia, cmlA1, golS, mdsA, mdsB, mdsC, mdtK, qacH, sdiA, sul2, sul3, and TEM-1 genes. Moreover, the presence of TEM-1, AAC(3)-IV, aadA2, APH(4)-Ia, cmlA1, dfrA12, floR, sul1, sul3, and tet(A) genes found within three IncFIB plasmids and one IncX1 plasmid highlight their possible transmission into the environment, which is a public health risk. In conclusion, the generated data using this new hybrid mapping strategy will contribute to the improvement of AMR monitoring and support the risk assessment of AMR dissemination.

Highlights

IntroductionIn addition to the direct cytotoxic effects of this deadly virus, bacterial co-infections and secondary infections have become prevalent and emergent, especially among patients admitted to intensive care units due to Microorganisms 2022, 10, 227
After trimming and adapter removal, the quality of the short reads (Figure 2A) and long reads (Figure 2B) of three S. enterica serovar Schwarzengrund isolates were assessed by FastQC and LongQC, respectively
antimicrobial resistance (AMR) genes localized on plasmids can be transferred and spread by horizontal gene transfer, their occurrence should be closely monitored

Summary

Introduction

In addition to the direct cytotoxic effects of this deadly virus, bacterial co-infections and secondary infections have become prevalent and emergent, especially among patients admitted to intensive care units due to Microorganisms 2022, 10, 227. Studies have shown that after viral infections, such as influenza or COVID19, both the innate and adaptive immune systems are impaired and thereby enhance the proliferation of potentially pathogenic bacterial species [3]. A study conducted by The Pew Charitable Trusts found that among 5838 hospital admissions from February through July 2020, more than half of hospital patients received antibiotics during the first six months of the pandemic to prevent secondary bacterial and fungal infections [4]

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