Objective: The study aims to investigate the characteristic baseline information about genetic lineages, drug-resistance genes, virulence genes and evolutionary relationships of food-borne Listeria monocytogenes (Lm) isolates from Nanshan district of Shenzhen. Methods: The whole genomes of 46 Lm isolates during 2009-2019 were extracted and sequenced (Illumina PE-150, 100×). The CLC Genomics Workbench 12.0 was used to assemble and align Lm genomes, analyze their housekeeping genes, drug-resistance genes and virulence genes, and construct a k-mer phylogenetic tree. Results: After assembly, all genomes satisfied analytical conditions (contigs N50>20 kb). The medians of GC content, gene count and gene size were 38.3%, 5 960 and 2 952 608 bp, respectively. Based on the Lm genomic reference database, the local k-mer phylogenetic tree had 14 clusters of which the genetic distance was wide. The 46 Lm isolates were classified as Lineage 1 (21), Lineage 2 (23) and Lineage 3 (2). The most common ST type of Lineage 1 was ST87, followed by ST3, ST59, ST224 and ST429, whereas the major ST types of Lineage 2 included ST8 and ST9, the rest being ST121, ST155, ST199, ST204 and ST321. However, Lineage 3 only had ST299. The part of Lm strains carried five drug-resistance genes, such as fosX (17), tetM (6), dfrG (4), catB3 (1) and mefA (1). Furthermore, all strains possessed nine virulence genes, including flaA, iap, actA, hly, mpl, prfA, plcA, plcB and inlB. Nevertheless, six isolates and three of them respectively carried the mutant inlA and inlJ, and other two isolates lacked inlC. Conclusion: The food-borne Lm isolates from Nanshan district of Shenzhen presented genetic and evolutionary diversity. Noted that the drug-resistant strains, which also owned abundant virulence genes with specific functions, could lead to serious infections, particularly those isolates from raw poultry and Flammulina velutipes. It was implied that the local region was at risk due to Listeriosis by food. This study offered reference for prevention, control and treatment of Lm infection to the Greater Bay Area.
目的： 分析深圳市南山区食源性单核细胞增多性李斯特菌（Lm）基因组遗传家系、耐药基因、毒力基因和进化关系的特征性基线信息。 方法： 对2009—2019年南山区食品中分离的46株Lm进行全基因组提取和二代测序（PE-150，100×），运用CLC Genomics Workbench 12.0软件组装、比对基因组及分析其管家基因、耐药基因、毒力基因和k-mer系统进化关系等特征。 结果： 46个Lm基因组组装后均满足分析条件（contigs N50>20 kb），平均GC含量为38.3%、预测基因数为5 960个、基因组大小为2 952 608 bp；南山区Lm全基因组k-mer系统发生树可见14簇，总体遗传距离较大，其遗传家系包括21株Lineage 1、23株Lineage 2和2株Lineage 3，Lineage 1以ST87为主，其余为ST3、ST59、ST224和ST429，Lineage 2以ST8和ST9为主，其余为ST121、ST155、ST199、ST204和ST321，Lineage 3只见ST299；发现本地区Lm携带fosX（17株）、tetM（6株）、dfrG（4株）、catB3（1株）和mefA（1株）5种耐药基因，均携带flaA、iap、actA、hly、mpl、prfA、plcA、plcB和inlB 九种毒力基因，同时有6株inlA与3株inlJ发生变异和2株inlC缺失。 结论： 深圳市南山区分离的食源性Lm呈现遗传进化多样性，携带耐药基因情况较为严重，特别是来源于生禽肉和金针菇的分离株，且功能明确的毒力基因丰富齐全。.