Genomic Determinants of Pathogenicity and Antimicrobial Resistance for 60 Global Listeria monocytogenes Isolates Responsible for Invasive Infections

Abstract

Listeria monocytogenes remains a significant public health threat, causing invasive listeriosis manifested as septicemia, meningitis, and abortion, with up to 30% of cases having a fatal outcome. Tracking the spread of invasive listeriosis requires an updated knowledge for virulence factors (VFs) and antimicrobial resistance features, which is an essential step toward its clinical diagnosis and treatment. Taking advantage of high-throughput genomic sequencing, we proposed that the differential genes based on the pathogenomic composition could be used to evaluate clinical observations and therapeutic options for listeriosis. Here, we performed the comparative genomic analysis of 60 strains from five continents with a diverse range of sources, representing serotypes 1/2a, 1/2b, 1/2c, and 4b, comprising lineage I and lineage II and including 13 newly contributed Chinese isolates from clinical cases. These strains were associated with globally distributed clonal groups linked with confirmed foodborne listeriosis outbreak and sporadic cases. We found that L. monocytogenes strains from clonal complex (CC) CC8, CC7, CC9, and CC415 carried most of the adherence and invasive genes. Conversely, CC1, CC2, CC4, and CC6 have the least number of adherence and invasive genes. Additionally, Listeria pathogenicity island-1 (LIPI-1), LIPI-2, intracellular survival, surface anchoring, and bile salt resistance genes were detected in all isolates. Importantly, LIPI-3 genes were harbored in CC3, CC224, and ST619 of the Chinese isolates and in CC1, CC4, and CC6 of other worldwide isolates. Notably, Chinese isolates belonging to CC14 carried antibiotic resistance genes (ARGs) against β-lactams (blaTEM-101, blaTEM-105) and macrolide (ermC-15), whereas CC7 and CC8 isolates harbored ARGs against aminoglycoside (aadA10_2, aadA6_1), which may pose a threat to therapeutic efficacy. Phylogenomic analysis showed that CC8, CC7, and CC5 of Chinese isolates, CC8 (Swiss and Italian isolates), and CC5 and CC7 (Canadian isolates) are closely clustered together and belonged to the same CC. Additionally, CC381 and CC29 of Chinese isolates shared the same genomic pattern as CC26 of Swiss isolate and CC37 of Canadian isolate, respectively, indicating strong phylogenomic relation between these isolates. Collectively, this study highlights considerable clonal diversity with well-recognized virulence and antimicrobial-resistant determinants among Chinese and worldwide isolates that stress to design improved strategies for clinical therapies.

First Report of Septicaemic Listeriosis in a Loggerhead Sea Turtle (Caretta caretta) Stranded along the Adriatic Coast: Strain Detection and Sequencing

“…Note that the presence of LIPI-4 genes, usually reported in hypervirulent strains, is usually associated with high tropism for neuronal and placental tissue [ 30 ]. Adhesive and invasive genes such as ami and aut were missing, in agreement with Shi and colleagues [ 34 ], who detected the absence of these genes in L. monocytogenes strains belonging to serogroup IVb. InlF , lntA , and vip genes were present as well.…”

“…lntA modulates the host’s INF-l-mediated immune response, and vip interacts with the host endoplasmic reticulum for cell invasion and signalling events during infection [ 32 ]. Listeriolysin S , representing LIPI-3, is responsible for L. monocytogenes ’s interaction with gut microbiota and is usually associated with serotype 4b, but it was missing in our strain [ 34 ]. The presence of SigB factors explains the strain’s ability to survive the acidic gastric environment.…”

Table_1.XLS

“…B. cereus was detected in 8.49% (91/1076) of all samples collected, out of which 65/91 (71.4%) were from boiled rice dishes, 6/91 (6.6%) were from boiled rice noodles, 13/91 (14.3%) were from fried rice noodles, 2/91 (2.2%) were from sticky rice roll, 3/91 (3.3%) were from boiled sticky rice dishes and 2/91 (2.2%) were from fried rice cake. According to previously published data, there are significant variances in the detection rate of B. cereus in various types of food samples from different regions of the world (Wang et al, 2019;Xu et al, 2020;Qiu et al, 2021;Shi et al, 2021;Wu et al, 2021). The total occurrence rate of B. cereus in our study was similar to a previous study in which B. cereus was isolated from dairy products, rice and flour products in China (Zhao et al, 2020).…”

Prevalence and antimicrobial-resistant characterization of Bacillus cereus isolated from ready-to-eat rice products in Eastern China

“…B. cereus was detected in 8.49% (91/1076) of all samples collected, out of which 65/91 (71.4%) were from boiled rice dishes, 6/91 (6.6%) were from boiled rice noodles, 13/91 (14.3%) were from fried rice noodles, 2/91 (2.2%) were from sticky rice roll, 3/91 (3.3%) were from boiled sticky rice dishes and 2/91 (2.2%) were from fried rice cake. According to previously published data, there are significant variances in the detection rate of B. cereus in various types of food samples from different regions of the world ( Wang et al, 2019 ; Xu et al, 2020 ; Qiu et al, 2021 ; Shi et al, 2021 ; Wu et al, 2021 ). The total occurrence rate of B. cereus in our study was similar to a previous study in which B. cereus was isolated from dairy products, rice and flour products in China ( Zhao et al, 2020 ).…”

“…Clustering analysis was based on the Dice similarity coefficient and the unweighted pair group method with arithmetic mean (UPGMA). The Hunter and Gaston Diversity Index (HGDI) was calculated to evaluate the discriminatory capability of ERIC-PCR ( Shi et al, 2021 ). Isolates that share 100% similarity of amplicon bands pattern were grouped into one genotype.…”