Salmonella is recognized as one of the most common microbial pathogens worldwide. The bacterium contains the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems, providing adaptive immunity against invading foreign nucleic acids. Previous studies suggested that certain bacteria employ the Cas proteins of CRISPR-Cas systems to target their own genes, which also alters the virulence during invasion of mammals. However, whether CRISPR-Cas systems in Salmonella have similar functions during bacterial invasion of host cells remains unknown. Here, we systematically analyzed the genes that are regulated by Cas3 in a type I-E CRISPR-Cas system and the virulence changes due to the deletion of cas3 in Salmonella enterica serovar Enteritidis. Compared to the cas3 gene wild-type (cas3 WT) Salmonella strain, cas3 deletion upregulated the lsrFGBE genes in lsr (luxS regulated) operon related to quorum sensing (QS) and downregulated biofilm-forming-related genes and Salmonella pathogenicity island 1 (SPI-1) genes related to the type three secretion system (T3SS). Consistently, the biofilm formation ability was downregulated in the cas3 deletion mutant (Δcas3). The bacterial invasive and intracellular capacity of Δcas3 to host cells was also reduced, thereby increasing the survival of infected host cells and live chickens. By the transcriptome-wide screen (RNA-Seq), we found that the cas3 gene impacts a series of genes related to QS, the flagellum, and SPI-1-T3SS system, thereby altering the virulence phenotypes. As QS SPI-1-T3SS and CRISPR-Cas systems are widely distributed in the bacteria kingdom, our findings extend our understanding of virulence regulation and pathogenicity in mammalian hosts for Salmonella and potentially other bacteria.

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Summary Background Salmonella enterica subspecies enterica serovar abortus equi (S. abortus equi) is well known as the aetiological agent of equine abortion. However, abortion caused by S. abortus equi has not been previously described in donkeys. Objectives To investigate whether S. abortus equi was correlated with an abortion outbreak consisting of 61 abortions. Study design Investigation of the clinical cases using pathoanatomical, bacteriological, serological and molecular approaches. Methods Autopsies on nine aborted foetuses were performed. Tissue specimens from seven aborted foetuses and two mares were cultured and subjected to detection of equine herpesvirus 1 (EHV‐1), equine herpesvirus 4 (EHV‐4) and equine arteritis virus (EAV) by polymerase chain reaction. The isolates were serotyped according to the Kaufmann−White scheme and analysed by multi‐locus sequence typing (MLST). Detection of EHV and EAV antibodies was performed in all pregnant mares. Results No obvious gross lesions were observed in the foetuses. Nine Gram‐negative isolates were obtained from all nine tissue samples and were identified as Salmonella spp. All of the isolates belonged to the B group, the O antigen epitope was 4, 12 and H antigen was not obtained. The isolates of Salmonella were characterised as sequence type (ST) 251. Detection of EHV‐1, EHV‐4 and EAV was negative. Main limitations The mechanism that causes abortion in donkeys needs further study and the lack of histological examination. Conclusion Salmonella abortus equi was isolated as the single agent and was responsible for the abortions. Equine practitioners should be aware of S. abortus equi infection as a cause of abortion in donkeys.