Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence

CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries

Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.

Relationship between CRISPR sequence type and antimicrobial resistance in avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is a primary cause of extraintestinal disease and respiratory infections in chickens; therefore, various antimicrobials applied via mass medication in farms to control APEC in Korea. In this study, we analyzed the relationship between CRISPR sequence type and antimicrobial resistance (AMR) in APEC isolates. Based on spacer distribution, a total of 103 CRISPR-positive APEC isolates were classified into 25 E. coli sequence types (ESTs), largely into two clusters that were correlated with phylogenetic groups: isolates appearing to have CRISPR 1 and/or 2 (93.2 %) and those having CRISPR 3 and 4 (6.8 %). Moreover, ESTs were divided into three AMR pattern-based groups: cephems-resistant group, non-cephems-resistant group, and antimicrobial sensitive group. There were significant differences among the groups (p < 0.05). Sixteen of the 25 ESTs had a significantly higher distribution of multidrug-resistant (MDR) isolates than the other ESTs (p < 0.05), and the ratio of MDR isolates was significantly higher than that of non-MDR isolates in the CRISPR 1 and 2 arrays (p < 0.05). A total of 9 protospacers were identified with protospacer, with protospacer 1 in CRISPR 1 being the most prevalent among the isolates (41.7 %). The protospacers of CRISPR 1 and 2 loci were associated with protection against external invaders such as bacteriophage or endogenous gene regulation. However, each protospacer of the CRISPR 3 and 4 loci originated from genes associated with AMR plasmids. These results indicate that CRISPR sequence type can improve AMR bacteria and enhance strategies for tackling the complexity of AMR in bacterial pathogens.

Genotypic correlation between Salmonella Enteritidis isolates from broiler breeders and hatchery flocks

In this study, Salmonella Enteritidis strains isolated from dust and environmental materials from different flocks located in Turkey’s Western Black Sea region were examined by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). A total of 59 S. Enteritidis strains isolated from broiler breeder and hatchery flocks, and one S. Enteritidis strain isolated from a stool sample of a farm worker were examined. PFGE analysis revealed two major PFGE groups and nine different macro restriction profiles. It was determined that 85% (51/60) of the strains were close to each other and comprised Group I. All S. Enteritidis strains had the same sequence type (ST): ST11. Isolation of strains with a single genotype suggests that there may be a cross transmission between the flocks.

Revisiting Persistent Salmonella Infection and the Carrier State: What Do We Know?

One characteristic of the few Salmonella enterica serovars that produce typhoid-like infections is that disease-free persistent infection can occur for months or years in a small number of individuals post-convalescence. The bacteria continue to be shed intermittently which is a key component of the epidemiology of these infections. Persistent chronic infection occurs despite high levels of circulating specific IgG. We have reviewed the information on the basis for persistence in S. Typhi, S. Dublin, S. Gallinarum, S. Pullorum, S. Abortusovis and also S. Typhimurium in mice as a model of persistence. Persistence appears to occur in macrophages in the spleen and liver with shedding either from the gall bladder and gut or the reproductive tract. The involvement of host genetic background in defining persistence is clear from studies with the mouse but less so with human and poultry infections. There is increasing evidence that the organisms (i) modulate the host response away from the typical Th1-type response normally associated with immune clearance of an acute infection to Th2-type or an anti-inflammatory response, and that (ii) the bacteria modulate transformation of macrophage from M1 to M2 type. The bacterial factors involved in this are not yet fully understood. There are early indications that it might be possible to remodulate the response back towards a Th1 response by using cytokine therapy.

Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato

Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I-IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.

Lactobacillus casei protects intestinal mucosa from damage in chicks caused by Salmonella pullorum via regulating immunity and the Wnt signaling pathway and maintaining the abundance of gut microbiota

Dysfunction of the intestinal mucosal barrier of chicks caused by Salmonella pullorum is of great harm to the poultry industry. Probiotics are recognized for their beneficial health-promoting properties, promoting maintenance of bowel epithelial integrity and host immune system homeostasis. Our previous research showed that Lactobacillus casei protects jejunal mucosa from injury in chicks infected with S. pullorum. However, the specific mechanisms underlying its protective properties are still not fully understood. In the present study, we aimed to explore the mechanisms underlying the protective effects of L. casei on the intestinal mucosal barrier of chicks infected with S. pullorum through histological, immunological, and molecular biology methods. The results indicated that L. casei significantly reduced the diarrhea rate, increased the daily weight gain, and maintained normal levels of IgA, IgM, and IgG in the serum of chicks infected with S. pullorum. Furthermore, we found that L. casei markedly improved the immunity of gut mucosa by regulating cytokine and chemokine receptor balance, elevating the number of intraepithelial lymphocytes, and hence effectively restraining bowel inflammation. Strikingly, feeding of infected chicks with L. casei notably boosted interleukin-22 expression to activate the Wingless-Int pathway, moderated diamine oxidase and D-lactic acid levels, diminished the generation of myosin light chain kinase, and expanded tight junction protein levels (Zonulin-1 and Claudin-1), strengthening the function of the gut mucosal epithelium. In addition, experiments using 16S rDNA sequencing also demonstrated that L. casei immensely weakened the adhesion of S. pullorum, mainly manifesting as improved diversity of the intestinal microbiota in the V4 area of infected chicks. Taken together, these results show that the application of L. casei may be a good strategy to regulate the intestinal inflammatory response of chicks infected with S. pullorum, providing new perspectives in producing antibiotic substitutes in poultry farms.

Survival of Salmonella Under Heat Stress is Associated with the Presence/Absence of CRISPR Cas Genes and Iron Levels

Clustered regularly interspaced short palindromic repeats (CRISPR) cas genes have been linked to stress response in Salmonella. Our aim was to identify the presence of CRISPR cas in Salmonella and its response to heat in the presence of iron. Whole genomes of Salmonella (n = 50) of seven serovars were compared to identify the presence of CRISPR cas genes, direct-repeats and spacers. All Salmonella genomes had all cas genes present except S. Newport 2393 which lacked these genes. Gene-specific primers were used to confirm the absence of these genes in S. Newport 2393. The presence/absence of CRISPR cas genes was further investigated among 469 S. Newport genomes from PATRIC with 283 genomes selected for pan-genome analysis. The response of eleven Salmonella strains of various serovars to gradual heat in ferrous and ferric forms of iron was investigated. A total of 32/283 S. Newport genomes that lacked all CRISPR cas genes clustered together. S. Newport 2393 was the most heat-sensitive strain at higher iron levels (200 and 220 pm) in ferrous and ferric forms of iron. The absence of CRISPR cas genes in S. Newport 2393 may contribute to its increase in heat sensitivity and iron may play a role in this. The high reduction in numbers of most Salmonella strains exposed to heat makes it unfeasible to extract RNA and conduct transcription studies. Further studies should be conducted to validate the survival of Salmonella when exposed to heat in the presence/absence of CRISPR cas genes and different iron levels.

CRISPR Typing of Salmonella Isolates from Different Resources

CRISPR typing is a newly developed method used to reveal the genetic relationship of bacterial isolates from different resources. For Salmonella, CRISPR typing can not only reveal the phylogenic difference among isolates belonging to the identical serotype, but also show good correspondence with Salmonella serotypes. Here we describe the protocol of CRISPR typing method used in Salmonella, and the approaches to analyze the genetic relationship among different strains.

Virulence Variation of Salmonella Gallinarum Isolates through SpvB by CRISPR Sequence Subtyping, 2014 to 2018

Simple Summary

Salmonella Gallinarum causes fowl typhoid in all ages of chickens, which results in economic loss of commercial chicken farms. The disease has been eradicated in many developed countries, but is still prevalent in Korea. In this study, we investigated virulence and genetic variation of S. Gallinarum from Korea, between 2014 and 2018. The results indicated that virulence was increased, which was associated with genetic change over time. Therefore, surveillance of genetic change associated with virulence increase is necessary for monitoring of S. Gallinarum isolates for dissemination.

Abstract

Salmonella Gallinarum is a Gram-negative bacteria that causes fowl typhoid, a septicemic disease with high morbidity and mortality that affects all ages of chickens. Although vaccines and antimicrobials have been used nationwide to eradicate the disease, the malady is still prevalent in Korea. In this study, we investigated the virulence and genetic variation of 116 S. Gallinarum isolates from laying hens between 2014 and 2018. A total of 116 isolates were divided into five Gallinarum Sequence Types (GST) through clustered regularly interspaced short palindromic repeats (CRISPR) subtyping method. The GSTs displayed changes over time. The 116 isolates showed no difference in virulence gene distribution, but the polyproline linker (PPL) length of the SpvB, one of the virulence factors of Salmonella spp., served as an indicator of S. Gallinarum pathogenicity. The most prevalent PPL length was 22 prolines (37.9%). The shortest PPL length (19 prolines) was found only in isolates from 2014 and 2015. However, the longest PPL length of 24 prolines appeared in 2018. This study indicates that PPLs of S. Gallinarum in Korea tend to lengthen over time, so the pathogenic potency of the bacteria is increasing. Moreover, the transition of GST was associated with PPL length extension over time. These results indicate that surveillance of changing GST and PPL length are necessary in the monitoring of S. Gallinarum isolates.

The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella

Salmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition and/or exchange of various virulence factors influences the evolutionary framework. To gain insights into evolution of Salmonella in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains differed in their CRISPR1-leader and cas operon features assorting into two main clades, CRISPR1-STY/cas-STY and CRISPR1-STM/cas-STM, comprising majorly typhoidal and non-typhoidal Salmonella serovars respectively. Serovars of these two clades displayed better relatedness, concerning CRISPR1-leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region could be through a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system. As opposed to broad-host-range, the host-specific serovars harbor fewer spacers. Mapping of protospacer sources suggested a partial correlation of spacer content with habitat diversity of the serovars. Some serovars like serovar Enteritidis and Typhimurium that inhabit similar environment/infect similar hosts hardly shared their protospacer sources.

Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012

Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0-4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0-10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.

Host and body site-specific adaptation of Lactobacillus crispatus genomes

Lactobacillus crispatus is a common inhabitant of both healthy poultry gut and human vaginal tract, and the absence of this species has been associated with a higher risk of developing infectious diseases. In this study, we analyzed 105 L. crispatus genomes isolated from a variety of ecological niches, including the human vaginal tract, human gut, chicken gut and turkey gut, to shed light on the genetic and functional features that drive evolution and adaptation of this important species. We performed in silico analyses to identify the pan and core genomes of L. crispatus, and to reveal the genomic differences and similarities associated with their origins of isolation. Our results demonstrated that, although a significant portion of the genomic content is conserved, human and poultry L. crispatus isolates evolved to encompass different genomic features (e.g. carbohydrate usage, CRISPR-Cas immune systems, prophage occurrence) in order to thrive in different environmental niches. We also observed that chicken and turkey L. crispatus isolates can be differentiated based on their genomic information, suggesting significant differences may exist between these two poultry gut niches. These results provide insights into host and niche-specific adaptation patterns in species of human and animal importance.

CRISPR-cas3 of Salmonella Upregulates Bacterial Biofilm Formation and Virulence to Host Cells by Targeting Quorum-Sensing Systems

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.

Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009-2017 in China

CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: - isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34 isolates from both Salmonella Typhimurium and Salmonella 4,[5],12:i:-. Among the isolates of ST34, TST4 was identified as the most common CRISPR type representing 86.5% of Salmonella 4,[5],12:i:- and 14.5 % of Salmonella Typhimurium mainly from pigs and humans. This study demonstrated that TST4-ST34 isolates were predominant in Salmonella 4,[5],12:i:-, and pig was the main reservoir for Salmonella 4,[5],12:i:- in China, which might have the potential to transmit to humans by pig production.

Loss and Gain in the Evolution of the Salmonella enterica Serovar Gallinarum Biovar Pullorum Genome

Pullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic epidemiological analysis of 97 S. Pullorum strains was carried out to reconstruct the phylogeny and transmission history of S. Pullorum. Further analysis demonstrated that functional gene loss and acquisition occurred simultaneously throughout the evolution of S. Pullorum, both of which reflected adaptation to the changing environment. The result of our study will be helpful in surveillance and prevention of pullorum disease.

Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the etiological agent of pullorum disease, causing white diarrhea with high mortality in chickens. There are many unsolved issues surrounding the epidemiology of S. Pullorum, including its origin and transmission history as well as the discordance between its phenotypic heterogeneity and genetic monomorphism. In this paper, we report the results of whole-genome sequencing of a panel of 97 S. Pullorum strains isolated between 1962 and 2014 from four countries across three continents. We utilized 6,795 core genome single nucleotide polymorphisms (SNPs) to reconstruct a phylogenetic tree within a spatiotemporal Bayesian framework, estimating that the most recent common ancestor of S. Pullorum emerged in ∼914 CE (95% confidence interval [95%CI], 565 to 1273 CE). The extant S. Pullorum strains can be divided into four distinct lineages, each of which is significantly associated with geographical distribution. The intercontinental transmissions of lineages III and IV can be traced to the mid-19th century and are probably related to the “Hen Fever” prevalent at that time. Further genomic analysis indicated that the loss or pseudogenization of functional genes involved in metabolism and virulence in S. Pullorum has been ongoing since before and after divergence from the ancestor. In contrast, multiple prophages and plasmids have been acquired by S. Pullorum, and these have endowed it with new characteristics, especially the multidrug resistance conferred by two large plasmids in lineage I. The results of this study provide insight into the evolution of S. Pullorum and prove the efficiency of whole-genome sequencing in epidemiological surveillance of pullorum disease.

IMPORTANCE Pullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic epidemiological analysis of 97 S. Pullorum strains was carried out to reconstruct the phylogeny and transmission history of S. Pullorum. Further analysis demonstrated that functional gene loss and acquisition occurred simultaneously throughout the evolution of S. Pullorum, both of which reflected adaptation to the changing environment. The result of our study will be helpful in surveillance and prevention of pullorum disease.

Virulence of Salmonella enterica serovar Pullorum isolates compared using cell-based and chicken embryo infection models

To reveal differences in virulence among strains of Salmonella enterica serovar Pullorum (S. Pullorum), we used 2 cell-based infection models and a chicken embryo infection model in this study. S. Pullorum strain S06004 was used to infect 4 different avian cell lines (HD-11, DF-1, LMH, DT-40), and the results showed that the infection of S06004 in both LMH and HD-11 cells was more stable than in DF-1 and DT-40 cells. Therefore, the HD-11 and LMH cell lines were used as the appropriate macrophage and epithelial cell models, respectively, to study the infection of S. Pullorum. Fifty strains isolated during the years 1962 to 2010 were then analyzed to compare their infection rates in HD-11 and LMH cells. The result showed that the infection rates of most strains were very similar to that of S06004, except for S9876 which displayed the highest infection rate among these strains. Based on the cell infection results, 10 strains were selected to be used in the chicken embryo infection model. Sixteen-day-old SPF chicken embryos were infected with the pathogen at a dose of 103 CFU/100 μL via allantoic cavity inoculation. The strains C79-13, 7101, and S06013 caused death of more than 80% embryos, whereas S09C12 and 6703 resulted less than 20% death. Thus, this study established cell-based infection models to screen S. Pullorum strains in vitro, and a chick embryo model to evaluate their in vivo virulence.

Analyses of prevalence and molecular typing reveal the spread of antimicrobial-resistant Salmonella infection across two breeder chicken farms

In this study, Salmonella prevalence and antimicrobial resistance were evaluated at various production stages in 2 geographically separated breeder farms (referred to as G and F). Day-old chicks for the breeder flock at farm F were purchased from farm G. A total of 219 Salmonella isolates, all identified as Salmonella enterica subsp. enterica serovar Enteritidis, were recovered from 1,430 samples (sick chicken carcasses and/or dead embryos). The isolation rates at breeder farms G and F were 10.53% (56/532) and 18.15% (163/898), respectively. Resistance to 4-6 antimicrobial agents was the most frequent phenotype during the laying stage at both farms, suggesting that chicks are exposed to higher risk of antimicrobial-resistant Salmonella infection during this stage of the breeding process. Using clustered regularly interspaced short palindromic repeat (CRISPR) typing, 5 CRISPR patterns were identified, out of which one pattern was shared by the 2 farms. In addition, pulsed-field gel electrophoresis (PFGE) typing result indicated that 2 clusters (PF-1 and PF-2) were shared among the 2 breeder farms, suggesting that strains were transmitted from breeder farm G to farm F via the trade of day-old chicks. Our findings suggested that the trade of day-old breeder chicks could be one of the potential Salmonella transmission routes, and antibiotics should be administered with caution during the laying stage.

Quinolone resistance phenotype and genetic characterization of Salmonella enterica serovar Pullorum isolates in China, during 2011 to 2016

Background

Pullorum disease, caused by Salmonella enterica serovar Pullorum (S. Pullorum), is one of the most important bacterial infections in the poultry industry in developing countries, including China. To examine the prevalence and characteristics of S. Pullorum, the Multilocus Sequence Typing (MLST) genotypes, fluoroquinolones resistance, and biofilm-forming abilities of S. Pullorum isolates were investigated, collected from 2011 to 2016 in China.

Results

Thirty S. Pullorum isolates collected from 2011 to 2016 were analyzed. Quinolones susceptibility testing showed that 90% of the isolates were resistant to the first generation of quinolines nalidixic acid, but the resistance rates to different fluoroquinolones agents were lower than 13.3%; for some there was even no resistance. Multilocus sequence typing (MLST) showed that ST-92 was the dominating genotype, accounting for 90.0% of all S. pullorum strains. The remaining three isolates were of the new reported sequence type ST-2151. Interestingly, the Asp87Gly substitution in quinolone resistance-determining regions (QRDR) of GyrA was only observed in the three strains of ST-2151, suggesting a potential correlation between Asp87Gly substitution and sequence type (p < 0.05). However, Asp87Gly substitution could not confer the resistant to ofloxacin and ciprofloxacin of these isolates. The plasmid-mediated quinolone resistance (PMQR) gene was not found in any of the tested isolates. Furthermore, an assay measuring biofilm-forming abilities showed that 46.7% of the isolates were non-biofilm producers, while 53.3% could form very weak biofilms, which might explain the relatively lower resistance to fluoroquinolones.

Conclusions

We reported a high resistance rate to the first generation of quinolines nalidixic acid and relatively low resistance rates to fluoroquinolones in S. Pullorum isolates. In addition, weak biofilm-forming abilities were found, which might be an important reason of the low fluoroquinolones resistance rates of S. Pullorum isolates. ST-92 was the dominating genotype demonstrated by MLST, and the new sequence type ST-2151 showed a potential correlation with Asp87Gly substitution in QRDR of GyrA. We believe the characterization of these S. Pullorum isolates will be helpful to develop prevention and control strategies.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1368-4) contains supplementary material, which is available to authorized users.

Induction of arthritis in chickens by infection with novel virulent Salmonella Pullorum strains

Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum (Salmonella Pullorum) is a host-specific serovar causing systemic infection with high mortality in young chicks. Pullorum disease is characterized by white diarrhea. However, arthritis has become increasingly frequent recently, particularly in southern China. The aim of the present study was to determine the pathogenesis and arthritis induction of new Salmonella Pullorum isolates. We isolated and identified five Salmonella Pullorum strains from broilers with bacterial arthritis and lameness in a commercial poultry farm. Four of five isolates were resistant to at least three classes of antibiotics and were defined as multidrug-resistant Salmonella Pullorum. All isolates had the same CRISPR sequence type and belonged to a single major cluster. The isolates exhibited high capability of biofilm formation, which may facilitate their dispersal and survival in hostile habitats, and showed high virulence based on embryo lethality and inoculation of newly hatched chicks. Tissue distribution analysis confirmed that SP1621 was more adapted to colonize the joint when compared to the white diarrhoea-causing Salmonella Pullorum reference strain S06004. Reproducible arthritis and typical joint lesions were observed in SP1621-infected chicks, and histopathological examination showed necrotic synovitis and cartilage tissue hyperplasia of the joint. Koch's postulates were confirmed when the novel Salmonella Pullorum strain was re-isolated from the joint tissues of experimentally inoculated chicks. These novel Salmonella Pullorum isolates have unique ability to induce arthritis in chickens, representing expanded pathogenic diversity in China. These results suggest the need for strict control strategies and new vaccines to prevent the disease.

CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization

The CRISPR-Cas system biologically serves as an adaptive defense mechanism against phages. However, there is growing interest in exploiting the hypervariable nature of the CRISPR locus, often of viral origin, for microbial typing and tracking. Moreover, the spacer content of any given strain provides a phage resistance profile. Large-scale CRISPR typing studies require an efficient method for showcasing CRISPR array similarities across multiple isolates. Historically, CRISPR arrays found in microbes have been represented by colored shapes based on nucleotide sequence identity and, while this approach is now routinely used, only scarce computational resources are available to automate the process, making it very time-consuming for large datasets. To alleviate this tedious task, we introduce CRISPRStudio, a command-line tool developed to accelerate CRISPR analysis and standardize the preparation of CRISPR array figures. It first compares nucleotide spacer sequences present in a dataset and then clusters them based on sequence similarity to assign a meaningful representative color. CRISPRStudio offers versatility to suit different biological contexts by including options such as automatic sorting of CRISPR loci and highlighting of shared spacers, while remaining fast and user-friendly.

The CRISPR-Cas system in Enterobacteriaceae

In nature, microorganisms are constantly exposed to multiple viral infections and thus have developed many strategies to survive phage attack and invasion by foreign DNA. One of such strategies is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. This defense mechanism is widespread in prokaryotes including several families such as Enterobacteriaceae. Much knowledge about the CRISPR-Cas system has been generated, including its biological functions, transcriptional regulation, distribution, utility as a molecular marker and as a tool for specific genome editing. This review focuses on these aspects and describes the state of the art of the CRISPR-Cas system in the Enterobacteriaceae bacterial family.

Insights into the Human Virome Using CRISPR Spacers from Microbiomes

Due to recent advances in next-generation sequencing over the past decade, our understanding of the human microbiome and its relationship to health and disease has increased dramatically. Yet, our insights into the human virome, and its interplay with important microbes that impact human health, is relatively limited. Prokaryotic and eukaryotic viruses are present throughout the human body, comprising a large and diverse population which influences several niches and impacts our health at various body sites. The presence of prokaryotic viruses like phages, has been documented at many different body sites, with the human gut being the richest ecological niche. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated proteins constitute the adaptive immune system of bacteria, which prevents attack by invasive nucleic acid. CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.

Genetics of CRISPR arrays in Salmonella Typhimurium 14028 associated with foreign DNA decay

Clustered regularly interspaced short palindromic repeats (CRISPRs) are a genetic locus of prokaryotes and contain highly conserved direct repeats, spacers, and CRISPR-associated genes. Spacers in CRISPRs are known as adaptive immune markers and reveal what types of phage or foreign DNA have been introduced in the past. The primary objective of this study was to analyze spacer sequences in CRISPR arrays of 15 Salmonella enterica subspecies and to determine if Salmonella CRISPRs are indeed involved in resistance to foreign DNAs. Using a bioinformatics algorithm, the CRISPR arrays of 15 subspecies of S. enterica were predicted. The transformation efficiencies of the wild-type and mutant strains lacking a space were determined using the plasmid harboring the same sequences with the space. Analysis of the CRISPR arrays indicated that S. Typhimurium encoded three possible CRISPR regions in the genome. Notably, 48 or 55 spacers were predicted in the genomes of S. Typhimurium 14028 and LT2 strains, respectively, and 39 were precisely identical. To confirm this prediction, the predicted CRISPR regions of S. Typhimurium 14028 were sequenced using the specific primers. Interestingly, a homology search of individual spacers found that the 2nd spacer of CRISPR 2 was nearly identical to a partial genome region of phage FSL SP-016. The mutant strain showed two to threefold increased transformation efficiency compared to that of the wild-type strain. These results demonstrate that the spacer sequence is dependent on genetic relations, especially for adaptive immunity against phage or foreign DNAs.

A rapid method to identify Salmonella enterica serovar Gallinarum biovar Pullorum using a specific target gene ipaJ

Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the pathogen of pullorum disease, which leads to severe economic losses in many developing countries. Traditional methods to identify S. enterica have relied on biochemical reactions and serotyping, which are time-consuming with accurate identification if properly carried out. In this study, we developed a rapid polymerase chain reaction (PCR) method targeting the specific gene ipaJ to detect S. Pullorum. Among the 650 S. Pullorum strains isolated from 1962 to 2016 all over China, 644 strains were identified to harbour ipaJ gene in the plasmid pSPI12, accounting for a detection rate of 99.08%. Six strains were ipaJ negative because pSPI12 was not found in these strains according to whole genome sequencing results. There was no cross-reaction with other Salmonella serotypes, including Salmonella enterica serovar Gallinarum biovar Gallinarum (S. Gallinarum), which show a close genetic relationship with S. Pullorum. This shows that the PCR method could distinguish S. Gallinarum from S. Pullorum in one-step PCR without complicated biochemical identification. The limit of detection of this PCR method was as low as 90 fg/μl or 10² CFU, which shows a high sensitivity. Moreover, this method was applied to identify Salmonella isolated from the chicken farm and the results were consistent with what we obtained from biochemical reactions and serotyping. Together, all the results demonstrated that this one-step PCR method is simple and feasible to efficiently identify S. Pullorum.

Genetic analysis and CRISPR typing of Salmonella enterica serovar Enteritidis from different sources revealed potential transmission from poultry and pig to human

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent serotypes in Salmonella isolated from poultry and the most commonly reported cause of human salmonellosis. In this study, we aimed to assess the genetic diversity of 329 S. Enteritidis strains isolated from different sources from 2009 to 2016 in China. Clustered regularly interspaced short palindromic repeat (CRISPR) typing was used to characterize these 262 chicken clinical isolates, 38 human isolates, 18 pig isolates, six duck isolates, three goose isolates and two isolates of unknown source. A total of 18 Enteritidis CRISPR types (ECTs) were identified, with ECT2, ECT8 and ECT4 as the top three ECTs. CRISPR typing identified ECT2 as the most prevalent ECT, which accounted for 41% of S. Enteritidis strains from all the sources except duck. ECT9 and ECT13 were identified in both pig and human isolates and revealed potential transmission from pig to human. A cluster analysis distributed 18 ECTs, including the top three ECTs, into four lineages with LI as the predominant lineage. Forty-eight out of 329 isolates were subjected to whole genome sequence typing, which divided them into four clusters, with Cluster I as the predominant cluster. Cluster I included 92% (34/37) of strains located in LI identified from the CRISPR typing, confirming the good correspondence between both typing methods. In addition, the CRISPR typing also revealed the close relationship between ECTs and isolated areas, confirming that CRISPR spacers might be obtained by bacteria from the unique phage or plasmid pools in the environment. However, further analysis is needed to determine the function of CRISPR-Cas systems in Salmonella and the relationship between spacers and the environment.

Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum

Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.