Identification and comparative analysis of a genomic island in Mycobacterium avium subsp. hominissuis

Mycobacterium avium subsp. hominissuis (MAH) is an environmental bacterium causing opportunistic infections. The objective of this study was to identify flexible genome regions in MAH isolated from different sources. By comparing five complete and draft MAH genomes we identified a genomic island conferring additional flexibility to the MAH genomes. The island was absent in one of the five strains and had sizes between 16.37 and 84.85 kb in the four other strains. The genes present in the islands differed among strains and included phage- and plasmid-derived genes, integrase genes, hypothetical genes, and virulence-associated genes like mmpL or mce genes.     

2型猪链球菌gene0969基因敲除突变体的构建及毒力分析

目的:构建2型猪链球菌强毒株05ZYH33毒力岛89K上的Ⅳ型分泌系统组分gene0969敲除突变体,初步分析其活性,为进一步研究猪链球菌假想毒力因子在致病中的作用提供实验基础。方法:以05ZYH33基因组为模板,PCR扩增gene0969基因的上下游片段;以穿梭质粒pSET1为模板,PCR扩增氯霉素抗性基因Cm;采用重叠PCR方法搭建3个片段,并克隆到自杀载体pSET4s上,构建基因敲除载体,通过同源重组构建gene0969突变体,再用小鼠感染模型对突变株和野生株的毒力进行比较。结果:获得了gene0969基因敲除突变体,并发现其毒力与野生型相比有下降趋势。结论:2型猪链球菌假想毒力因子gene0969可能与毒力有关,其作用和机制值得进一步分析。     

Mutations in the Gene Encoding the Ancillary Pilin Subunit of the Streptococcus suis srtF Cluster Result in Pili Formed by the Major Subunit Only

Pili have been shown to contribute to the virulence of different Gram-positive pathogenic species. Among other critical steps of bacterial pathogenesis, these structures participate in adherence to host cells, colonization and systemic virulence. Recently, the presence of at least four discrete gene clusters encoding putative pili has been revealed in the major swine pathogen and emerging zoonotic agent Streptococcus suis. However, pili production by this species has not yet been demonstrated. In this study, we investigated the functionality of one of these pili clusters, known as the srtF pilus cluster, by the construction of mutant strains for each of the four genes of the cluster as well as by the generation of antibodies against the putative pilin subunits. Results revealed that the S. suis serotype 2 strain P1/7, as well as several other highly virulent invasive S. suis serotype 2 isolates express pili from this cluster. However, in most cases tested, and as a result of nonsense mutations at the 5′ end of the gene encoding the minor pilin subunit (a putative adhesin), pili were formed by the major pilin subunit only. We then evaluated the role these pili play in S. suis virulence. Abolishment of the expression of srtF cluster-encoded pili did not result in impaired interactions of S. suis with porcine brain microvascular endothelial cells. Furthermore, non-piliated mutants were as virulent as the wild type strain when evaluated in a murine model of S. suis sepsis. Our results show that srtF cluster-encoded, S. suis pili are atypical compared to other Gram-positive pili. In addition, since the highly virulent strains under investigation are unlikely to produce other pili, our results suggest that pili might be dispensable for critical steps of the S. suis pathogenesis of infection.     

Antimicrobial activity of nisin against the swine pathogen Streptococcus suis and its synergistic interaction with antibiotics

Streptococcus suis serotype 2 is known to cause severe infections in pigs, including meningitis, endocarditis and pneumonia. Furthermore, this bacterium is considered an emerging zoonotic agent. Recently, increased antibiotic resistance in S. suis has been reported worldwide. The objective of this study was to evaluate the potential of nisin, a bacteriocin of the lantibiotic class, as an antibacterial agent against the pathogen S. suis serotype 2. In addition, the synergistic activity of nisin in combination with conventional antibiotics was assessed. Using a plate assay, the nisin-producing strain Lactococcus lactis ATCC 11454 proved to be capable of inhibiting the growth of S. suis (n = 18) belonging to either sequence type (ST)1, ST25, or ST28. In a microdilution broth assay, the minimum inhibitory concentration (MIC) of purified nisin ranged between 1.25 and 5 μg/mL while the minimum bactericidal concentration (MBC) was between 5 and 10 μg/mL toward S. suis. The use of a capsule-deficient mutant of S. suis indicated that the presence of this polysaccharidic structure has no marked impact on susceptibility to nisin. Following treatment of S. suis with nisin, transmission electron microscopy observations revealed lysis of bacteria resulting from breakdown of the cell membrane. A time-killing curve showed a rapid bactericidal activity of nisin. Lastly, synergistic effects of nisin were observed in combination with several antibiotics, including penicillin, amoxicillin, tetracycline, streptomycin and ceftiofur. This study brought clear evidence supporting the potential of nisin for the prevention and treatment of S. suis infections in pigs.     

猪链球菌2型ABC转运蛋白gene0910敲除突变体的构建及活性分析

目的:构建猪链球菌2型(Streptococcus suis type 2)强毒株05ZYH3389K毒力岛上的ABC转运蛋白gene0910敲除突变体,并初步分析其活性,为进一步研究猪链球菌假想毒力因子在致病中的作用提供实验基础。方法:以猪链球菌2型05ZYH33基因组为模板,扩增gene0910两侧各约500bp左右的片段为上下游同源臂,以pSET1质粒为模板,扩增氯霉素抗性基因Cm为中间片段,采用重叠PCR方法搭建三个片段,并克隆到自杀载体pSET4S上,构建基因敲除的载体。电转化05ZYH33感受态细胞,经30℃双交换和40℃质粒丢失,最后点板法筛选出基因敲除突变体△0910。对突变株和野生株的生物学活性及小鼠的致病性进行了初步比较。结果:PCR分析和测序结果均显示gene0910完全被氯霉素抗性基因Cm所替代,基因敲除突变体构建成功。结论:突变株的生物学活性和对小鼠的致病性与野生株相比差异不显著。     

A Zebrafish Larval Model to Assess Virulence of Porcine Streptococcus suis Strains

Streptococcus suis is an encapsulated Gram-positive bacterium, and the leading cause of sepsis and meningitis in young pigs resulting in considerable economic losses in the porcine industry. It is also considered an emerging zoonotic agent. In the environment, both avirulent and virulent strains occur in pigs, and virulent strains appear to cause disease in both humans and pigs. There is a need for a convenient, reliable and standardized animal model to assess S. suis virulence. A zebrafish (Danio rerio) larvae infection model has several advantages, including transparency of larvae, low cost, ease of use and exemption from ethical legislation up to 6 days post fertilization, but has not been previously established as a model for S. suis. Microinjection of different porcine strains of S. suis in zebrafish larvae resulted in highly reproducible dose- and strain-dependent larval death, strongly correlating with presence of the S. suis capsule and to the original virulence of the strain in pigs. Additionally we compared the virulence of the two-component system mutant of ciaRH, which is attenuated for virulence in both mice and pigs in vivo. Infection of larvae with the ΔciaRH strain resulted in significantly higher survival rate compared to infection with the S10 wild-type strain. Our data demonstrate that zebrafish larvae are a rapid and reliable model to assess the virulence of clinical porcine S. suis isolates.     

Genome-wide identification of novel genomic islands that contribute to Salmonella virulence in mouse systemic infection

Salmonella pathogenicity islands are inserted into the genome by horizontal gene transfer and are required for expression of full virulence. Here, we performed tRNA scanning of the genome of Salmonella enterica serovar Typhimurium and compared it with that of nonpathogenic Escherichia coli in order to identify genomic islands that contribute to Salmonella virulence. Using deletion analysis, we identified four genomic islands that are required for virulence in the mouse infection model. One of the newly identified pathogenicity islands was the pheV- tRNA-located genomic island, which is comprised of 26 126 bp, and encodes 22 putative genes, including STM3117–STM3138. We also showed that the pheV tRNA-located genomic island is widely distributed among different nontyphoid Salmonella serovars. Furthermore, genes including STM3118–STM3121 were identified as novel virulence-associated genes within the pheV- tRNA-located genomic island. These results indicate that a Salmonella -specific pheV- tRNA genomic island is involved in Salmonella pathogenesis among the nontyphoid Salmonella serovars.     

猪链球菌2型强毒株S.suis 05ZY和弱毒株S.suis 1940的比较转录谱分析

目的:比较猪链球菌2型强毒株S.suis 05ZY和弱毒株S.suis 1940毒力相关基因转录水平的差异,为进一步研究强毒株S.suis 05ZY毒力增强的原因提供实验基础。方法:分别提取S.suis 05ZY和S.suis 1940的RNA,反转录成cDNA并纯化,用Cy5或Cy3标记,与猪链球菌全基因组DNA芯片进行杂交,扫描芯片进行数据分析,比较二者在转录水平上的差异基因。结果:编码溶血素、精氨酸氨基肽酶的基因分别上调4.4和6.0倍,参与荚膜多糖合成的相关基因cps2H、cps2I、cps2J和一些可能的毒力相关基因ofs、dpr、SSU05₀196、SSU05₀272、SSU05₁408-1409均发生转录水平的上调。结论:溶血素、荚膜多糖、精氨酸氨基肽酶及一些可能的毒力因子在转录水平的上调很可能与S.suis 05ZY的毒力增强有关。     

The involvement of sortase A in high virulence of STSS-causing Streptococcus suis serotype 2

Sortase A (SrtA), originally identified as a transpeptidase in Staphylococcus aureus, plays key roles in full virulence of pathogenic bacteria. In silico genome-wide search suggested a srtA homologue from 05ZYH33, a Chinese human isolate of streptococcal toxic shock syndrome (STSS)-causing Streptococcus suis serotype 2 (S. suis 2, SS2). An isogenic srtA mutant (ΔsrtA) of 05ZYH33 strain was obtained by homologous recombination. Immunofluorescence analysis revealed that two known virulence-associated surface proteins featuring Leu-Pro-X-Thr-Gly motif, muramidase-released protein and surface antigen one, were absent in the ΔsrtA. Piglet infection experiments showed that deletion of srtA attenuated the full virulence of 05ZYH33 strain, and impaired its colonizing potential in specific organs. Furthermore, the ΔsrtA displayed significant reduction in adherence to human cells (Hep-2 and human umbilical vein endothelial cells). Collectively, we concluded that SrtA was involved in the virulence manifestation of STSS-causing SS2. Jiaqi Tang, Changjun Wang designed the study; Changjun Wang, Feng Zheng, Ming Li, Youjun Feng, Yaqing Dong, Gong Cheng, Jing Wang, Dan Hu, Xiaodan Feng, Fuquan Hu, and Junchao Ge performed the experiments; Changjun Wang, Ming Li, Youjun Feng, Feng Zheng, Yaqing Dong, Gong Cheng, Xiuzhen Pan, Di Liu, and Min Cao analyzed the data; Changjun Wang, Jiaqi Tang, Youjun Feng, and Ming Li wrote the paper.     

Lysogenic Streptococcus suis Isolate SS2-4 Containing Prophage SMP Showed Increased Mortality in Zebra Fish Compared to the Wild-Type Isolate

Streptococcus suis (S. suis) infection is considered to be a major problem in the swine industry worldwide. Based on the capsular type, 33 serotypes of S. suis have been described, with serotype 2 (SS2) being the most frequently isolated from diseased piglets. Little is known, however, about the pathogenesis and virulence factors of S. suis. Research on bacteriophages highlights a new area in S. suis research. A S. suis serotype 2 bacteriophage, designated SMP, has been previously isolated in our laboratory. Here, we selected a lysogenic isolate in which the SMP phage was integrated into the chromosome of strain SS2-4. Compared to the wild-type isolate, the lysogenic strain showed increased mortality in zebra fish. Moreover the sensitivity of the lysogenic strain to lysozyme was seven times higher than that of the wild-type.     

Comprehensive molecular,genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40

Background

Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type.

Results

We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).

Conclusion

Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1367-x) contains supplementary material, which is available to authorized users.     

Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

Background

Acinetobacter baumannii is an important nosocomial pathogen that poses a serious health threat to immune-compromised patients. Due to its rapid ability to develop multidrug resistance (MDR), A. baumannii has increasingly become a focus of attention worldwide. To better understand the genetic variation and antibiotic resistance mechanisms of this bacterium at the genomic level, we reported high-quality draft genome sequences of 8 clinical isolates with various sequence types and drug susceptibility profiles.

Results

We sequenced 7 MDR and 1 drug-sensitive clinical A. baumannii isolates and performed comparative genomic analysis of these draft genomes with 16 A. baumannii complete genomes from GenBank. We found a high degree of variation in A. baumannii, including single nucleotide polymorphisms (SNPs) and large DNA fragment variations in the AbaR-like resistance island (RI) regions, the prophage and the type VI secretion system (T6SS). In addition, we found several new AbaR-like RI regions with highly variable structures in our MDR strains. Interestingly, we found a novel genomic island (designated as GI_BJ4) in the drug-sensitive strain BJ4 carrying metal resistance genes instead of antibiotic resistance genes inserted into the position where AbaR-like RIs commonly reside in other A. baumannii strains. Furthermore, we showed that diverse antibiotic resistance determinants are present outside the RIs in A. baumannii, including antibiotic resistance-gene bearing integrons, the bla_OXA-23-containing transposon Tn2009, and chromosomal intrinsic antibiotic resistance genes.

Conclusions

Our comparative genomic analysis revealed that extensive genomic variation exists in the A. baumannii genome. Transposons, genomic islands and point mutations are the main contributors to the plasticity of the A. baumannii genome and play critical roles in facilitating the development of antibiotic resistance in the clinical isolates.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1163) contains supplementary material, which is available to authorized users.     

Identification of Genes and Genomic Islands Correlated with High Pathogenicity in Streptococcus suis Using Whole Genome Tilling Microarrays

Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST), ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP) ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs). Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP.     

Identification of a Novel Virulence-Related Gene in Streptococcus suis Type 2 Strains

The trag is a novel infection-related factor identified using in vivo-induced antigen technology (IVIAT) from SS2 expression libraries with swine convalescent sera. PCR-based studies of various S. suis strains collected from different sources revealed that the trag gene was present in all the virulent SS2 strains, but absent in the avirulent T15 strain. PCR and Southern hybridization analyses of a trag-knockout strain created through homologous recombination confirmed the coding sequence of trag replaced by spc ^R cassette in the ?trag mutant. Zebrafish was used to identify the role of trag in SS2 virulence. The reduction of virulence in the trag mutant compared to the wild-type in animal model systems, laid the foundation for further studies.     

Characterization of Streptococcus suis serotype 2 blood infections using RT-qPCR to quantify glutamate dehydrogenase copy numbers

This study characterized the dynamic distribution of bacteria in the blood of pigs infected with Streptococcus suis serotype 2 using specific primers and a TaqMan probe designed to amplify the highly conserved S. suis serotype 2 glutamate dehydrogenase (GDH) gene sequences. Gene copy numbers were used to determine the concentration of bacteria in the blood of infected pigs over time using established TaqMan real-time quantitative PCR methodologies (RT-qPCR). The results showed that the detection limit of the RT-qPCR was 10 GDH gene copies. The advantages of utilizing this approach are the high levels of specificity, sensitivity and reproducibility. Bacteria were detected in the blood of infected pigs after 24 h post infection and S. suis GDH gene copies in the experimental group were highest (10^4.15) on day 7 post infection. Data presented in this report demonstrate that the TaqMan RT-qPCR detection method can be used to characterize the dynamic changes occurring during S. suis serotype 2 blood infections in Bama minipigs thereby facilitating research associated with defining pathogenic mechanisms associated with this organism.     

Prevalence of Streptococcus suis Genotypes in Wild Boars of Northwestern Germany

Invasive serotype 2 (cps2⁺) strains of Streptococcus suis cause meningitis in pigs and humans. Four case reports of S. suis meningitis in hunters suggest transmission of S. suis through the butchering of wild boars. Therefore, the objective of this study was to investigate the prevalence of potentially human-pathogenic S. suis strains in wild boars. S. suis was isolated from 92% of all tested tonsils (n = 200) from wild boars. A total of 244 S. suis isolates were genotyped using PCR assays for the detection of serotype-specific genes, the hemolysin gene sly, and the virulence-associated genes mrp and epf. The prevalence of the cps2⁺ genotype among strains from wild boars was comparable to that of control strains from domestic pig carriers. Ninety-five percent of the cps2⁺ wild boar strains were positive for mrp, sly, and epf*, the large variant of epf. Interestingly, epf* was significantly more frequently detected in cps2⁺ strains from wild boars than in those from domestic pigs; epf* is also typically found in European S. suis isolates from humans, including a meningitis isolate from a German hunter. These results suggest that at least 10% of wild boars in Northwestern Germany carry S. suis strains that are potentially virulent in humans. Additional amplified fragment length polymorphism analysis supported this hypothesis, since homogeneous clustering of the epf* mrp⁺ sly⁺ cps2⁺ strains from wild boars with invasive human and porcine strains was observed.     

Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics

Background

Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general.

Results

In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species.

Conclusions

Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.     

Differential fluctuation in virulence and VOC profiles among different cultures of entomopathogenic fungi

Insect-passaged cultures of entomopathogenic fungi grown on potato dextrose agar media have been shown to have altered virulence and profiles of volatile compounds. The present study demonstrated the pathogenic status of FS₀ (in vitro) and FS₁ and FS₂ (insect-passaged cultures grown on PDA) cultures of Metarhizium anisopliae (strains 406 and 02049) and Beauveria bassiana by a non-choice assay, in which filter paper was inoculated with fungal spores at a concentration of 1 × 10⁷ spores/ml. The FS₁ and FS₂ cultures of M. anisopliae strain 02049 and B. bassiana produced conidia with high virulence, and the volatile profiles of these conidia comprised relatively lower percentages of branched-alkanes than conidia from the FS₀ cultures. In contrast, the conidia from an FS₀ culture of M. anisopliae strain 406 had somewhat elevated virulence levels, but their volatile profile had <2% branched-alkanes. The FS₁ and FS₂ cultures of M. anisopliae strain 406 did not gain virulence, and these cultures showed a decline in virulence along with major alteration of their volatile profiles. Their volatile profiles mainly comprised branched-alkanes. The volatile profiles of the FS₁ and FS₂ cultures lacked n-tetradecane, which was an important component of all the virulent cultures. Four compounds, 2-phenylpropenal, 2,5,5-trimethyl-1-hexene, n-tetradecane and 2,6-dimethylheptadecane, were detected only from the virulent cultures, suggesting that low LT₅₀ values were probably due to the production of these compounds. This is the first report to characterize volatiles from FS₀, FS₁ and FS₂ cultures of entomopathogenic fungi; its utility in different aspects opens an interesting area for further investigations.