Genome sequence of Cronobacter sakazakii BAA-894 and comparative genomic hybridization analysis with other Cronobacter species

Uncovering the pathogenic mechanisms of Cronobacter turicensis: A dual transcriptomics study using a zebrafish larvae model

PURPOSE

Cronobacter (C.) is an emerging opportunistic pathogen representing a significant cause of mortality in neonatal patients with bacteremia and meningitis. The pathobiology of Cronobacter mediated meningitis has primarily been investigated using in vitro models. In this study, we used zebrafish to investigate in vivo the infection strategy of the sepsis/meningitis-causing strain C. turicensis z3032 (LMG 23827T) and the immune response of zebrafish larvae after central nervous system (CNS) invasion. Global gene expression profiles of both organisms were analyzed using RNA-Seq.

METHODS

Injection of bacteria into the yolk sac resulted in proliferation of bacteria and translocation to different tissues, including the brain. Infected larval heads were obtained by microdissection and dual RNA-sequencing was performed on host and pathogen simultaneously.

RESULTS

A total of 1432 genes in C. turicensis z3032 and 80 genes in zebrafish were found to be differentially expressed. Upregulated virulence genes in C. turicensis included those encoding for denitrification and anaerobic respiration, chemotaxis, surface structures, and secretion systems. In zebrafish, transcriptional changes included inflammatory processes, cytokine mediated signaling pathways, and NF-kB signaling as the primary GO categories for upregulated genes in response to infection.

CONCLUSION

The dual transcriptomics approach provided a unique opportunity to create a comprehensive catalog of differentially expressed genes in both the pathogen and the host, offering new insights into the infection strategies of C. turicensis and zebrafish immune response.

Isolation of Pathogenic Cronobacter Species as Bacteriological Risks Indicator in Powdered Infant Formula Available to Deprived Infants in Lagos Metropolis, Nigeria

Powdered infant formula (PIF) is rich in nutrients that support the survival and growth of bacteria that trigger food safety disorders in deprived infants through life-threatening illnesses. The study aims to examine and identify the incidence of pathogenic bacteria of concern in PIF upon reconstitution in lukewarm water. A total of 172 samples consisting of 38 brands of PIF available in the Lagos metropolis were sampled, suspended in water (10 g in 100 mL), and bacteria strains were isolated using combinational enrichment and selective culture techniques. Pure bacterial strains were characterized and identified based on their physiology and 16S rRNA gene sequence homology. While 85 bacterial strains were isolated from the enriched culture system, 20 strains were selectively isolated based on tolerance to sodium deoxycholate. Approximately 13% of the selected bacteria were identified as Cronobacter spp., exhibiting virulence traits including extracellular protease production, coagulation and proteolysis of casein, haem-agglutination, and β-haemolysis of human blood. Approximately 82% of the Cronobacter strains tolerated NaCl (10%) and bile salt; and exhibited resistance to cefotaxime, ceftriaxone, gentamicin, and Amoxicillin-clavulanic acid antibiotics. The presence of Cronobacter spp. in 13% of the PIF brands available to infants calls for concern about the safety of deprived infants that might be fed with such PIF. Consequently, PIF safety alerts need to be activate while further studies on critical points at which the pathogens get introduced to the PIFs need to be identified.

Microbiological survey and genomic analysis of Cronobacter sakazakii strains isolated from US households and retail foods

Cronobacter species are opportunistic pathogens that are capable of causing morbidity and mortality, particularly in infants. Although the transmission dynamics involved in Cronobacter infections remain largely unknown, contaminated powdered infant formula (PIF) has been linked to 30% of Cronobacter sakazakii cases involving invasive illness in infants. As several lines of evidence have implicated the domestic environment in PIF contamination, we undertook a microbiological survey of homes (N = 263) across the US. Cronobacter spp. and C. sakazakii were isolated from 36.1% and 24.7% of US homes, respectively, with higher recovery rates observed for floor and kitchen surfaces. Multi-locus sequence typing indicated that the dominant strain was C. sakazakii ST4, the sequence type most commonly associated with neonatal meningitis. For comparison purposes, retail foods (N = 4,009) were also surveyed, with the highest contamination frequencies (10.1%-26.3%) seen for nut products, seeds, and grains/baked goods/flours. The sequence type profile of isolates recovered from homes mirrored that of isolates recovered from retail foods, with increased representation of ST1, ST4, ST13, ST17, and ST40. Analysis of 386 whole genomic sequences revealed significant diversity. Redundancies were only observed for isolates recovered from within the same domicile, and there were no identical matches with sequences archived at the NCBI pathogen database. Genes coding for putative virulence and antibiotic resistance factors did not segregate with clinically significant sequence types. Collectively, these findings support the possibility that contamination events occurring within the home should not be overlooked as a contributor to community-onset Cronobacter infections.

IMPORTANCE

Cronobacter sakazakii is an opportunistic pathogen that can cause significant morbidity and mortality in neonates. Its transmission dynamics are poorly understood, though powered infant formula (PIF) is thought to be the major transmission vehicle. How the PIF becomes contaminated remains unknown. Our survey shows that roughly 1/4 of US homes are contaminated with Cronobacter sakazakii, particularly in the kitchen setting. Our analyses suggest that the domestic environment may contribute to contamination of PIF and provides insights into mitigating the risk of transmission.

Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Antimicrobial resistance (AMR) is responsible for the spread and persistence of bacterial infections. Surveillance of AMR in healthy individuals is usually not considered, though these individuals serve as reservoirs for continuous disease transmission. Therefore, it is essential to conduct epidemiological surveillance of AMR in healthy individuals to fully understand the dynamics of AMR transmission in Nigeria. Thirteen multidrug-resistant Citrobacter spp., Enterobacter spp., Klebsiella pneumoniae, and Escherichia coli isolated from stool samples of healthy children were subjected to whole genome sequencing (WGS) using Illumina and Oxford nanopore sequencing platforms. A bioinformatics analysis revealed antimicrobial resistance genes such as the pmrB_Y358N gene responsible for colistin resistance detected in E. coli ST219, virulence genes such as senB, and ybtP&Q, and plasmids in the isolates sequenced. All isolates harbored more than three plasmid replicons of either the Col and/or Inc type. Plasmid reconstruction revealed an integrated tetA gene, a toxin production caa gene in two E. coli isolates, and a cusC gene in K. quasivariicola ST3879, which induces neonatal meningitis. The global spread of AMR pathogenic enteric bacteria is of concern, and surveillance should be extended to healthy individuals, especially children. WGS for epidemiological surveillance will improve the detection of AMR pathogens for management and control.

Electrotransformation of Foodborne Pathogen Cronobacter sakazakii by a Simple Method

Cronobacter sakazakii is an opportunistic foodborne pathogen that mainly infects infants and immunocompromised people, with a high mortality rate. However, the efficient transformation method of this bacterium has not been systematically reported. In this study, we developed a fast and efficient transformation method for C. sakazakii by cold sucrose treatment. Compared with CaCl2 or glycerol treatment, the transformation efficiency of this method is significantly high when bacteria were cultured overnight at 42°C before cold sucrose treatment. Furthermore, applying this method, we successfully knocked out the pppA gene by direct electroporation. Collectively, our study provides a simple, time-saving, and efficient method for competent cell preparation of C. sakazakii, which is conducive to the further research of C. sakazakii.

Transcriptomic analysis reveals novel desiccation tolerance mechanism of Cronobacter based on type VI secretion system inhibition

Cronobacter malonaticus (C. malonaticus) is a food-borne pathogen inducing severe infections both in infants and adults, and it could survive in dry powdered infant formula (PIF) for a long time, implying its strong tolerance to desiccation. However, the thorough molecular mechanism of resistance to desiccation remains elusive. When C. malonaticus was exposed to desiccation conditions (7, 15, and 30 d), transcriptomic analysis provided a universal adaptation strategy to withstand desiccation with the increased compatible solutes accumulation, activated stress resistance-related regulators, suppressed protein export and bacterial secretion system, and reduced other unessential survival functions including adhesion, invasion, virulence, and flagellar motility. Importantly, type VI secretion system (T6SS) genes exhibited significantly downregulated expressions, as well as markedly increased survival and viability of their mutants after desiccation treatment, revealing the negative regulation of T6SS in desiccation tolerance. Meanwhile, the decreased expressions of T6SS structure genes in other six species further confirmed the vital role of T6SS in desiccation tolerance of Cronobacter spp. Thus, our studies present a novel hypothesis of desiccation resistance in Cronobacter based on type VI secretion system inhibition, causing the reduction of macromolecule secretion such as effectors and hyperosmolality development within the cytomembrane, which allow Cronobacter to survive in desiccation.

Genomic Characterisation of Multidrug-Resistant Pathogenic Enteric Bacteria from healthy children in Osun State, Nigeria

Antimicrobial resistance (AMR) has been established to be a significant driver for the persistence and spread of bacterial infections. It is, therefore, essential to conduct epidemiological surveillance of AMR in healthy individuals to understand the actual dynamics of AMR in Nigeria. Multi-drug resistant Klebsiella quasivariicola (n=1), Enterobacter hormaechei (n=1), and Escherichia coli (n=3) from stool samples of healthy children were subjected to whole genome sequencing using Illumina Nextseq1000/2000 and Oxford nanopore. Bioinformatics analysis reveals antimicrobial resistance, virulence genes, and plasmids. This pathogenic enteric bacteria harbored more than three plasmid replicons of either Col and/or Inc type associated with outbreaks and AMR resistant gene pmrB responsible for colistin resistance. Plasmid reconstruction revealed an integrated tetA gene responsible for tetracycline resistance, and caa gene responsible for toxin production in two of the E.coli isolates, and a cusC gene known to induce neonatal meningitis in the K. quasivariicola ST3879. The global spread of MDR pathogenic enteric bacteria is a worrying phenomenon, and close surveillance of healthy individuals, especially children, is strongly recommended to prevent the continuous spread and achieve the elimination and eradication of these infections. Molecular epidemiological surveillance using whole genome sequencing (WGS) will improve the detection of MDR pathogens in Nigeria.

Effects of ESA_00986 Gene on Adhesion/Invasion and Virulence of Cronobacter sakazakii and Its Molecular Mechanism

Cronobacter sakazakii is an opportunistic Gram-negative pathogen that has been identified as a causative agent of severe foodborne infections with a higher risk of mortality in neonates, premature infants, the elderly, and immunocompromised populations. The specific pathogenesis mechanisms of C. sakazakii, such as adhesion and colonization, remain unclear. Previously, we conducted comparative proteomic studies on the two strains with the stronger and weaker infection ability, respectively, and found an interesting protein, ESA_00986, which was more highly expressed in the strain with the stronger ability. This unknown protein, predicted to be a type of invasitin related to invasion, may be a critical factor contributing to its virulence. This study aimed to elucidate the precise roles of the ESA_00986 gene in C. sakazakii by generating gene knockout mutants and complementary strains. The mutant and complementary strains were assessed for their biofilm formation, mobility, cell adhesion and invasion, and virulence in a rat model. Compared with the wild-type strain, the mutant strain exhibited a decrease in motility, whereas the complementary strain showed comparable motility to the wild-type. The biofilm-forming ability of the mutant was weakened, and the mutant also exhibited attenuated adhesion to/invasion of intestinal epithelial cells (HCT-8, HICE-6) and virulence in a rat model. This indicated that ESA_00986 plays a positive role in adhesion/invasion and virulence. This study proves that the ESA_00986 gene encodes a novel virulence factor and advances our understanding of the pathogenic mechanism of C. sakazakii.

Emerging of Multidrug-Resistant Cronobacter sakazakii Isolated from Infant Supplementary Food in China

Cronobacter is a foodborne pathogen associated with severe infections in restricted populations and particularly with high mortality in neonates and infants. The prevalence and antimicrobial resistance (AMR) phenotype of Cronobacter cultured from powdered infant formula and supplementary food were studied. The virulence factors, AMR genes, and genomic environments of the multidrug-resistant isolates were further studied. A total of 1,055 Cronobacter isolates were recovered from 12,105 samples of powdered infant formula and supplementary food collected from 29 provinces between 2018 and 2019 in China. Among these, 1,048 isolates were from infant supplementary food and 7 were from powdered infant formula. Regarding antimicrobial resistance susceptibility, 11 (1.0%) isolates were resistant and two showed resistance to four antimicrobials (ampicillin [AMP], tetracycline [TET], sulfamethoxazole-trimethoprim [SXT], and chloramphenicol [CHL]), defined as MDR. These two MDR isolates were subsequently identified as Cronobacter sakazakii sequence type 4 (ST4) (C. sakazakii Crono-589) and ST40 (C. sakazakii Crono-684). Both MDR isolates contain 11 types of virulence genes and 7 AMR genes on their genomes. Meanwhile, the IncFIB plasmids of both MDR C. sakazakii isolates also harbored 2 types of virulence genes. Results of the genomic comparative analysis indicated that food-associated C. sakazakii could acquire antimicrobial resistance determinants through horizontal gene transfer (HGT). IMPORTANCE As a foodborne pathogen, Cronobacter can cause serious infections in restricted populations and lead to death or chronic sequelae. Although a number of investigations showed that Cronobacter isolates are susceptible to most antimicrobial agents, MDR Cronobacter isolates, isolated mainly from clinical cases but occasionally from foods, have been reported in recent years. In this study, we successfully identified two MDR Cronobacter sakazakii isolates from infant foods based on nationwide surveillance and genome sequencing in China. Genomic analysis revealed that these two MDR C. sakazakii strains acquired resistance genes from other species via different evolution and transmission routes. It is important to monitor MDR C. sakazakii isolates in infant foods, and appropriate control measures should be taken to reduce the contamination with and transmission of this MDR bacterium.

Virulence, antimicrobial susceptibility, and phylogenetic analysis of Cronobacter sakazakii isolates of food origins from Jordan

AIMS

to characterize a collection of Cronobacter sakazakii isolates collected from various origins in Jordan.

METHODS AND RESULTS

the isolates were characterized using 16S rRNA sequencing, DNA microarray, multi-locus sequence typing (MLST), O-serotyping, virulence gene identification, and antibiotic susceptibility testing. The identities and phylogenetic relatedness revealed that C. sakazakii sequence type 4 (ST4) and Csak O:1 serotype was the most prevalent STs and serovars among these C. sakazakii strains. PCR screening of putative virulence genes showed that the siderophore-interacting protein gene (sip) and iron acquisition gene clusters (eitCBAD and iucABCD/iutA) were the most detected genes with noticeable variability in the type 6 secretion system (T6SS) and filamentous hemagglutinin/adhesion (FHA) gene loci. The antibiotic resistance profiles revealed that the majority of the isolates were susceptible to all antibiotics used despite harboring a class C β-lactamase resistance gene.

CONCLUSIONS

the results described in this report provide additional insights about the considerable genotypic and phenotypic heterogeneity within C. sakazakii.

SIGNIFICANCE AND IMPACT OF THE STUDY

the information reported in this study might be of great value in understanding the origins of C. sakazakii isolates, in addition to their diversity and variability, which might be helpful in preventing future outbreaks of this pathogen.

Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies

Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.

African cereal fermentations: A review on fermentation processes and microbial composition of non-alcoholic fermented cereal foods and beverages

Africa has a rich tradition of cereal fermentations to produce diverse products including baked goods, porridges, non-alcoholic beverages and alcoholic beverages. Diversity also relates to the choice of the fermentation substrates, which include wheat, maize, teff, sorghum and millet, and the fermentation processes that are used in food production. For fermentation processes that are used in baking and brewing, it is well established that the composition of fermentation microbiota and thus the impact of fermentation on product quality is determined by the choice of fermentation conditions. This link has not been systematically explored for African cereal fermentations. This review therefore aims to provide an overview on the diversity of African fermented cereal products, and to interrogate currently available literature data with respect to the impact of fermentation substrate and fermentation processes on the assembly of fermentation microorganisms and product quality.

Insights into the mechanisms of Cronobacter sakazakii virulence

Cronobacter species have adapted to survive harsh conditions, particularly in the food manufacture environment, and can cause life-threatening infections in susceptible hosts. These opportunistic pathogens employ a multitude of mechanisms to aid their virulence throughout three key stages: environmental persistence, infection strategy, and systemic persistence in the human host. Environmental persistence is aided by the formation of biofilms, development of subpopulations, and high tolerance to environmental stressors. Successful infection in the human host involves several mechanisms such as protein secretion, motility, quorum sensing, colonisation, and translocation. Survival inside the host is achieved via competitive acquisition and utilization of minerals and metabolites respectively, coupled with host immune system evasion and antimicrobial resistance (AMR) mechanisms. Across the globe, Cronobacter sakazakii is associated with often fatal systemic infections in populations including neonates, infants, the elderly and the immunocompromised. By providing insight into the mechanisms of virulence utilised by this pathogen across these three stages, this review identifies current gaps in the literature. Further research into these virulence mechanisms is required to inform novel mitigation measures to improve global food safety with regards to this food-borne pathogen.

Complete genome sequences and genomic characterization of five plasmids harbored by environmentally persistent Cronobacter sakazakii strains ST83 H322 and ST64 GK1025B obtained from powdered infant formula manufacturing facilities

Background

Cronobacter sakazakii is a foodborne pathogen that causes septicemia, meningitis, and necrotizing enterocolitis in neonates and infants. The current research details the full genome sequences of two extremely persistent C. sakazakii strains (H322 and GK1025B) isolated from powdered infant formula (PIF) manufacturing settings. In addition, the genetic attributes associated with five plasmids, pH322_1, pH322_2, pGK1025B_1, pGK1025B_2, and pGK1025B_3 are described.

Materials and Methods

Using PacBio single-molecule real-time (SMRT^®) sequencing technology, whole genome sequence (WGS) assemblies of C. sakazakii H322 [Sequence type (ST)83, clonal complex [CC] 83) and GK1025B (ST64, CC64) were generated. Plasmids, also sequenced, were aligned with phylogenetically related episomes to determine, and identify conserved and missing genomic regions.

Results

A truncated ~ 13 Kbp type 6 secretion system (T6SS) gene cluster harbored on virulence plasmids pH322_2 and pGK1025B_2, and a second large deletion (~ 6 Kbp) on pH322_2, which included genes for a tyrosine-type recombinase/integrase, a hypothetical protein, and a phospholipase D was identified. Within the T6SS of pH322_2 and pGK1025B_2, an arsenic resistance operon was identified which is in common with that of plasmids pSP291_1 and pESA3. In addition, PHASTER analysis identified an intact 96.9 Kbp Salmonella SSU5 prophage gene cluster in pH322_1 and pGK1025B_1 and showed that these two plasmids were phylogenetically related to C. sakazakii plasmids: pCS1, pCsa767a, pCsaC757b, pCsaC105731a. Plasmid pGK1025B_3 was identified as a novel conjugative Cronobacter plasmid. Furthermore, WGS analysis identified a ~ 16.4 Kbp type 4 secretion system gene cluster harbored on pGK1025B_3, which contained a phospholipase D gene, a key virulence factor in several host–pathogen diseases.

Conclusion

These data provide high resolution information on C. sakazakii genomes and emphasizes the need for furthering surveillance studies to link genotype to phenotype of strains from previous investigations. These results provide baseline data necessary for future in-depth investigations of C. sakazakii that colonize PIF manufacturing facility settings and genomic analyses of these two C. sakazakii strains and five associated plasmids will contribute to a better understanding of this pathogen's survival and persistence within various “built environments” like PIF manufacturing facilities.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-022-00500-5.

Role of sigma factor RpoS in Cronobacter sakazakii environmental stress tolerance

Cronobacter sakazakii is a food-borne, conditionally pathogenic bacterium that mainly infects neonates, especially premature infants. Previous studies have indicated that an important route of infection for C. sakazakii is through infant formula, suggesting a high stress resistance of the bacterium. RpoS is a σ-factor that is closely related to the bacterial resistance mechanisms. In this study, a C. sakazakii BAA894 model strain was used. An rpoS-deficient mutant strain Δrpos was constructed using Red homologous recombination, and the differences between the mutant and the wild-type strains were compared. To investigate the functions of the rpoS gene, the membrane formation and cell wall properties of the strains were studied, and the tolerance of each strain to acid, osmotic pressure, desiccation, and drug resistance were compared. The results showed that the membrane formation ability in the mutant strain was increased, auto-aggregation was enhanced, motility, acid resistance and hyperosmotic resistance were alternated to different degrees, and desiccation resistance was stronger than observed in the wild type grown in LB medium but weaker than the wild type cultured in M9 medium. These results showed that rpoS is involved in environmental stress resistance in C. sakazakii BAA894. Finally, transcriptome analysis verified that the deletion of the rpoS gene caused differential expression of resistance-related genes and instigated changes in related metabolic pathways. These messenger RNA results were consistent with the functional experimental results and help explain the phenotypic changes observed in the mutant strain.

Null mutation in sspA of Cronobacter sakazakii influences its tolerance to environmental stress

Cronobacter sakazakii is a known foodborne opportunistic pathogen that can affect the intestinal health of infants. Despite undergoing complex manufacturing processes and low water concentration in the finished product, infant formula has been associated with Cronobacter infections, suggesting that C. sakazakii's pathogenicity may be related to its tolerance to stress. In this study, the effect of the stringent starvation protein A (SspA), which plays an important role in E. coli cellular survival under environmental stresses, on the stress tolerance of C. sakazakii BAA894 was investigated by creating an sspA-knockout mutant. The effects of this mutation on the acid, desiccation and drug tolerance were assessed, and results showed that acid tolerance decreased, while desiccation tolerance increased in LB and decreased in M9. Moreover, the MICs of 10 antibiotics in LB medium and 8 antibiotics in M9 medium were determined and compared of the wild-type and ΔsspA. Transcriptome analysis showed that 27.21% or 37.78% of the genes in ΔsspA were significantly differentially expressed in LB or M9 media, the genes relevant to microbial metabolism in diverse environments and bacterial chemotaxis were detailed analyzed. The current study contributes towards an improved understanding of the role of SspA in C. sakazakii BAA894 stress tolerance.

Genetic Diversity and Structure of Rear Edge Populations of Sorbus aucuparia (Rosaceae) in the Hyrcanian Forest

Sorbus aucuparia (Rosaceae) is a small tree species widely distributed in Eurasia. The Hyrcanian forest is the southernmost distribution limit of this species. Severe habitat degradation and inadequate human interventions have endangered the long-term survival of this species in this region, and it is necessary to develop and apply appropriate management methods to prevent the loss of its genetic diversity. In this study, we used 10 SSR markers in order to evaluate the genetic diversity of this taxon. Leaf samples were collected from five known populations of S. aucuparia throughout its distribution area in the Hyrcanian forest. Expected heterozygosity ranged from 0.61 (ASH) to 0.73, and according to the M-ratio, all populations showed a significant reduction in effective population size, indicating a genetic bottleneck. Global FST was not statistically significant and attained the same values with and without excluding null alleles (ENA) correction (FST = 0.12). Bayesian analysis performed with STRUCTURE defined two genetic clusters among the five known populations, while the results of discriminant analysis of principal components (DAPC) identified three distinct groups. The average proportion of migrants was 22. In general, the gene flow was asymmetrical, with the biggest differences between immigration and emigration in Barzekoh and Asbehriseh. The Mantel test showed that there was no significant correlation between genetic distance (FST) and geographic distance in S. aucuparia. The best pathway for theoretical gene flow is located across the coast of the Caspian Sea and significant spatial autocorrelation was observed in only one population. In order to reduce the extinction risk of very small and scattered populations of S. aucuparia in the Hyrcanian forest, it is very important to establish and/or enhance the connectivity through habitat restoration or genetic exchange.

Characterization of a gene cluster containing four genes relevant to biosynthesis of inner core of lipopolysaccharide in Cronobacter sakazakii

Many genes in the biosynthetic pathway of lipopolysaccharide in Cronobacter sakazakii have not been identified. In this study, we demonstrate that an operon containing four genes ESA_RS18945, ESA_RS18950, ESA_RS18955, and ESA_RS18960 is responsible for L-glycero-D-mannoheptose addition on the inner core of lipopolysaccharide in C. sakazakii. The proteins encoded by these four genes are homologous to E. coli WaaQ, WaaC, WaaF, and WaaD. Lipopolysaccharide from the deletion mutants of ESA_RS18945, ESA_RS18950, ESA_RS18955, and ESA_RS18960 (named as △RS18945, △RS18950, △RS18955 and △RS18960, respectively) were analyzed by SDS-PAGE. △RS18945 synthesized lipopolysaccharide with similar length to the wildtype BAA-894, whereas △RS18950, △RS18955, and △RS18960 synthesized much shorter lipopolysaccharide. This suggests that the enzyme encoded by ESA_RS18945 might function as E. coli WaaQ on the sidechain of lipopolysaccharide. When E. coli WaaC, WaaF, and WaaD were overexpressed in △RS18950, △RS18955, and △RS18960, respectively, the full length of lipopolysaccharide was recovered. Mass spectrometry analysis indicates that △RS18950 and △RS18960 only synthesized Kdo₂ -lipid A, confirming that enzymes encoded by ESA_RS18950 and ESA_RS18960 have similar functions to E. coli WaaC and WaaD, respectively. Hep-Kdo₂ -lipid A with a phosphoethanolamine was produced in △RS18955, suggesting that the enzyme encoded by ESA_RS18955 has similar function to E. coli WaaF.

Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Milk

Cronobacter spp. are opportunistic pathogens of the Enterobacteriaceae family. The organism causes infections in all age groups, but the most serious cases occur in outbreaks related to neonates with meningitis and necrotizing enterocolitis. The objective was to determine the in silico and in vitro putative virulence factors of six Cronobacter sakazakii strains isolated from powdered milk (PM) in the Czech Republic. Strains were identified by MALDI-TOF MS and whole-genome sequencing (WGS). Virulence and resistance genes were detected with the Ridom SeqSphere+ software task template and the Comprehensive Antibiotic Resistance Database (CARD) platform. Adherence and invasion ability were performed using the mouse neuroblastoma (N1E-115 ATCCCRL-2263) cell line. The CRISPR-Cas system was searched with CRISPRCasFinder. Core genome MLST identified four different sequence types (ST1, ST145, ST245, and ST297) in six isolates. Strains 13755-1B and 1847 were able to adhere in 2.2 and 3.2 × 106 CFU/mL, while 0.00073% invasion frequency was detected only in strain 1847. Both strains 13755-1B and 1847 were positive for three (50.0%) and four virulence genes, respectively. The cpa gene was not detected. Twenty-eight genes were detected by WGS and grouped as flagellar or outer membrane proteins, chemotaxis, hemolysins, and invasion, plasminogen activator, colonization, transcriptional regulator, and survival in macrophages. The colistin-resistance-encoding mcr-9.1 and cephalothin-resis-encoding blaCSA genes and IncFII(pECLA) and IncFIB(pCTU3) plasmids were detected. All strains exhibited CRISPR matrices and four of them two type I-E and I-F matrices. Combined molecular methodologies improve Cronobacter spp. decision-making for health authorities to protect the population.

Proteomics profiles of Cronobacter sakazakii and a fliF mutant: Adherence and invasion in mouse neuroblastoma cells

Cronobacter sakazakii is an opportunistic foodborne pathogen associated with necrotizing enterocolitis, bacteremia, and meningitis in infants. A comparative proteomic study of C. sakazakii ATCC BAA-894 (CS WT) and a fliF::Tn5 mutant was performed, including the ability of both strains to adhere to and invade N1E-115 cells. To achieve this goal, a nonmotile C. sakazakii‬ ATCC BAA-894 fliF::Tn5 (CS fliF::Tn5) strain was generated using an EZ-Tn5 <KAN-2>Tnp Transposome kit. Analysis of differential protein expression showed that 81.49% (361/443) of the proteins were expressed in both strains, 8.35% (37/443) were exclusively expressed in the CS WT strain, and 10.16% (45/443) were exclusively expressed in the CS fliF::Tn5 strain. The main exclusively expressed proteins in the CS WT strain were classified into the "cell motility" and "signal transduction mechanisms" subcategories. The proteins exclusively expressed in the CS fliF::Tn5 strain were classified into the following subcategories: "intracellular trafficking, secretion, and vesicular transport", "replication, recombination, and repair", "nucleotide transport and metabolism", "carbohydrate transport and metabolism", "coenzyme transport and metabolism", and "lipid transport and metabolism". Expression of the Cpa protein was detected in both strains, but Cpa was more abundant in the CS WT strain than in the CS fliF::Tn5 strain. A significant increase (p = 0.0001) in adherence to N1E-115 cells was observed in the nonmotile CS fliF::Tn5 strain (31.3 × 10⁶ CFU/mL) compared to the CS WT strain (14.5 × 10⁶ CFU/mL). Additionally, the CS WT strain showed a 0.17% invasion frequency in N1E-115 cells, which was significantly higher (p = 0.01) than that of the nonmotile CS fliF::Tn5 strain. In conclusion, the proteins involved in the motility were mainly identified by proteomic analysis in the CS WT strain compared to the CS fliF::Tn5 strain. Our data indicate that flagella are required to promote the invasion of N1E-115 cells and that the absence of flagella significantly increases the adherence to N1E-115 cells.

Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses

Cronobacter species are opportunistic pathogens capable of causing life-threatening infections in humans, with serious complications arising in neonates, infants, immuno-compromised individuals, and elderly adults. The genus is comprised of seven species: Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite a multiplicity of genomic data for the genus, little is known about likely transmission vectors. Using DNA microarray analysis, in parallel with whole genome sequencing, and targeted PCR analyses, the total gene content of two C. malonaticus, three C. turicensis, and 14 C. sakazaki isolated from various filth flies was assessed. Phylogenetic relatedness among these and other strains obtained during surveillance and outbreak investigations were comparatively assessed. Specifically, microarray analysis (MA) demonstrated its utility to cluster strains according to species-specific and sequence type (ST) phylogenetic relatedness, and that the fly strains clustered among strains obtained from clinical, food and environmental sources from United States, Europe, and Southeast Asia. This combinatorial approach was useful in data mining for virulence factor genes, and phage genes and gene clusters. In addition, results of plasmidotyping were in agreement with the species identity for each strain as determined by species-specific PCR assays, MA, and whole genome sequencing. Microarray and BLAST analyses of Cronobacter fly sequence datasets were corroborative and showed that the presence and absence of virulence factors followed species and ST evolutionary lines even though such genes were orthologous. Additionally, zebrafish infectivity studies showed that these pathotypes were as virulent to zebrafish embryos as other clinical strains. In summary, these findings support a striking phylogeny amongst fly, clinical, and surveillance strains isolated during 2010–2015, suggesting that flies are capable vectors for transmission of virulent Cronobacter spp.; they continue to circulate among United States and European populations, environments, and that this “pattern of circulation” has continued over decades.

The Characterization of Two-Component System PmrA/PmrB in Cronobacter sakazakii

Cronobacter sakazakii is an opportunistic Gram-negative pathogen that could cause meningitis and necrotizing enterocolitis. Several Gram-negative bacteria use the PmrA/PmrB system to sense and adapt to environmental change by resistance to cationic antimicrobial peptides of host immune systems. The PmrA/PmrB two-component system regulates several genes to modify LPS structure in the bacterial outer membrane. The role of PmrA/PmrB of C. sakazakii has been studied within the current study. The results suggest that PmrA/PmrB plays a crucial role in modifying LPS structure, cationic antimicrobial peptide susceptibility, cell membrane permeability and hydrophobicity, and invading macrophage.

The Secretion of Toxins and Other Exoproteins of Cronobacter: Role in Virulence, Adaption, and Persistence

: Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capable of causing both intestinal and systemic human disease. This review describes common virulence themes shared among the seven Cronobacter species and describes multiple exoproteins secreted by Cronobacter, many of which are bacterial toxins that may play a role in human disease. The review will particularly concentrate on the virulence factors secreted by C. sakazakii, C. malonaticus, and C. turicensis, which are the primary human pathogens of interest. It has been discovered that various species-specific virulence factors adversely affect a wide range of eukaryotic cell processes including protein synthesis, cell division, and ion secretion. Many of these factors are toxins which have been shown to also modulate the host immune response. These factors are encoded on a variety of mobile genetic elements such as plasmids and transposons; this genomic plasticity implies ongoing re-assortment of virulence factor genes which has complicated our efforts to categorize Cronobacter into sharply defined genomic pathotypes.

Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species where C. sakazakii Homologs Follow Sequence Type Lineages

Cronobacter species are a group of foodborne pathogenic bacteria that cause both intestinal and systemic human disease in individuals of all age groups. Little is known about the mechanisms that Cronobacter employ to survive and persist in foods and other environments. Toxin-antitoxin (TA) genes are thought to play a role in bacterial stress physiology, as well as in the stabilization of horizontally-acquired re-combinatorial elements such as plasmids, phage, and transposons. TA systems have been implicated in the formation of a persistence phenotype in some bacterial species including Escherichia coli and Salmonella. This project's goal was to understand the phylogenetic relatedness among TA genes present in Cronobacter. Preliminary studies showed that two typical toxin genes, fic and hipA followed species evolutionary lines. A local database of 22 TA homologs was created for Cronobacter sakazakii and a Python version 3 shell script was generated to extract TA FASTA sequences present in 234 C. sakazakii genomes previously sequenced as part of Center for Food Safety and Applied Nutrition's (CFSAN) GenomeTrakr project. BLAST analysis showed that not every C. sakazakii strain possessed all twenty-two TA loci. Interestingly, some strains contained either a toxin or an antitoxin component, but not both. Five common toxin genes: ESA_00258 (parDE toxin-antitoxin family), ESA_00804 (relBE family), ESA_01887 (relBE family), ESA_03838 (relBE family), and ESA_04273 (YhfG-Fic family) were selected for PCR analysis and the primers were designed to detect these genes. PCR analysis showed that 55 of 63 strains possessed three of these genes Sequence analysis identified homologs of the target genes and some of the strains were PCR-negative for one or more of the genes, pointing to potential nucleotide polymorphisms in those loci or that these toxin genes were absent. Phylogenetic studies using a Cronobacter pan genomic microarray showed that for the most part TAs follow species evolutionary lines except for a few toxin genes possessed by some C. malonaticus and C. universalis strains; this demonstrates that some TA orthologues share a common phylogeny. Within the C. sakazakii strains, the prevalence and distribution of these TA homologs by C. sakazakii strain BAA-894 (a powdered infant formula isolate) followed sequence-type evolutionary lineages. Understanding the phylogeny of TAs among the Cronobacter species is essential to design future studies to realize the physiological mechanisms and roles for TAs in stress adaptation and persistence of Cronobacter within food matrices and food processing environments.

Multicenter Study of Cronobacter sakazakii Infections in Humans, Europe, 2017

Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe and the extent of clonality for outbreak detection. National coordinators representing 24 countries in Europe were requested to submit all human C. sakazakii isolates collected during 2017 to a study center in Austria. Testing at the center included species identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, subtyping by whole-genome sequencing (WGS), and determination of antimicrobial resistance. Eleven countries sent 77 isolates, including 36 isolates from 2017 and 41 historical isolates. Fifty-nine isolates were confirmed as C. sakazakii by WGS, highlighting the challenge of correctly identifying Cronobacter spp. WGS-based typing revealed high strain diversity, indicating absence of multinational outbreaks in 2017, but identified 4 previously unpublished historical outbreaks. WGS is the recommended method for accurate identification, typing, and detection of this pathogen.

Whole Genome Sequencing-Based Comparison of Food Isolates of Cronobacter sakazakii

Cronobacter sakazakii is an emerging foodborne pathogen, which is linked to life-threatening infections causing septicemia, meningitis, and necrotizing enterocolitis. These infections have been epidemiologically connected to ingestion of contaminated reconstituted powder infant formula. Even at low water activity C. sakazakii can survive for a long time; it is capable of protective biofilm formation and occasionally shows high virulence and pathogenicity even following stressful environmental conditions. Hence it is a challenging task for the food industry to control contamination of food ingredients and products through the entire production chain, since an increasing number of severe food-related outbreaks of C. sakazakii infections has been observed. The seemingly great capability of C. sakazakii to survive even strict countermeasures combined with its prevalence in many food ingredients requires a greater in depth understanding of its virulence factors to master the food safety issues related to this organism. In this context, we present the whole genome sequence (WGS) of two different C. sakazakii isolated from skimmed milk powder (C7) and ready-to-eat salad mix (C8), respectively. These are compared to other, already sequenced, C. sakazakii genomes. Sequencing of the fusA allele revealed that both isolates were C. sakazakii. We investigated the molecular characteristics of both isolates relevant for genes associated with pathogenesis and virulence factors, resistance to stressful environmental conditions (e.g., osmotic and heat), survival in desiccation as well as conducted a comparative genomic analysis. By using multi-locus sequence typing (MLST), the genetic type of both isolates is assessed and the number of unique genes is determined. DNA of C. sakazakii C8 is shown to hold a novel and unique sequence type; the number of unique genes identified in the genomic sequence of C. sakazakii C7 and C8 were 109 and 188, respectively. Some of the determined unique genes such as the rhs and VgrG genes are linked to the Type VI Secretion System cluster, which is associated with pathogenicity and virulence factors. Moreover, seven genes encoding for multi-drug resistance were found in both isolates. The finding of a number of genes linked to producing capsules and biofilm are likely related to the observed resistance to desiccation.

Composition and Origin of the Fermentation Microbiota of Mahewu, a Zimbabwean Fermented Cereal Beverage

Mahewu is a fermented cereal beverage produced in Zimbabwe. This study determined the composition and origin of mahewu microbiota. The microbiota of mahewu samples consisted of 3 to 7 dominant strains of lactobacilli and two strains of yeasts. Enterobacteriaceae were not detected. Candida glabrata was present in high cell counts from samples collected in summer but not from samples collected in winter. Millet malt is the only raw ingredient used in the production of mahewu and is a likely source of fermentation microbiota; therefore, malt microbiota was also analyzed by culture-dependent and high-throughput 16S rRNA gene sequencing methodologies. Millet malt contained 8 to 19 strains of Enterobacteriaceae, lactobacilli, bacilli, and very few yeasts. Strain-specific quantitative PCR assays were established on the basis of the genome sequences of Lactobacillus fermentum FUA3588 and FUA3589 and Lactobacillus plantarum FUA3590 to obtain a direct assessment of the identity of strains from malt and mahewu. L. fermentum FUA3588 and FUA3589 were detected in millet malt, demonstrating that millet malt is a main source of mahewu microbiota. Strains which were detected in summer were not detected in samples produced at the same site in winter. Model mahewu fermentations conducted with a 5-strain inoculum consisting of lactobacilli, Klebsiella pneumoniae, and Cronobacter sakazakii demonstrated that lactobacilli outcompete Enterobacteriaceae, which sharply decreased in the first 24 h. In conclusion, mahewu microbiota is mainly derived from millet malt microbiota, but minor components of malt microbiota rapidly outcompete Enterobacteriaceae and Bacillus species during fermentation.IMPORTANCE This study provides insight into the composition and origin of the microbiota of mahewu and the composition of millet malt microbiota. Fermentation microbiota are often hypothesized to be derived from the environment, but the evidence remains inconclusive. Our findings confirm that millet malt is the major source of mahewu microbiota. By complementing culture methods with high-throughput sequencing of 16S rRNA amplicons and strain-specific quantitative PCR, this study provides evidence about the source of mahewu microbiota, which can inform the development of starter cultures for mahewu production. The study also documents the fate of Enterobacteriaceae during the fermentation of mahewu. There are concerns regarding the safety of traditionally prepared mahewu, and this requires in-depth knowledge of the fermentation process. Therefore, this study elucidated millet malt microbiota and identified cultures that are able to control the high numbers of Enterobacteriaceae that are initially present in mahewu fermentations.

Occurrence of virulence factors in Cronobacter sakazakii and Cronobacter malonaticus originated from clinical samples

BACKGROUND

Cronobacter spp. are Gram-negative, facultative-anaerobic, non-spore forming, enteric coliform bacteria, which belongs to the Enterobacteriaceae family. Cronobacter spp. are opportunistic pathogens that have brought rare but life-threatening infections such as meningitis, necrotizing enterocolitis and bloodstream infections in neonates and infants. Information on the diversity, pathogenicity and virulence of Cronobacter species obtained from various sources is still relatively scarce and fragmentary. The aim of this study was to examine and analyse different pathogenicity and virulence factors among C. sakazakii and C. malonaticus strains isolated from clinical samples.

METHODS

The thirty-six clinical Cronobacter strains have been used in this study. This bacterial collection consists of 25 strains of C. sakazakii and 11 strains of C. malonaticus, isolated from different clinical materials. Seven genes (ompA, inv, sip, aut, hly, fliC, cpa) were amplified by PCR. Moreover, the motility and the ability of these strains to adhere and invade human colorectal adenocarcinoma (HT-29) and mouse neuroblastoma (N1E-115) cell lines were investigated.

RESULTS

Our results showed that all tested strains were able to adhere to both used cell lines, HT-29 and N1E-115 cells. The invasion assay showed that 66.7% (24/36) of isolates were able to invade N1-E115 cells while 83% (30/36) of isolates were able to invade HT-29 cells. On the average, 68% of the C. sakazakii strains exhibited seven virulence factors and only 18% in C. malonaticus. All strains amplified ompA and fliC genes. The other genes were detected as follow: sip 97% (35/36), hlyA 92% (33/36), aut 94% (34/36), cpa 67% (24/36), and inv 69% (25/36).

CONCLUSIONS

C. sakazakii and C malonaticus strains demonstrate the diversity of the virulence factors present among these pathogens. It is necessary to permanently monitor the hospital environment to appropriately treat and resolve cases associated with disease. Furthermore, in-depth knowledge is needed about the source and transmission vehicles of pathogens in hospitals to adopt pertinent prevention measures.

Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains

Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from the USA, the Middle East, China, and the Republic of Korea. The average genome size of the C. sakazakii genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins involved in osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as virulence-related and heat shock-related proteins. Interestingly, a metabolic island comprised of a variably-sized xylose utilization operon was found within the spice-associated C. sakazakii genomes, which supports the hypothesis that plants may serve as transmission vectors or alternative hosts for Cronobacter species. The presence of the genes identified in this study can support the remarkable phenotypic traits of C. sakazakii such as the organism's capabilities of adaptation and survival in response to adverse growth environmental conditions (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses provided insights into many aspects of physiology and evolutionary history of this important foodborne pathogen.

Silver nanoparticles: A novel antibacterial agent for control of Cronobacter sakazakii

Silver nanoparticles (AgNP) have been widely applied because of their broad spectrum of antimicrobial activities against bacteria, fungi, and viruses. However, little research has been done to evaluate their effects on Cronobacter sakazakii, an opportunistic pathogen usually infecting infants and having a high fatality rate. The aims of this work were to investigate the antibacterial property of novel, synthesized, positively charged silver nanoparticles against C. sakazakii and to discuss the potential antibacterial mechanisms involved. In this study, the spherical and face-centered cubic silver nanoparticles had a mean particle size of 31.2 nm and were synthesized by reducing Ag⁺ using citrate and dispersed by glycerol and polyvinylpyrrolidone (PVP) under alkaline conditions. Minimum inhibitory concentrations (MIC) and inhibition zone tests showed that the AgNP exhibited strong antibacterial activity against 4 tested C. sakazakii strains with mean MIC of 62.5 to 125 mg/L and average inhibition zone diameters of 13.8 to 16.3 mm. Silver nanoparticles caused cell membrane injury accompanied by adsorption of AgNP onto the cell surface, as shown by changes in cell morphology, cell membrane hyperpolarization, and accelerated leakage of intracellular reducing sugars and proteins outward from the cytoplasm. In addition, dysfunction of the respiratory chain was induced after treatment with AgNP, which was supported by a decrease in intracellular ATP and inhibition of related dehydrogenases. This research indicates that AgNP could be a novel and efficient antibacterial agent to control C. sakazakii contamination in environments producing powdered infant formulas from milk.

Survival of Cronobacter in powdered infant formula and their variation in biofilm formation

Cronobacter is a ubiquitous Gram-negative pathogen bacterium capable of surviving in low water activity environments, in particular powdered infant formula (PIF). Seven Cronobacter strains representing four different species (C. sakazakii, n = 4; C. malonaticus, n = 1; C. muytjensii, n = 1; C. turicensis, n = 1) were subjected to dry stress and stored in PIF at room temperature. The resulting survivor curves showed that Cronobacter sp. can survive for extended periods of at least 3 months with a significant, but moderate, variability regarding the level of resistance between species; however, no correlation was evident regarding the origin of strains. These results are evaluated with regard to other key characteristics, including genomic profiles and biofilm formation capacities of the strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Cronobacter can survive extended periods of at least 3 months in PIF, with moderately significant interspecific variability in desiccation resistance. Results are evaluated with regard to genomic profiles and biofilm formation capacities of the strains, and contribute to an improved understanding of the environmental persistence of Cronobacter in contaminated PIF, and subsequent risk to infant exposure.

Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

Background

Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven Cronobacter species is thought to be largely absent in Cronobacter sakazakii (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other C. sakazakii strains.

Results

In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 C. sakazakii strains tested could utilize malonate. Zebrafish embryo infection studies showed that C. sakazakii ST64 strains are as virulent as other Cronobacter species. Parallel whole genome sequencing (WGS) and MA showed that the strains phylogenetically grouped as a separate clade among the Csak species cluster. Additionally, these strains possessed the Csak O:2 serotype. The nine-gene, ~ 7.7 kbp malonate utilization operon was located in these strains between two conserved flanking genes, gyrB and katG. Plasmidotyping results showed that these strains possessed the virulence plasmid pESA3, but in contrast to the USA ST64 Csak strains, ST64 Csak strains isolated from sources in Europe and the Middle East, did not possess the type six secretion system effector vgrG gene.

Conclusions

Until this investigation, the presence of malonate-positive Csak strains, which are associated with foods and clinical cases, was under appreciated. If this trait was used solely to identify Cronobacter strains, many strains would likely be misidentified. Parallel WGS and MA were useful in characterizing the total genome content of these Csak O:2, ST64, malonate-positive strains and further provides an understanding of their phylogenetic relatedness among other virulent C. sakazakii strains.

Electronic supplementary material

The online version of this article (10.1186/s13099-018-0238-9) contains supplementary material, which is available to authorized users.

Genes involved in tolerance to osmotic stress by random mutagenesis in Cronobacter malonaticus

Cronobacter malonaticus is one of the opportunistic food-borne pathogens in powdered infant formula and has unusual abilities to survive under environmental stresses such as osmotic conditions. However, the genes involved in osmotic stress have received little attention in C. malonaticus. Here, genes involved in osmotic stress were determined in C. malonaticus using a transposon mutagenesis approach. According to the growth of mutants (n = 215) under 5.0% NaCl concentration, the survival of 5 mutants under osmotic stress was significantly decreased compared with that of the wild type strain. Five mutating sites, including potassium efflux protein KefA, inner membrane protein YqjF, peptidylprolyl isomerase, Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase, and oligogalacturonate lyase were successfully identified. In addition, the biofilm formation of 5 mutants was determined using crystal violet staining, scanning electron microscopy, and confocal laser scanning microscopy, and the biofilms of 5 mutants significantly decreased within 72 h compared with that of wild type strain. This is the first report to determine the genes involved in osmotic tolerance in C. malonaticus. The findings provided valuable information for deep understanding of the mechanism of survival of C. malonaticus under osmotic stress, and a possible relationship between biofilm formation and tolerance to osmotic stress was also demonstrated in C. malonaticus.

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

Background

Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative, have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree.

Results

We have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.

Conclusions

xenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2038-0) contains supplementary material, which is available to authorized users.

Microbial Source Tracking of Cronobacter spp

Being able to track bacterial pathogens is essential for epidemiological purposes as well as monitoring in-house production facilities. Common bacterial pathogens, such as Salmonella serovars, are already been well defined, and their detection methods are very advanced. However, this will not be the case for emergent bacterial pathogens, as was the case for Cronobacter. The clinical significance of the organism is due to its association with rare sporadic infections in adults, and severe life-threatening outbreaks of necrotizing enterocolitis and meningitis in newborn babies. The main recognized route of infection being through the consumption of contaminated reconstituted powdered infant formula. Key to the advances in being able to track this organism during formula production and outbreaks in neonatal intensive care units has been the use of DNA sequence-based methods, and most recently those which profile whole-genome sequences. This chapter considers how the latest DNA sequence-based methods in genotyping Cronobacter serve as a model for analyzing emergent bacterial pathogens in the future. The methods considered will initially highlight the limitations of phenotyping, then advance from the DNA probe-based methods for serotyping through to DNA sequence-based methods, especially multilocus sequence typing which is supported by an open access database. Finally the development of typing methods based on whole-genomes sequences, CRISPR-cas array profiling and SNP analysis, will be covered. The overall perspective is that emergent pathogens need to be investigated with the most advanced methods in order for robust and reliable control measures to be adopted.

Antibiotic Susceptibility of Cronobacter spp. Isolated from Clinical Samples

Cronobacter spp. have been recognized as causative agents of various severe infections in pre-term or full-term infants as well as elderly adults suffering from serious underlying disease or malignancy. A surveillance study was designed to identify antibiotic resistance among clinical Cronobacter spp. strains, which were isolated from patients of two hospitals between May 2007 and August 2013. Altogether, 52 Cronobacter spp. isolates were analyzed. Although MALDI-TOF mass spectrometry recognized all Cronobacter sakazakii and Cronobacter malonaticus strains, it could not identify Cronobacter muytjensii strain. Nevertheless, all strains were identified as Cronobacter spp. using multilocus sequence typing (MLST). Strains were tested against 17 types of antibiotics, using the standard microdilution method according to the 2018 European Committee on Antimicrobial Susceptibility Testing criteria. Three Cronobacter species were identified as C. sakazakii (n = 33), C. malonaticus (n = 18), and C. muytjensii (n = 1); all isolates were susceptible to all tested antibiotics. All strains were PCR-negative for bla_TEM, bla_SHV, and bla_CTX-M β-lactamase genes, as well. Even though the results of this study showed that Cronobacter spp. isolates were pan-susceptible, continued antibiotic resistance surveillance is warranted.

Updates on the Cronobacter Genus

There has been considerable concern related to Cronobacter spp. in foods, especially due to their highlighted association with neonatal infections through the ingestion of reconstituted powdered infant formula (PIF). This concern resulted in improved microbiological criteria recommendations by the Codex Alimentarius Commission and revised WHO advice on the preparation of infant feeds. In recent years, the diversity of the genus has been well described, and various detection and typing methods have been developed. This review considers our current knowledge of the genus and how DNA-sequence-based methods have contributed considerably to research into improved detection methods and more reliable identification procedures, genotyping schemes, and genomic analysis. The broader occurrence of Cronobacter in food ingredients, finished products, and food manufacturing environments is covered. This review also highlights the significance of clonal lineages in microbial source tracking and the use of CRISPR-cas array profiling.

Characterisation of Cronobacter strains isolated from hospitalised adult patients

Bacteria belonging to the genus Cronobacter are opportunistic pathogens known for causing rare but serious infections in neonates, including meningitis, necrotising enterocolitis and sepsis. Cronobacter infections occur also in adult populations, however, they generally have milder manifestations and their prevalence is uncertain. In this study, the presence of Cronobacter strains from adult patients in the University Hospital in Bratislava was investigated and overall 18 confirmed isolates from 321 patients (5.3%) were recovered. No Cronobacter positive sample was detected in 215 sputum samples from outpatients. The highest occurrence of Cronobacter strains was observed from stroke patients and this may be associated with an abnormal swallowing ability. The isolated strains belonged to the species Cronobacter sakazakii and Cronobacter malonaticus. In silico genotyping (MLST, CRISPR-cas array profiling) of whole genome sequences assigned the strains to three different MLST clones. The majority (12/18) of the isolated strains were sequence type ST513 or single locus variants ST514 and ST515, thereby being members of C. sakazakii pathovar clonal complex CC4. However, according to core genome MLST analysis the ST513-ST515 strains created a unique cluster substantially different from other CC4 strains. The isolated strains were susceptible to 18 tested antibiotics. All strains possess a genomic island encoding for increased thermal tolerance. As Cronobacter strains are frequently present in dried foods of plant origin, spread of a specific clone within a hospital may be caused by food transmission and may be facilitated by its tolerance to environmental stresses such as desiccation and temperature.

Inactivation of Cronobacter malonaticus cells and inhibition of its biofilm formation exposed to hydrogen peroxide stress

Presence of Cronobacter malonaticus in powdered infant formula (PIF) poses a high risk to infant and public health. Cronobacter malonaticus has been widely distributed in food and food processing environments, and the true origin of C. malonaticus in PIF is poorly understood. Control and prevention of C. malonaticus is necessary for achieving microbial safety of PIF. However, little information about decontamination of C. malonaticus is available. In this study, effects of hydrogen peroxide on inactivation and morphological changes of C. malonaticus cells were determined. Furthermore, inhibitory effects of H₂O₂ on biofilm formation in C. malonaticus were also performed. Results indicated that H₂O₂ could completely inactivate C. malonaticus in sterile water with 0.06% H₂O₂ for 25 min, 0.08% H₂O₂ for 15 min, and 0.10% for 10 min, respectively, whereas the survival rates of C. malonaticus in tryptic soy broth medium significantly increased with the same treatment time and concentration of H₂O₂. In addition, morphological changes of C. malonaticus cells, including cell shrinkage, disruption of cells, cell intercession, and leakage of intercellular material in sterile water after H₂O₂ treatment, were more predominant than those in tryptic soy broth. Finally, significant reduction in biofilm formation by H₂O₂ was found using crystal violet staining, scanning electron microscopy, and confocal laser scanning microscopy detection compared with control samples. This is the first report to determine the effects of H₂O₂ on C. malonaticus cells and biofilm formation. The findings provided valuable information for practical application of H₂O₂ for decontamination of C. malonaticus in dairy processing.

DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling

The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST), capsular profiling of the K-antigen and colanic acid (CA) biosynthesis regions, and CRISPR-cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC) 1 and 4, sequence types (ST) 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis, C. dublinensis and C. universalis. The majority of CRISPR-cas types across the genus was the I-E (Ecoli) type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo) type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.

Potential factors involved in virulence of Cronobacter sakazakii isolates by comparative transcriptome analysis

Cronobacter species are important foodborne pathogens causing severe infections in neonates through consumption of contaminated powdered infant formula. However, the virulence-associated factors in Cronobacter are largely unknown. In this study, the transcriptome analysis between highly virulent Cronobacter sakazakii G362 and attenuated L3101 strains was used to reveal the potential factors involved in virulence. The total transcripts were grouped into 20 clusters of orthologous group categories and summarized in 3 gene ontology categories (biological process, cellular component, and molecular function). In addition, the differentially expressed genes (DEG) between these isolates were analyzed using Volcano plots and gene ontology enrichment. The predominant DEG were flagella-associated genes such as flhD, motA, flgM, flgB, and fliC. Furthermore, the expression abundance of outer membrane protein or lipoprotein genes (ompW, slyB, blc, tolC, and lolA), potential virulence-related factors (hlyIII and hha), and regulation factors (sdiA, cheY, Bss, fliZ) was also significantly different between G362 and L3101. Interestingly, 3 hypothetical protein genes (ESA_01022, ESA_01609, and ESA_00609) were found to be expressed only in G362. Our findings provide valuable transcriptomic information about potential virulence factor genes, which will be needed in future molecular biology studies designed to understand the pathogenic mechanism of Cronobacter.

Evaluation of Whole Genome Mapping as a Fast and Automated Molecular Epidemiological Tool for the Study of Cronobacter spp. in Powdered Infant Formula Processing Facilities

Cronobacter has been identified as the causative agent of outbreaks or sporadic cases of meningitis, necrotizing enterocolitis, and septicemia associated with powdered infant formula. Food processing environments may provide a possible contamination route. The purpose of this study was to evaluate whole genome mapping (WGM) as a fast and automated molecular epidemiological method for characterizing Cronobacter spp. in the processing environment. This is the first study indicating the applicability of WGM to Cronobacter. WGM was compared with ribotyping, which is often used as an automated typing tool, and with pulsed-field gel electrophoresis, which is a well-known and highly discriminating tool that is also based on restriction site analysis. The comparison of the three tools was carried out on a subset of Cronobacter isolates collected from 2011 to 2014 through a monitoring program. The performance characteristics of WGM have not yet been described; therefore, in the current study its performance was evaluated based on five criteria: typeability, reproducibility, stability, epidemiological concordance, and the discrimination power. WGM was shown to produce typeable, reproducible, and stable results. With a similar cut-off of 98%, WGM was shown to have a discriminatory power equivalent to pulsed-field gel electrophoresis and higher than ribotyping. Future studies are needed to confirm the indicated cut-off level of 98%.