Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively

Turning trash into treasure: Hermetia illucens microbiome and biodegradation of industrial side streams

Black soldier fly larvae (BSFL) have attracted attention due to their ability to upcycle various biological side streams into valuable biomass, such as proteins, lipids, and chitin. In this study, we investigated the impact of high-fiber diets on larval growth performance and the shift of microbes in the gut. We tested empty fruit bunches (EFB), potato pulp (PP), and cottonseed press cake (CPC), with chicken feed (CF) used as a control diet. We found that larvae reared on the EFB, PP, and CPC were smaller than control larvae at the end of development due to the low nutritional value of the diets. However, survival rates of more than 90% were observed regardless of the diet. We used a cultivation-dependent approach to analyze the microbial community in the gut of BSFL, isolated, and identified a total of 329 bacterial strains. Bacillaceae were most frequently isolated from larvae reared on the high-fiber EFB diet. These isolates were predicted to degrade cellulose in silico and this was subsequently confirmed in vitro using the Congo Red assay. Whereas the members of Enterobacteriaceae and Morganellaceae were mostly found in guts of larvae reared on the high-protein diets CPC and CF. We conclude that the gut microbiome plays a crucial role in the digestion of fiber-rich plant organic material, thereby enabling the BSFL to successfully complete their life cycle also on substrates with low nutritional value. As a result, BSFL convert industrial side streams into valuable biomass, reducing waste and promoting sustainability.

IMPORTANCE

Organic side streams from various industries pose a challenge to the environment. They are often present in huge amounts and are mostly discarded, incinerated, used for biogas production, or as feed for ruminant animals. Many plant-based side streams contain difficult-to-digest fiber as well as anti-nutritional or even insecticidal compounds that could harm the animals. These challenges can be addressed using black soldier fly larvae, which are known to degrade various organic substrates and convert them into valuable biomass. This will help mitigate agro-industrial side streams via efficient waste management and will contribute to the more economical and sustainable farming of insects.

Genomic Analysis of Cronobacter condimenti s37: Identification of Resistance and Virulence Genes and Comparison with Other Cronobacter and Closely Related Species

Cronobacter condimenti are environmental commensals that have not been associated with any clinical infections. To date, they are the least understood and described Cronobacter species within the genus. The objective of this study was to use a draft genome sequence (DGS) of the Cronobacter condimenti strain s37 to screen for genes encoding for antibiotic resistance, virulence, response to environmental stress, and biofilm formation. The strain was isolated in Poland from commercial small radish sprouts. This is the second genome of this species available in the GenBank database. The comparative genome analysis (cgMLST) of C. condimenti s37 with other Cronobacter spp. including the pathogenic species C. sakazakii and the plant-associated closely related genera Franconibacter and Siccibacter was also performed. The assembled and annotated genome of the C. condimenti s37 genome was 4,590,991 bp in length, with a total gene number of 4384, and a GC content of 55.7%. The s 37 genome encoded for genes associated with resistance to stressful environmental conditions (metal resistance genes: zinc, copper, osmotic regulation, and desiccation stress), 17 antimicrobial resistance genes encoding resistance to various classes of antibiotics and 50 genes encoding for the virulence factors. The latter were mainly genes associated with adhesion, chemotaxis, hemolysis, and biofilm formation. Cg-MLST analysis (3991 genes) revealed a greater similarity of C. condimenti s37 to S. turicensis, F. pulveris, and C. dublinensis than to other species of the genus Cronobacter. Studies on the diversity, pathogenicity, and virulence of Cronobacter species isolated from different sources are still insufficient and should certainly be continued. Especially the analysis of rare strains such as s37 is very important because it provides new information on the evolution of these bacteria. Comparative cgMLST analysis of s37 with other Cronobacter species, as well as closely related genera Franconibacter and Siccibacter, complements the knowledge on their adaptability to specific environments such as desiccation.

Effect of glutathione-transport-related gene gsiD on desiccation tolerance of Cronobacter sakazakii and its related regulatory mechanism

The outstanding desiccation tolerance of Cronobacter sakazakii (C. sakazakii) enables long-term persistence in food products with low-water activity to increase the infection risk, especially in low-birth-weight, immuno-compromised neonates, and infants less than 4 weeks of age. In our previous study, the disruption of glutathione transport-related gene gsiD by transposon was found to significantly increase its inactivation rate under drying stress challenges. However, the mechanism underlying the association between glutathione transport and desiccation tolerance of C. sakazakii remains to be clarified. In this study, the mechanism underlying their association was investigated in detail by constructing the gsiD gene deletion mutant. gsiD gene deletion was found to cause the dysfunction of the glutathione transport system GsiABCD and the limitation of glutathione import. The resulting decrease in intracellular glutathione caused the decreased potassium ions uptake and increased potassium ions efflux, inhibited the proline synthesis process, limited extracellular glutathione utilization, increased oxidant stress, reduced biofilm formation, and increased outer membrane permeability, which may be the main reasons for the significant reduction of the desiccation tolerance of C. sakazakii.IMPORTANCEContributing to its superior environmental adaptability, Cronobacter sakazakii can survive under many abiotic stress conditions. The outstanding desiccation tolerance makes this species persist in low-water activity foods, which increases harm to humans. For decades, many studies have focused on the desiccation tolerance of C. sakazakii, but the existing research is still insufficient. Our study found that gsiD gene deletion inhibited glutathione uptake and further decreased intracellular glutathione content, causing a decrease in desiccation tolerance and biofilm formation and an increase in outer membrane permeability. Moreover, the expression level of relative genes verified that gsiD gene deletion made the mutant not conducive to surviving in dry conditions due to restricting potassium ions uptake and efflux, inhibiting the conversion of glutamate to compatible solute proline, and increasing the oxidative stress of C. sakazakii. The above results enrich our knowledge of the desiccation tolerance mechanism of C. sakazakii.

High-affinity truncated aptamers for detection of Cronobacter spp with magnetic separation-assisted DNAzyme-driven 3D DNA walker

After optimizing the original aptamer sequence by truncation strategy, a magnetic separation-assisted DNAzyme-driven 3D DNA walker fluorescent aptasensor was developed for detecting the food-borne pathogen Cronobacter species. Iron oxide magnetic nanoparticles (MNPs) modified with a hybrid of truncated aptamer probe and DNAzyme strand (AP-E1) denoted as MNPs@AP-E1, were employed as capture probes. Simultaneously, a DNAzyme-driven 3D-DNA walker was utilized as the signal amplification element. The substrate strand (Sub) was conjugated with the gold nanoparticles (AuNPs), resulting in the formation of AuNPs@Sub, which served as a 3D walking track. In the presence of the target bacteria and Mg2+, E1-DNAzyme was activated and moved along AuNPs@Sub, continuously releasing the signal probe. Under optimized conditions, a strong linear correlation was observed for Cronobacter sakazakii (C. sakazakii) in the concentration range 101 to 106 CFU mL-1, with a low detection limit of 2 CFU mL-1. The fluorescence signal responses for different Cronobacter species exhibited insignificant differences, with a relative standard deviation of 3.6%. Moreover, the aptasensor was successfully applied to determine  C. sakazakii in real samples with recoveries of 92.86%-108.33%. Therefore, the novel method could be a good candidate for ultra-sensitive and selective detection of Cronobacter species without complex manipulation.

Characterization of Cronobacter sakazakii and Cronobacter malonaticus Strains Isolated from Powdered Dairy Products Intended for Consumption by Adults and Older Adults

The objective of this study was to characterize Cronobacter spp. and related organisms isolated from powder dairy products intended for consumption by adults and older adults using whole-genome sequencing (WGS), and to identify genes and traits that encode antibiotic resistance and virulence. Virulence (VGs) and antibiotic resistance genes (ARGs) were detected with the Comprehensive Antibiotic Resistance Database (CARD) platform, ResFinder, and MOB-suite tools. Susceptibility testing was performed using disk diffusion. Five presumptive strains of Cronobacter spp. were identified by MALDI-TOF MS and ribosomal MLST. Three C. sakazakii strains were of the clinical pathovar ST1, one was ST31, and the remaining isolate was C. malonaticus ST60. In addition, Franconibacter helveticus ST345 was identified. The C. sakazakii ST1 strains were further distinguished using core genome MLST based on 2831 loci. Moreover, 100% of the strains were resistant to cefalotin, 75% to ampicillin, and 50% to amikacin. The C. sakazakii ST1 strains were multiresistant (MDR) to four antibiotics. Additionally, all the strains adhered to the N1E-115 cell line, and two invaded it. Eighteen ARGs mainly involved in antibiotic target alteration and antibiotic efflux were detected. Thirty VGs were detected and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, and genes involved in metabolism and stress. The pESA3, pSP291-1, and pCMA1 plasmids were detected, and the prevalent mobile genetic elements (MGEs) were ISEsa1, ISEc52, and IS26. The isolates of C. sakazakii and C. malonaticus exhibited multiresistance to antibiotics, harbored genes encoding various antibiotic resistance proteins, and various virulence factors. Consequently, these contaminated powdered dairy products pose a risk to the health of hypersensitive adults.

Screening of Antibiotic and Virulence Genes from Whole Genome Sequenced Cronobacter sakazakii Isolated from Food and Milk-Producing Environments

The objective of this study was to use whole-genome sequencing (WGS) to screen for genes encoding for antibiotic resistance, fitness and virulence in Cronobacter sakazakii strains that had been isolated from food and powdered-milk-producing environments. Virulence (VGs) and antibiotic-resistance genes (ARGs) were detected with the Comprehensive Antibiotic Resistance Database (CARD) platform, ResFinder and PlasmidFinder tools. Susceptibility testing was performed using disk diffusion. Fifteen presumptive strains of Cronobacter spp. were identified by MALDI-TOF MS and ribosomal-MLST. Nine C. sakazakii strains were found in the meningitic pathovar ST4: two were ST83 and one was ST1. The C. sakazakii ST4 strains were further distinguished using core genome MLST based on 3678 loci. Almost all (93%) strains were resistant to cephalotin and 33% were resistant to ampicillin. In addition, 20 ARGs, mainly involved in regulatory and efflux antibiotics, were detected. Ninety-nine VGs were detected that encoded for OmpA, siderophores and genes involved in metabolism and stress. The IncFIB (pCTU3) plasmid was detected, and the prevalent mobile genetic elements (MGEs) were ISEsa1, ISEc52 and ISEhe3. The C. sakazakii isolates analyzed in this study harbored ARGs and VGs, which could have contributed to their persistence in powdered-milk-producing environments, and increase the risk of infection in susceptible population groups.

Siccibacter colletis as a member of the plant growth-promoting rhizobacteria consortium to improve faba-bean growth and alleviate phosphorus deficiency stress

The rhizosphere is a hot spot and a source of beneficial microorganisms known as plant growth-promoting rhizobacteria (PGPR). From the alfalfa (Medicago sativa) rhizosphere, 115 bacteria were isolated, and from the screening for PGP traits, 26 interesting isolates were selected as PGP rhizobacteria for the next tests. The objective of this study was to use a consortium of PGPR to enhance the growth of faba-bean under phosphate (P) deficiency by taking advantage of their ability to release phosphorus from rock phosphate (RP). Several examined strains were found to have a relatively high activity on P solubilization, auxin, siderophore, ammoniac production, antifungal activity, and the ability to tolerate hypersalinity and water stress. 16S rRNA gene sequencing of the collection revealed six different genera, including Bacillus (46.15%), Siccibacter (23.07%), and Acinetobacter (15.38%) which were identified as the most abundant. Three of the interesting strains (Siccibacter colletis, Enterobacter huaxiensis, and Pantoea sp.) showed high plant growth promotion traits and no antagonism with Rhizobium laguerreae. These three bacteria were retained to establish a rhizobia-including consortium. The inoculation of faba-bean plants with the consortium improved growth parameters as root and shoot dried biomasses and some physiological criteria (chlorophyll content and P uptake under low P availability conditions), and the increase reached 40%. Our study could be the first report of faba-bean growth promotion by a multi-strain PGPR-rhizobia consortium involving S. colletis, E. huaxiensis, and Pantoea sp. Thus, this consortium could be recommended for faba-bean inoculation, particularly under P-limiting conditions.

Thermal tolerance of Cronobacter sakazakii and Cronobacter pulveris in reconstituted infant milk formula

Background

Cronobacter sspecies are the most significant foodborne pathogen in infant milk formula (IMF). These pathogens have been incriminated in severe forms of neonatal meningitis, sepsis, and necrotizing enterocolitis with a high mortality rate.

Aim

This study was performed to elucidate the effect of heat stress on Cronobacter spp. (C. sakazakii and C. pulveris) in reconstituted IMF (RIMF).

Methods

The reconstituted formula was inoculated with five C. sakazakii isolates and four C. pulveris isolates separately. The nine isolates of Cronobacter spp. were heated in RIMF at 48°C, 52°C, 56°C, 60°C, 64°C, and 66°C. The D- and z-values were determined by using linear regression analysis.

Results

The D-values of all isolates of C. sakazakii (CS1, CS3, CS4, CS5, and CS6) at 48°C, 52°C, 56°C, 60°C, 64°C, and 66°C were in the ranges 7.29-23.47, 2.77-15.50, 0.62-1.04, 0.62-1.02, 0.62-1.00, 0.62-1.00 minutes, respectively; while, the z-values extended from 2.50°C to 4.28°C. The D- values of C. pulveris isolates (CP1, CP2, CP3, CP4) were in the ranges 7.60-22.32, 1.42-8.45, 0.62-1.08, 0.62-0.78, 0.62-0.78, 0.62-0.79 minutes at 48°C, 52°C, 56°C, 60°C, 64°C, 66°C, respectively and the calculated z-values ranged from 3.33°C to 4.89°C.

Conclusion

This study may contribute to improving the understanding of the behavior of C. sakazakii and C. pulveris isolates in RIMF at various heat stress temperatures and may participate in the effective control of these pathogens in infant food production.

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.

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.

Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile

This study characterized five Cronobacter spp. and six Salmonella spp. strains that had been isolated from 155 samples of powdered infant formula (PIF) sold in Chile and manufactured in Chile and Mexico in 2018–2020. Two strains of Cronobacter sakazakii sequence type (ST) ST1 and ST31 (serotypes O:1 and O:2) and one strain of Cronobacter malonaticus ST60 (O:1) were identified. All Salmonella strains were identified as Salmonella Typhimurium ST19 (serotype O:4) by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST (cgMLST). The C. sakazakii and C. malonaticus isolates were resistant to cephalothin, whereas the Salmonella isolates were resistant to oxacillin and ampicillin. Nineteen antibiotic resistance genes were detected in the C. sakazakii and C. malonaticus isolates; the most prevalent were mcr-9.1, bla_CSA, and bla_CMA. In Salmonella, 30 genes encoding for aminoglycoside and cephalosporin resistance were identified, including aac(6′)-Iaa, β-lactamases ampH, ampC1, and marA. In the Cronobacter isolates, 32 virulence-associated genes were detected by WGS and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, invasion, plasminogen activator, colonization, transcriptional regulator, survival in macrophages, use of sialic acid, and toxin-antitoxin genes. In the Salmonella strains, 120 virulence associated genes were detected, adherence, magnesium uptake, resistance to antimicrobial peptides, secretion system, stress protein, toxin, resistance to complement killing, and eight pathogenicity islands. The C. sakazakii and C. malonaticus strains harbored I-E and I-F CRISPR-Cas systems and carried Col(pHHAD28) and IncFIB(pCTU1) plasmids, respectively. The Salmonella strains harbored type I-E CRISPR-Cas systems and carried IncFII(S) plasmids. The presence of C. sakazakii and Salmonella in PIF is a health risk for infants aged less than 6 months. For this reason, sanitary practices should be reinforced for its production and retail surveillance.

Diversity and phylogeny of the bacterial strains isolated from nodules of fenugreek (Trigonella foenum-graecum L.) in Iran

The diversity of fenugreek (Trigonella foenum-graecum L.) microsymbionts has been barely studied even though it is of great interest for being a spice and a medicinal plant. Here we analyzed fifty-nine bacterial strains isolated from fenugreek nodules originating from different geographic and climatic areas of Iran. Most of these strains exhibit phenotypic characteristics compatible with rhizobia and they nodulate fenugreek. Analysis of the recA and atpD genes shows that representative strains of ERIC-BOX-PCR groups cluster with the type strains of Ensifer meliloti and Ensifer kummerowiae as well as with strains capable of nodulating different Trigonella species found in other countries. The closeness of E. meliloti and E. kummerowiae suggests there is a need to revise the taxonomic status of the latter species. The nodC gene analysis shows that most Trigonella-nodulating strains belong to the symbiovar meliloti except those nodulating Trigonella arcuata in China, which belong to the symbiovar rigiduloides. This analysis shows that the type strains of E. kummerowiae, E. meliloti and E. medicae belonged to three well-defined groups within the symbiovar meliloti, with the Iranian strains belonging to the E. kummerowiae subgroup. The small group of strains unable to nodulate fenugreek isolated in this study belong to Enterobacter cloacae, reported for the first time as being a possible endophyte of fenugreek nodules.

Reclassification of Enterobacter sp. FY-07 as Kosakonia oryzendophytica FY-07 and Its Potential to Promote Plant Growth

Precise classification of bacteria facilitates prediction of their ecological niche. The genus Enterobacter includes pathogens of plants and animals but also beneficial bacteria that may require reclassification. Here, we propose reclassification of Enterobacter FY-07 (FY-07), a strain that has many plant-growth-promoting traits and produces bacterial cellulose (BC), to the Kosakonia genera. To re-examine the taxonomic position of FY-07, a polyphasic approach including 16S rRNA gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, determination of DNA G + C content, average nucleotide identity based on BLAST, in silico DNA–DNA hybridization and analysis of phenotypic features was applied. This polyphasic analysis suggested that Enterobacter sp. FY-07 should be reclassified as Kosakonia oryzendophytica FY-07. In addition, the potential of FY-07 to promote plant growth was also investigated by detecting related traits and the colonization of FY-07 in rice roots.

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.

Roseitranquillus sediminis gen. nov., sp. nov. a novel genus and species of the family Rhodobacteraceae, isolated from sediment of an Arctic fjord

A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain MCCB 386^T was isolated from sediment samples collected from Kongsfjorden, an Arctic fjord. The strain MCCB 386^T showed growth at 4-37 °C (optimum 27°C) in the presence of 1-8% NaCl (w/v, optimum 3.5%) and at pH 6.0-8.0 (optimum pH 7.0). The major fatty acids were C_18:1ω7c (54.0%) and 11-methyl C_18:1ω7c (22.6%). The dominant respiratory quinone was Q-10. The major polar lipids comprised of phosphatidylcholine (PC), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphoglycolipid (PGL), one unidentified aminolipid, two glycolipids and two unidentified lipids. The genomic G+C content of the strain MCCB 386^T was 68.1 mol%. The 16 S rRNA gene sequences based phylogenetic analysis of MCCB 386^T showed that Psychromarinibacter halotolerans YBW34^T (95.88%) is the most closely related species. In addition, overall genome relatedness indices (OGRI) of MCCB 386^T with closely related strains were lower than threshold level for species and genus delineation. The analysis of Biosynthetic Gene clusters (BGCs) revealed the potential of this strain for production of novel bioactive secondary metabolites. As per polyphasic taxonomic characterisation, strain MCCB 386^T represents a novel species of a novel genus for which the name Roseitranquillus sediminis gen. nov., sp. nov. is suggested. The type strain of the species is MCCB 386^T (= JCM 33,538^T= KACC 21,531^T).

A simple and sensitive aptasensor with rolling circle amplification for viable Cronobacter sakazakii detection in powdered infant formula

Cronobacter sakazakii is a foodborne, emerging opportunistic pathogen that causes severe bacteremia, necrotizing enterocolitis, and sepsis with a mortality rate of up to 80%. In this study, we developed a simple and sensitive fluorescent turn-off aptasensor with rolling circle amplification assay for viable C. sakazakii detection in powdered infant formula. The results showed that the proposed aptasensor has good performance and specificity for detecting viable C. sakazakii in pure culture and powdered infant formula samples within 3 h. Under the optimal reaction conditions, there is a linear relationship between fluorescent intensity at 490 nm and logarithmic concentration of C. sakazakii in the range of 2.7 × 10⁵ to 2.7 × 10² cfu/mL, with a limit of detection of 2.7 × 10² cfu/mL in pure culture. The proposed aptasensor achieved a recovery of 104 to 111% in pure culture, and 96 to 107% in spiked powdered infant formula samples. The proposed aptasensor does not require complicated DNA extraction steps or antibodies, and can be performed at 37°C, making it a convenient and sensitive strategy for C. sakazakii detection.

Profiling the Virulence and Antibiotic Resistance Genes of Cronobacter sakazakii Strains Isolated From Powdered and Dairy Formulas by Whole-Genome Sequencing

Cronobacter sakazakii is an enteropathogen that causes neonatal meningitis, septicemia, and necrotizing enterocolitis in preterm infants and newborns with a mortality rate of 15 to 80%. Powdered and dairy formulas (P-DF) have been implicated as major transmission vehicles and subsequently the presence of this pathogen in P-DF led to product recalls in Chile in 2017. The objective of this study was to use whole genome sequencing (WGS) and laboratory studies to characterize Cronobacter strains from the contaminated products. Seven strains were identified as C. sakazakii, and the remaining strain was Franconibacter helveticus. All C. sakazakii strains adhered to a neuroblastoma cell line, and 31 virulence genes were predicted by WGS. The antibiograms varied between strains. and included mcr-9.1 and bla CSA genes, conferring resistance to colistin and cephalothin, respectively. The C. sakazakii strains encoded I-E and I-F CRISPR-Cas systems, and carried IncFII(pECLA), Col440I, and Col(pHHAD28) plasmids. In summary, WGS enabled the identification of C. sakazakii strains and revealed multiple antibiotic resistance and virulence genes. These findings support the decision to recall the contaminated powdered and dairy formulas from the Chilean market in 2017.

Bacterial endosymbiont inhabiting Leucaena leucocephala leaves and their antioxidant and antidiabetic potential

OBJECTIVES

Research on endosymbionts is emerging globally and is considered as a potential source of bioactive phytochemicals. The present study examines the antioxidant and antidiabetic of the endophytic crude extract isolated from Leucaena leucocephala leaves.

METHODS

Endophytic bacteria were isolated from the leaves of L. leucocephala and 16S rRNA gene sequencing was used to establish their identity. The in vitro antioxidant effect of endophytic crude extract (LL) was evaluated using 2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) free radical scavenging methods. The in vitro antidiabetic properties of LL were evaluated using α-amylase and α-glucosidase enzyme inhibition assay.

RESULTS

The isolated endophytic bacteria were identified as Cronobacter sakazakii. LL displayed potent free radical scavenging effect against ABTS and DPPH radicals with an inhibitory concentration 50% (IC₅₀) value of 17.49 ± 0.06 and 11.3 ± 0.1 μg/mL respectively. LL exhibited α-amylase and α-glucosidase inhibition with an IC₅₀ value of 23.3 ± 0.08 and 23.4 ± 0.1 μg/mL respectively compared to the standard drug (acarbose). Both glucose loaded normoglycemic rats and STZ induced diabetic rats treated with LL (200 mg/kg) exhibited a considerable reduction in blood glucose levels p<0.01 after 8 h of treatment when compared to normal and diabetic control rats respectively.

CONCLUSIONS

Thus, the study shows that LL has a wellspring of natural source of antioxidants, and antidiabetic agents and phytoconstituents present in endophytes could be the rich source for bioactive compounds.

Inactivation Efficacy of 405 nm LED Against Cronobacter sakazakii Biofilm

The objectives of this study were to evaluate the inactivation efficacy of a 405-nm light-emitting diode (LED) against Cronobacter sakazakii biofilm formed on stainless steel and to determine the sensitivity change of illuminated biofilm to food industrial disinfectants. The results showed that LED illumination significantly reduced the population of viable biofilm cells, showing reduction of 2.0 log (25°C), 2.5 log (10°C), and 2.0 log (4°C) between the non-illuminated and LED-illuminated groups at 4 h. Images of confocal laser scanning microscopy and scanning electron microscopy revealed the architectural damage to the biofilm caused by LED illumination, which involved destruction of the stereoscopic conformation of the biofilm. Moreover, the loss of biofilm components (mainly polysaccharide and protein) was revealed by attenuated total reflection Fourier-transformed infrared spectroscopy, and the downregulation of genes involved in C. sakazakii biofilm formation was confirmed by real time quantitative PCR analysis, with greatest difference observed in fliD. In addition, the sensitivity of illuminated-biofilm cells to disinfectant treatment was found to significantly increased, showing the greatest sensitivity change with 1.5 log reduction between non-LED and LED treatment biofilms in the CHX-treated group. These results indicated that 405 nm LED illumination was effective at inactivating C. sakazakii biofilm adhering to stainless steel. Therefore, the present study suggests the potential of 405 nm LED technology in controlling C. sakazakii biofilms in food processing and storage, minimizing the risk of contamination.

Franconibacter sp., 1MS: A New Strain in Decolorization and Degradation of Azo Dyes Ponceau S Red and Methyl Orange

The aim of the present study is focused on the decolorization and degradation of azo dyes Ponceau S Red and Methyl Orange by a bacterial strain isolated from the gold mining district of San Martin de Loba, South of Bolivar (Colombia) sediment samples and identified as Franconibacter sp. 1MS (GenBank: MT568543) based on phenotypic and genotypic methods. A higher percentage of decolorization at 100 mg/L concentration, 37 °C, and pH 7 was recorded at 120 h of incubation period for both dyes. The UV-vis, Fourier transform infrared spectroscopy, and gas chromatography-mass spectrometry analysis of the original dyes and their degraded metabolites confirmed that the decolorization was due to degradation. The proposed metabolic pathways for biodegradation of both dyes have been elucidated, which showed the formation of five intermediate metabolites, namely, N,N-dimethylbenzyl-1,4-diamine, sulfonamide, 1,4-diaminobenzene, 2,5-diaminobenzenesulfonic acid, and 1-amino-2-naphthol, which are not only highly toxic but also be able to be converted through metabolic activation into mutagenic, carcinogenic, and/or teratogenic species. The phytotoxicity studies of the original dye and degraded metabolites were tested on Phaseolus vulgaris and divulged that the degraded metabolites have toxic effects. An effective phytostimulation was observed in Ponceau S Red, which could be attributed to its capacity for enrichment of the culture medium with essential nutrients, a favorable environment for the growth of the plant.

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.

Comparative Proteomic Analysis of Adhesion/Invasion Related Proteins in Cronobacter sakazakii Based on Data-Independent Acquisition Coupled With LC-MS/MS

Cronobacter sakazakii is foodborne pathogen that causes serious illnesses such as necrotizing enterocolitis, meningitis and septicemia in infants. However, the virulence determinants and mechanisms of pathogenicity of these species remain unclear. In this study, multilocus sequence typing (MLST) was performed on 34 C. sakazakii strains and two strains with the same sequence type (ST) but distinct adhesion/invasion capabilities were selected for identification of differentially expressed proteins using data-independent acquisition (DIA) proteomic analysis. A total of 2,203 proteins were identified and quantified. Among these proteins, 210 exhibited differential expression patterns with abundance ratios ≥3 or ≤0.33 and P values ≤0.05. Among these 210 proteins, 67 were expressed higher, and 143 were expressed lower in C. sakazakii SAKA80220 (strongly adhesive/invasive strain) compared with C. sakazakii SAKA80221 (weakly adhesive/invasive strain). Based on a detailed analysis of the differentially expressed proteins, the highly expressed genes involved in flagellar assembly, lipopolysaccharide synthesis, LuxS/AI-2, energy metabolic pathways and iron-sulfur cluster may be associated with the adhesion/invasion capability of C. sakazakii. To verify the accuracy of the proteomic results, real-time qPCR was used to analyze the expression patterns of some genes at the transcriptional level, and consistent results were observed. This study, for the first time, used DIA proteomic to investigate potential adhesion/invasion related factors as a useful reference for further studies on the pathogenic mechanism of C. sakazakii.

Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27^T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain RZME27^T clustered with the type strains of Neorhizobium galegae and Pseudorhizobium pelagicum from the family Rhizobiaceae. This family encompasses several genera establishing symbiosis with legumes, but the genes involved in nodulation and nitrogen fixation are absent in its genome. Nevertheless, genes related to plant colonization, such as those involved in motility, chemotaxis, quorum sensing, exopolysaccharide biosynthesis and hydrolytic enzymes production were found. The comparative pangenomic analyses showed that 78 protein clusters present in the strain RZME27^T were not found in the type strains of its closest relatives N. galegae and P. pelagicum. The calculated average nucleotide identity (ANI) values between the strain RZME27^T and the type strains of N. galegae and P. pelagicum were 75.61% and 75.1%, respectively, similar or lower than those found for other genera from family Rhizobiaceae. Several phenotypic differences were also found, highlighting the absence of the fatty acid C_19:0 cyclo ω8c and propionate assimilation. These results support the definition of a novel genus and species named Endobacterium cerealis gen. nov. sp. nov. whose type strain is RZME27^T.

Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses

The genus Izhakiella was established and designated as a member of the family Enterobacteriaceae in 2016. Although the taxonomical classification of most members in this family has been relatively resolved after two reclassifications in 2016 and 2017, the classification of the genus Izhakiella remains ambiguous. In this study, a polyphasic approach was used to provide evidence supporting the fact that the genus Izhakiella should no longer be considered a member of Enterobacteriaceae and proposes its reclassification into the family Erwiniaceae. The phylogenetic tree of type species in the families Enterobacteriaceae and Erwiniaceae based on the sequences of the 16S rRNA gene, rpoB housekeeping gene, and the whole-genome comprising the 92 core genes revealed that the genus Izhakiella forms a phylogenetic lineage within the family Erwiniaceae. The average nucleotide identity (ANI) value of the type species with genus Izhakiella was found to be higher for the family Erwiniaceae than that for the family Enterobacteriaceae. Notably, 12 conserved signature indels (CSIs) that are exclusively shared among the Erwiniaceae clade members were found in the type strains of the genus Izhakiella. Based on these analyses, this study suggests the reclassification of I. capsodis and I. australiensis into the family Erwiniaceae.

Siccibacter turicensis from Kangaroo Scats: Possible Implication in Cellulose Digestion

Microbiota in the kangaroo gut degrade cellulose, contributing to the kangaroo’s energy and survival. In this preliminary study, to discover more about the gut microbes that contribute to the survival of kangaroos, cellulose-degrading bacteria were isolated from kangaroo scats by selection on solidified media containing carboxymethyl cellulose as the main carbon source. One frequently occurring aerobic bacterium was Siccibacter turicensis, a microbe previously isolated in fruit powder and from a patient with angular cheilitis. The whole genome sequence of the kangaroo isolate was obtained using the Illumina MiSeq platform. Its sequence shared 97.98% identity of the S. turicensis Type strain, and the ability of the Type strain to degrade cellulose was confirmed. Analysis of the genomic data focused on the cellulose operon. In addition to genes from the operon, we suggest that a gene following the operon may have an important role in regulating cellulose metabolism by signal transduction. This is the first report of S. turicensis found within microbiota of the animal gut. Because of its frequent presence in the kangaroo gut, we suggest that S. turicensis plays a role in cellulose digestion for kangaroos.

Microbiological Quality of Powdered Infant Formula in Latin America

ABSTRACT

Cronobacter is a bacterial genus that includes seven species, and the species Cronobacter sakazakii is most related to meningitis and septicemia in infants associated with powdered infant formula (PIF). The objectives of this study were to evaluate the presence of C. sakazakii and to determine the microbiological quality of PIF for infant consumption. To do this, a total of 128 PIF samples were analyzed in four brands and countries (Chile, Mexico, Holland, and Brazil), considering three types of PIF: premature (PIF1), infant (PIF2), and follow-up (PIF3). Aerobic plate counts (APC) and Enterobacteriaceae (ENT) were assessed in accordance with Chilean official standards. The outer membrane protein A (ompA) gene was amplified to detect Cronobacter spp. and the fusA gene was amplified to identify C. sakazakii by using the PubMLST Web site and BLAST (NCBI). The antibiotic resistance profile was performed according to the Clinical and Laboratory Standards Institute standards. The pathogen was quantified by the most probable number (MPN). The results showed that APC median values for PIF1, PIF2, and PIF3 were 3.2, 4.9, and 4.8 log CFU g-1, respectively. The APC were higher in PIF2 (P < 0.01) from Holland (P < 0.01) in the commercial brand 4 (P < 0.01). The ENT median values in PIF1, PIF2, and PIF3 were 1.8, 1.5, and 1.7 log CFU g-1, respectively. Five strains of C. sakazakii and one strain of Cronobacter malonaticus were identified as having values between 0.023 and 2.3 MPN/g. All strains (100%) harbored the ompA, plasminogen activator (cpa), and hemolysin (hly) virulence genes. To conclude, C. sakazakii was found in four PIF samples from four Chilean products and one from Mexico, which is distributed throughout America. C. sakazakii strains exhibit virulence factors and resistance to ampicillin, thus posing a risk when PIFs are consumed by infants.

HIGHLIGHTS

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.

Georhizobium profundi gen. nov., sp. nov., a piezotolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench

A novel alphaproteobacterium, strain WS11T, was isolated from a deep-sea sediment sample collected from the New Britain Trench. The full-length 16S rRNA gene of strain WS11T had the highest sequence similarity of 97.6 % to Rhizobium subbaraonis JC85T, followed by Mycoplana ramosa DSM 7292T (96.9 %) and Rhizobium azooxidifex Po 20/26T (96.8 %). Phylogenetic analysis of concatenated 16S rRNA, atpD and recA gene sequences showed that strain WS11T was deeply separated from the species within the family Rhizobiaceae. Phylogenomic analysis based on the whole-genome protein sequences showed that strain WS11T formed an independent monophyletic branch in the family Rhizobiaceae, paralleled with the species in the families Brucellaceae and Phyllobacteriaceae within the order Rhizobiales. Cells were Gram-stain-negative, oxidase- and catalase-positive, and aerobic short rods (1.5-2.4×0.9-1.0 µm). Growth was observed at salinities ranging from 0 to 5% (optimum, 1 %), from pH 6.5 to 9 (optimum, pH 7) and at temperatures between 20 and 30 °C (optimum, 28 °C). Strain WS11T was piezotolerant, growing optimally at 0.1 MPa (range 0.1-70 MPa). The main fatty acid was summed feature 8 (C18 : 1 ω7c/C18  : 1 ω 6c). The sole respiratory quinone was ubiquinone-10 (Q-10). The predominant polar lipids were phosphatidylcholine, two unidentified aminophospholipids and an unidentified phospholipid. The genome size was about 4.36 Mbp and the G+C content was 62.3 mol%. The combined genotypic and phenotypic data show that strain WS11T represents a novel species of a novel genus in the family Rhizobiaceae, for which the name Georhizobium profundi gen. nov., sp. nov. is proposed (type strain WS11T=MCCC 1K03498T=KCTC 62439T).

Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant

The family Enterobacteriaceae is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family Enterobacteriaceae, isolated from a wound infection of an adult patient, in Sweden. Initial phenotypic and genotypic analyses identified the strain as a member of the family Enterobacteriaceae but could not assign it to any previously described species. The complete 16S rRNA gene sequence showed highest similarity (98.8%) to four species. Whole genome sequencing followed by in silico DNA-DNA similarity analysis and average nucleotide identity (ANI) analysis confirmed that strain CCUG 66741 represents a novel taxon. Sequence comparisons of six house-keeping genes (16S rRNA, atpD, dnaJ, gyrB, infB, rpoB) with those of the type strains of the type species of related genera within the family Enterobacteriaceae indicated that the strain embodies a novel species within the family. Phylogenomic analyses (ANI-based and core genome-based phylogeny) showed that strain CCUG 66741 forms a distinct clade, representing a novel species of a distinct, new genus within the family Enterobacteriaceae, for which the name Scandinavium goeteborgense gen. nov., sp. nov. is proposed, with CCUG 66741^T as the type strain (= CECT 9823^T = NCTC 14286^T). S. goeteborgense CCUG 66741^T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.

Prevalence and Genetic Diversity of Cronobacter Species Isolated From Four Infant Formula Production Factories in China

The aim of this study was to investigate the prevalence and genotypic characteristics of Cronobacter isolated from powdered infant formula (PIF) manufacturing facilities and to identify a potential source of contamination. A total of 42 Cronobacter isolates (5%) were detected in 835 environmental samples collected during the surveillance study. These isolates included C. sakazakii (n = 37), C. malonaticus (n = 3), and C. turicensis (n = 2). The isolates were divided into 14 sequence types (STs) by multi-locus sequence typing (MLST) and 21 pulsotypes (PTs) using pulsed-field gel electrophoresis (PFGE). The dominant C. sakazakii sequence types were ST3 (n = 12) and ST21 (n = 10), followed by ST136 (n = 6). The major PTs were PT22 (n = 12) and PT17 (n = 4) based on 100% similarity. Strains isolated from samples collected at the same production facility showed closer phylogenetic relation than those collected from distinct facilities. The result of extensive traceback sampling showed that PIF residues (PIF dust in production areas), fluid beds, drying areas, floors, and soil samples collected adjacent to the production facilities were the primary positive areas for Cronobacter. The present study outlines an effective approach to determine prevalence and genetic diversity of Cronobacter isolates associated with contamination of PIF.

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.

Characterization of the Desiccation Tolerance of Cronobacter sakazakii Strains

Strong desiccation tolerance is an outstanding feature of Cronobacter sakazakii and can enable the bacterium to survive in a dry food matrix (such as milk powder) for a long time. Therefore, contamination of food possessing low water activity with C. sakazakii can increase the risk of infection in human beings, particularly in neonates and infants. However, the mechanism underlying the desiccation tolerance property of C. sakazakii is largely unknown. In this study, the desiccation tolerance characteristics of 42 C. sakazakii strains were analyzed. Simultaneously, the sequence types and biofilm formation abilities of the strains were investigated, and their correlations with desiccation tolerance were analyzed. The results showed no significant correlation between desiccation tolerance and sequence type. However, there was a positive correlation between biofilm formation ability and desiccation tolerance. Raman spectroscopy was employed to investigate the biofilm formed by strains with distinct desiccation tolerance levels, and the results showed that the levels of polysaccharide, proteins and carotenoid might play important roles in the resistance to dry environments. In addition, 10 genes involved in osmoprotectant synthesis or transport were selected, and their differential expression in strains with diverse desiccation tolerance levels was compared to investigate whether these genes were responsible for cytoprotection in the dry environment. The results revealed a great difference in gene expression among strains with different desiccation tolerance levels, suggesting that these genes play a regulatory role in the resistance of C. sakazakii to dry environments. Our study provides a useful reference for follow-up studies investigating the mechanism of desiccation tolerance in C. sakazakii.

Lelliottia aquatilis sp. nov., isolated from drinking water

Five beige-pigmented, oxidase-negative bacterial isolates, 6331-17^T, 6332-17, 6333-17, 6334-17 and 9827-07, isolated either from a drinking water storage reservoir or drinking water in 2006 and 2017 in Germany, were examined in detail applying by a polyphasic taxonomic approach. Cells of the isolates were rod-shaped and Gram-stain-negative. Comparison of the 16S rRNA gene sequences of these five isolates showed highest sequence similarities to Lelliottia amnigena (99.98 %) and Lelliottia nimipressuralis (99.99 %). Multilocus sequence analyses based on concatenated partial rpoB, gyrB, infB and atpD sequences confirmed the clustering of these isolates with Lelliottia species, but also revealed a clear distinction to the closest related type strains. Analysis of the genome sequences of these isolates indicated >70 % in silico DNA-DNA hybridization and high average nucleotide identities between strains. Nevertheless, they showed only <70 and <95 % similarity to the type strains of these two Lelliottia species. The fatty acid profiles of these isolates were very similar and consisted of the major fatty acids C16:0, C17 : 0cyclo, C15 : 0iso 2-OH/C16 : 1ω7c and C18 : 1ω7c. In addition, physiological/biochemical tests revealed high phenotypic similarity to each other. These cumulative data indicate that these isolates represent a novel Lelliottia species, for which the name Lelliottia aquatilis sp. nov. is proposed, with strain 6331-17^T (=CCM 8846^T=CIP 111609^T=LMG 30560^T) as the type strain.

Cronobacter Species in Powdered Infant Formula and Their Detection Methods

Cronobacter species have been associated with disease outbreaks and sporadic infections, particularly in premature and immunocompromised infants. Cronobacter species can cause foodborne infections such as neonatal meningitis, septicaemia and necrotising enterocolitis. Accordingly, there is an urgent need to control and monitor the Cronobacter species in food, especially in powdered infant formula (PIF) and other baby foods. Therefore, in this review, the isolation and prevalence of Cronobacter species in infant food including PIF and the recent advance of detection methods are discussed for the better understanding on the current research status of Cronobacter species.

Draft Genome Sequence of the First Documented Clinical Siccibacter turicensis Isolate in Austria

The nonpathogenic species Siccibacter turicensis is closely related to members of the food-associated pathogenic genus Cronobacter and has been detected in fruit powders, formula, spices, and herbs. Here, we report on the first clinical isolate of S. turicensis, recovered from the labial angle of a patient with angular cheilitis.

Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp.  oharae, E.  hormaechei subsp.  steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E.  hormaechei subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp.  oharae, E.  hormaechei subsp.  steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E.  hormaechei subsp.  hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

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.