Invited review: Stress resistance of Cronobacter spp. affecting control of its growth during food production

Distribution characteristics and seasonal variation of microbial communities in powdered infant formula processing environment

The powdered infant formula (PIF) processing environment, as an industrial production site, provides a habitat conducive to microbial aggregation and colonization. However, the distribution and dynamics of microbial communities within this environment remain inadequately characterized. In this study, microbial community analysis was conducted using high-throughput sequencing on samples collected from the full production chain of 8 PIF factories. The sampling encompassed various types (raw milk, staff, air, equipment, wall and ground, and others) during two different seasons (summer and winter). The microbial diversity, composition, and dominant species varied across different groups. Potential source tracking analysis revealed close interactions between staff, air, and surface samples, indicating a potential risk of microbial transfer between staff and the processing environment. The β-nearest taxon index based null model showed that stochastic processes predominantly governed microbial community assembly across all groups. Positive interspecies interactions within the network structure, observed across different seasons and sample types, played a vital role in stabilizing and assembling microbial communities. Notably, the microbiota association networks of summer were more complex but demonstrated higher susceptibility to external disturbances. Conversely, the network structure of surface samples was more robust than that of other types of samples. These findings have improved our understanding of the microbial community distribution patterns in PIF processing environments, facilitating the prospective prediction and assessment of potential microbial sources and contamination risks in the processing chain, which in turn guides the implementation of refined control measures.

OmpR-mediated activation of the Type Vl secretion system drives enhanced acid tolerance in Cronobacter

Cronobacter (7 species) are prevalent foodborne pathogens with a remarkable capacity to adapt to acidic environments. This resilience enables them to persist in both food matrices and host organisms. Here we investigated the role of the 2-component system (TCS) response regulator OmpR in the acid tolerance of Cronobacter. Under acid stress, Cronobacter malonaticus (C. malonaticus) demonstrated significantly elevated expression of ompR and type VI secretion system (T6SS) genes, as well as a marked decrease in the survival of OmpR or T6SS-structure gene mutants, indicating the pivotal role of OmpR and T6SS in acid tolerance. Notably, OmpR markedly enhanced the T6SS expression by binding specifically to its promoter, and the activated T6SS expedited adaptation to acidic environments and facilitated biofilm formation, thereby aiding Cronobacter's survival under acidic conditions. Moreover, knocking out ompR in 6 additional Cronobacter species resulted in decreased T6SS expression and tolerance to acid stress than their wild-type strains, which further solidifies the widespread nature of the acid tolerance mechanism predicated on the activation of T6SS by OmpR in Cronobacter spp. A comprehensive understanding of the adaptation mechanisms employed by Cronobacter spp. in acidic conditions will provide a theoretical foundation for managing their contamination in acidic food matrices and preventing infection outbreaks in the infant gastrointestinal tract.

Effects of mscM Gene on Desiccation Resistance in Cronobacter sakazakii

Cronobacter sakazakii, an opportunistic foodborne pathogen, has a strong resistance to osmotic stress and desiccation stress, but the current studies cannot elucidate this resistance mechanism absolutely. A mechanosensitive channel MscM was suspected of involving to desiccation resistance mechanism of C. sakazakii. To investigate the specific molecular mechanism, the mscM mutant strain (ΔmscM) was constructed using the homologous recombination method, and the cpmscM complementary strain was obtained by gene complementation, followed by the analysis of the difference between the wild-type (WT), mutant, and complementary strains. Compared to the wild-type bacteria (WT), the inactivation rate of the ΔmscM strain decreased by 15.83% (p < 0.01) after desiccation stress. The absence of the mscM gene led to an increase in the membrane permeability of mutant strains. Through turbidity assay, it was found that the intracellular content of potassium ion (K+) of the ΔmscM strain increased by 2.2-fold (p < 0.05) compared to the WT strain, while other metal ion contents, including sodium ion (Na+), calcium ion (Ca2+), and magnesium ion (Mg2+), decreased by 48.45% (p < 0.001), 24.29% (p < 0.001), and 26.11% (p < 0.0001), respectively. These findings indicate that the MscM channel primarily regulates cell membrane permeability by controlling K+ efflux to maintain the homeostasis of intracellular osmotic pressure and affect the desiccation tolerance of bacteria. Additionally, the deletion of the mscM gene did not affect bacterial growth and motility but impaired surface hydrophobicity (reduced 20.52% compared to the WT strain, p < 0.001), adhesion/invasion capability (reduced 26.03% compared to the WT strain, p < 0.001), and biofilm formation ability (reduced 30.19% compared to the WT strain, p < 0.05) of the bacteria. This study provides a reference for the role of the mscM gene in the desiccation resistance and biofilm formation of C. sakazakii.

Inactivation of Lipopolysaccharide-Biosynthesizing Genes Altered Lipids Composition and Intensity in Cronobacter sakazakii

Gram-negative bacteria possess an asymmetric outer membrane, where the outer leaflet consists of LPSs and the inner leaflet comprises phospholipids. Cronobacter sakazakii, an opportunistic milk-borne pathogen that causes severe neonatal meningitis and bacteremia, displays diverse lipopolysaccharide (LPS) structures. As a barrier of the bacterial cell, LPSs likely influenced C. sakazakii resistance to environment stresses; however, there are no research reports on this aspect, hindering the development of novel bactericidal strategies overcoming the pathogen's resilience. In the present study, therefore, C. sakazakii BAA894 and two LPS mutants (ΔlpxM and ΔwaaC) were employed to investigate its influences. The ΔwaaC mutant showed lower resistance to acidic, alkali, oxidative, and osmotic stresses compared to the wild-type strain BAA894, and the ΔlpxM mutant exhibited lower desiccation resistance but higher osmotic resistance. To uncover potential reasons for these differences, comparative lipidomics was conducted. The results showed that compared to BAA894, both mutants showed drastic changes in lipid quantity, and many changed lipids were unsaturated. Additionally, eleven lipid classes exhibited significant variation in the relative content. In particular, the polyunsaturated TGs with double bonds at 5, 7, 12, and 14 displayed significant variation between the wild type and two mutants. Our study is the first to reveal that the changes in the LPS structure of C. sakazakii resulted in altered lipid profiles and intensities, which may be a critical biochemical basis for bacterial resistance to harsh stresses.

Cronobacter sakazakii lysozyme inhibitor LprI mediated by HmsP and c-di-GMP is essential for biofilm formation and virulence

Cronobacter sakazakii poses a significant threat, particularly to neonates and infants. Despite its strong pathogenicity, understanding of C. sakazakii biofilms and their role in infections remains limited. This study investigates the roles of HmsP and c-di-GMP in biofilm formation and identifies key genetic and proteomic elements involved. Gene knockout experiments reveal that HmsP and c-di-GMP are linked to biofilm formation in C. sakazakii. Comparative proteomic profiling identifies the lysozyme inhibitor protein LprI, which is downregulated in hmsP knockouts and upregulated in c-di-GMP knockouts, as a potential biofilm formation factor. Further investigation of the lprI knockout strain shows significantly reduced biofilm formation and decreased virulence in a rat infection model. Additionally, LprI is demonstrated to bind extracellular DNA, suggesting a role in anchoring C. sakazakii within the biofilm matrix. These findings enhance our understanding of the molecular mechanisms underlying biofilm formation and virulence in C. sakazakii, offering potential targets for therapeutic intervention and food production settings.IMPORTANCECronobacter sakazakii is a bacterium that poses a severe threat to neonates and infants. This research elucidates the role of the lysozyme inhibitor LprI, modulated by HmsP and c-di-GMP, and uncovers a key factor in biofilm formation and virulence. The findings offer crucial insights into the molecular interactions that enable C. sakazakii to form resilient biofilms and persist in hostile environments, such as those found in food production facilities. These insights not only enhance our understanding of C. sakazakii pathogenesis but also identify potential targets for novel therapeutic interventions to prevent or mitigate infections. This work is particularly relevant to public health and the food industry, where controlling C. sakazakii contamination in powdered infant formula is vital for safeguarding vulnerable populations.

Multiplex Determination of K-Antigen and Colanic Acid Capsule Variants of Cronobacter sakazakii

Cronobacter sakazakii is associated with the ingestion of contaminated reconstituted powdered infant formula (PIF), resulting in necrotizing enterocolitis, sepsis and meningitis in neonatal infants. Potential virulence determinants include the variable capsular polysaccharides; K-antigen and colanic acid (CA). Strains encoding for the capsule variant K2:CA2 have been strongly associated with neonatal meningitis cases. This study aimed to develop and apply a multiplex PCR assay to determine C. sakazakii K-antigen and colanic acid types. Twenty-six strains of C. sakazakii which had previously been isolated from food and environmental sources were used. These cover 18 multilocus sequence types and four serotypes. Based on our research findings, we have identified two K-antigen types present. Specifically, the K1-antigen was observed in sequence types ST1, ST8, ST20, ST23, ST64, ST198, ST263, ST264 and ST406, while the K2-antigen was present in ST4, ST9, ST12, ST13, ST136, ST233, ST245 and ST405. Additionally, we detected colanic acid (CA) type 1 in sequence types ST1, ST8, ST9, ST20, ST245 and ST405, and colanic acid (CA) type 2 in ST4, ST12, ST13, ST23, and ST64. We compared the predicted K-antigen and colanic acid types with the entire genome sequences of the strains. The comparison showed complete agreement between the PCR amplification results and the genomic analysis of the K-antigen and colanic acid-encoding regions. This assay is a useful tool for rapid identification of C. sakazakii, K-antigen and colanic acid types, in routine diagnoses and foodborne investigations. In addition, it will contribute to our knowledge of virulence factors associated with life-threatening neonatal meningitis.

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.

Microbiological hazards in infant and toddler food in China: A comprehensive study between 2004 and 2022

Infant and toddler food (ITF), including powdered infant and follow-up formula (PIFF) and complementary food (CF), provides the majority of early-life nutrients for young children. As infants and toddlers are more vulnerable to foodborne diseases, the safety concern of ITF is the ultimate priority. However, nationwide surveillance for the presence of hazards, specifically microbiological hazards, in the Chinese ITF is partially known, posing a significant knowledge gap for risk ranking. Most importantly, the related regional surveys were largely published in Chinese, making the data unavailable for global sharing. To bridge these gaps, we screened 5,306 publications and conducted a comprehensive meta-analysis for microbiological hazards using 129 qualified studies. The four most reported microbiological hazards in ITF were Bacillus cereus (13.4 %), Cronobacter (4.8 %), Staphylococcus aureus (1.3 %), and Salmonella (1.1 %). B. cereus is a risk factor in ITF, specifically in PIFF, cereals, and ready-to-eat food. The prevalence of B. cereus was high in Northern and Southern China, while the prevalence of Cronobacter was high in Central China. Cronobacter is a microbiological hazard, specifically in PIFF, with a prevalence of 3.0 %. Interestingly, the prevalence dynamics of Cronobacter and B. cereus in ITF were rising and stable, respectively, whereas the prevalence of S. aureus and Salmonella decreased over time. Together, our analysis will promote the global sharing of these critical findings and may guide future policy making.

Persistence of microbiological hazards in food and feed production and processing environments

Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.

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.

Co-culture of Cronobacter sakazakii and Staphylococcus aureus: Explore the influence of mixed biofilm formation and regulation of Cronobacter sakazakii biofilm formation genes

Bacterial biofilm is a protective matrix composed of metabolites secreted by bacteria that envelop bacteria. By forming a biofilm, bacteria can considerably improve their environmental tolerance. In food-related processing environment, different types of microorganisms are often present in biofilms. The main contaminating strain in the powdered infant formula (PIF) processing environment, Cronobacter sakazakii and Staphylococcus aureus continues to pollute the PIF processing environment after biofilm production. This study selected Cronobacter sakazakii with a weak biofilm-forming ability as one of the test organisms. The coexistence of Cronobacter sakazakii and Staphylococcus aureus on the surface of production equipment was simulated to analyze the interaction. Biofilm formation in the co-culture group was significantly higher than the others. In-depth study of the effect of Staphylococcus aureus on the biofilm formation genes of Cronobacter sakazakii. Results show two bacteria can coexist on the surface of a metal device, forming a more compact hybrid biofilm structure. Under co-culture conditions, S. aureus increased bcsA and fliD expression in Cronobacter sakazakii, whereas decreased bcsC expression. Signaling molecules produced by Staphylococcus aureus (Autoinducer 2) significantly promoted the biofilm formation of Cronobacter sakazakii at the concentration of 0-500 ng/mL (0.099-0.177) and up-regulated the expression of bcsA, filD and flhD genes.

A Method to Directly Identify Cronobacter sakazakii in Liquid Medium by MALDI-TOF MS

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been widely used as an emerging technology for the rapid identification of microorganisms. Cronobacter sakazakii (C. sakazakii) is a food-borne pathogen of particular importance to the powdered infant formula (PIF) processing environment due to its high lethality in infants. However, the traditional solid spotting detection method of pretreating samples for MALDI-TOF MS leads only to qualitative detection of C. sakazakii. We developed a new, low-cost, robust liquid spotting pretreatment method and used a response surface methodology to optimize its parameters. The applicability, accuracy, and quantitative potential were measured for different types of samples. The optimal parameters of this method were as follows: a volume of 70% formic acid of 25 μL, treatment with ultrasound at 350 W for 3 min, and a volume of acetonitrile added of 75 μL. These conditions led to the highest identification score for C. sakazakii (1926.42 ± 48.497). This method was found to detect bacteria accurately and reproducibly. When 70 strains of C. sakazakii isolates were analyzed with this method, the identification accuracy was 100%. The detection limit of C. sakazakii in environmental and PIF samples was 4.1 × 10¹ cfu/mL and 2.72 × 10³ cfu/mL, respectively.

Identification, Typing and Drug Resistance of Cronobacter spp. in Powdered Infant Formula and Processing Environment

Cronobacter spp. is a food-borne pathogenic microorganism that can cause serious diseases such as meningitis, sepsis, and necrotizing colitis in infants and young children. Powdered infant formula (PIF) is one of the main contamination routes, in which the processing environment is an important source of pollution. In this investigation, 35 Cronobacter strains isolated from PIF and its processing environment were identified and typed by 16S rRNA sequencing and multilocus sequence typing (MLST) technology. A total of 35 sequence types were obtained, and three new sequence types were isolated for the first time. The antibiotic resistance was analyzed, showing that all isolates were resistant to erythromycin but sensitive to ciprofloxacin. Multi-drug resistant strains accounted for 68.57% of the total, among which Cronobacter strains with the strongest drug resistance reached 13 multiple drug resistance. Combined with transcriptomics, 77 differentially expressed genes related to drug resistance were identified. The metabolic pathways were deeply excavated, and under the stimulation of antibiotic conditions, Cronobacter strains can activate the multidrug efflux system by regulating the expression of chemotaxis-related genes, thus, secreting more drug efflux proteins to enhance drug resistance. The study of drug resistance of Cronobacter and its mechanism has important public health significance for the rational selection of existing antibacterial drugs, the development of new antibacterial drugs to reduce the occurrence of bacterial resistance, and the control and treatment of infections caused by Cronobacter.