Diversity of Cronobacter genus isolated between 1970 and 2019 on the American continent and genotyped using multi-locus sequence typing.

This study aimed to evaluate the Cronobacter spp. strains isolated on the American continent and characterized using multi-locus sequence typing (MLST) available in the PubMLST database and current literature. From 465 Cronobacter spp. strains, the majority (n = 267, 57.4%) was from North America, mainly from USA (n = 234) and 198 (42.6%) were from South America, mainly from Brazil (n = 196). A total of 232 (49.9%) were isolated from foods, 102 (21.9%) from environmental, 87 (18.7%) from clinical, 27 (5.8%) from PIF, one from water (0.2%) and 16 (3.5%) from unknown sources. A total of five species were represented: Cronobacter sakazakii (374, 80.4%), Cronobacter malonaticus (41, 8.8%), Cronobacter dublinensis (29, 6.2%), Cronobacter turicensis (16, 3.5%) and Cronobacter muytjensii (5, 1.1%). The strains with complete MLST profile (n = 345) were assigned to 98 STs, a ratio of 3.5 strain by ST found and the calculated Simpson`s index was 0.93. The strains showed a high diversity and after eBURST analysis, 30 STs (n = 189) formed 12 single and/or double-locus variant clonal complexes (CC). A total of 38 STs (38.7%) were associated with clinical cases of infection, including well established C. sakazakii CC 1, 4, 8 and 83; C. malonaticus ST60, 307, 394 and 440; and C. sakazakii ST 12 and 494.

Applicability of Enterobacteriaceae and coliforms tests as indicators for Cronobacter in milk powder factory environments.

The emergence of Cronobacter as an important potential pathogen for newborn children and its occurrence in powdered infant formulae has generated a need to develop new management practices for this food group. This includes reduction of the prevalence of Cronobacter in manufacturing environments which can be a source of Cronobacter. This study was performed to assess the suitability of qualitative and quantitative Enterobacteriaceae and coliforms indicator tests for the presence and prevalence of Cronobacter. Environmental swabs (205) from five milk powder factories were examined. The qualitative indicator tests had good sensitivity but they lacked specificity for reliable routine use. Logistic regression analyses revealed a significant relationship between the quantitative indicator tests and Cronobacter prevalence, where the Enterobacteriaceae count was a slightly stronger predictor for Cronobacter than the coliforms count. The optimum test sensitivity (81%) and specificity (66%) was obtained when the indicator count thresholds were set at ≥1 cfu/cm2. However, since 11% of samples were Cronobacter positive when counts of Enterobacteriaceae and coliforms were less than 1 cfu/cm2, specific testing for Cronobacter is advised in addition to Enterobacteriaceae testing to minimise risk of transfer of Cronobacter from the factory environment into powdered infant formulae products.

Cytotoxicity profile of Cronobacter species isolated from food and clinical specimens in Brazil.

AIMS: The objective of this study was to evaluate the cytotoxic activity of Cronobacter strains isolated from foods (n = 50) and clinical samples (n = 6) in Brazil and genotype selected strains (n = 18) using multi-locus sequence typing (MLST) METHODS AND RESULTS: The cytotoxic activity of C. sakazakii (n = 29), C. dublinensis (n = 13), C. malonaticus (n = 6), C. turicensis (n = 6) and C. muytjensii (n = 2) was screened using Vero, RK13, Hep2c, NCTC clone 929 and BHK-21 cell lines. Selected Cronobacter strains were assigned to C. sakazakii ST 21, C. turicensis ST 252, C. sakazakii ST 647, and three newly assigned STs: C. turicensis STs 738-740. The maximum death caused by non-heat-treated filtrates was 20·4, 86·2, 47·0 and 84·0%, in Vero, RK13, Hep2c and NCTC clone 929 cells, respectively. These were caused by C. sakazakii strains C291 and C292 (ST 494) which had been isolated during neonatal Cronobacter meningitis infection, and C110 (ST 395) isolated from flaxseed flour. Thermal treatment (100°C/20 min) significantly reduced the cytotoxicity activity in NCTC clone 929 and Vero cells (P ≤ 2 × 10-6 ), but not in RK13 (P = 0·12) and Hep2c (P = 0·85), indicating the cytotoxin(s) were probably proteinaceous. Electron microscopy revealed that cytotoxic compounds from C. sakazakii induced several cell death characteristics, including loss of cell-cell contact, microvilli reduction and cellular lysis. Autophagic vacuoles and mitochondrial damage were the most common ultrastructural features observed. CONCLUSIONS: It was concluded that Cronobacter strains, especially C. sakazakii, could produce heat-labile cytotoxic compounds in cell filtrates. SIGNIFICANCE AND IMPACT OF THE STUDY: This study providing insights into the pathogenesis of the Cronobacter genus. Cytotoxins were identified in excreted filtrates of C. sakazakii strains isolated from food and clinical specimens. The presence of Cronobacter strains that can produce cytotoxins in foods can be a potential threat to human health and highlight the need for high levels of hygiene.

Cronobacter spp. isolated from aquatic products in China: Incidence, antibiotic resistance, molecular characteristic and CRISPR diversity.

Cronobacter species (Cronobacter spp.) are important foodborne pathogens that can infect and cause serious life-threatening diseases in infants and immunocompromised elderly. This study aimed to acquire data on Cronobacter spp. contamination of aquatic products in China from 2011 to 2016. In total, 800 aquatic products were tested, and the overall contamination rate for Cronobacter spp. was 3.9% (31/800). The average contamination level of the positive samples was 2.05 MPN/g. Four species and nine serotypes were identified among 33 isolates, of which the C. sakazakii serogroup O1 (n = 9) was the primary serotype. The majority of Cronobacter spp. strains harbored highest resistance against cephalothin (84.8%), followed by tetracycline (6.1%), trimethoprim/sulfameth-oxazole (3.0%) and chloramphenicol (3.0%). Two isolates were resistant to three antibiotics. In total, 26 sequence types and 33 CRISPR types (including 6 new STs and 26 new CTs) were identified, which indicates the extremely high diversity of Cronobacter spp. in aquatic products. Pathogenic C. sakazakii ST4, ST1, and C. malonaticus ST7 were also observed. Overall, this large-scale study revealed the relatively low prevalence and high genetic diversity of Cronobacter spp. in aquatic products in China, and the findings provide valuable information that can guide the establishment of effective measures for the control and precaution of Cronobacter spp. in aquatic products during production processes.

Prevalence, genetic analysis and CRISPR typing of Cronobacter spp. isolated from meat and meat products in China.

Cronobacter spp. are important foodborne pathogens that infections occur in all age groups, especially cause serious life-threatening diseases in infants. This study aimed to acquire data on Cronobacter spp. contamination of meat and meat products (n = 588) in China during 2011 to 2016, and investigated the use of CRISPR typing technology as an approach for characterizing the genetics of Cronobacter spp. The overall contamination rate for Cronobacter spp. was determined to be 9.18% (54/588). Of the positive samples, 90.74% (49/54) had <10 MPN/g, with duck samples had a relatively high contamination rate (15.69%, 8/51) and highest contamination level (28.90 MPN/g). Four species and nine serotypes were identified among 69 isolates, of which C. sakazakii was the major species (n = 50) and C. sakazakii serogroup O1 and O2 (n = 17) were the primary serotypes. The majority of Cronobacter spp. strains were found to be susceptible to most antibiotics except exhibited high resistance to cephalothin (76.81%, 53/69), and total two multi-drug resistant C. sakazakii strains were isolated from duck. The genetic diversity of Cronobacter spp. was remarkably high, as evidenced by the identification of 40 sequence types (STs) and 60 CRISPR types (CTs). C. sakazakii ST64 (n = 7) was the predominant genotype and was further divided into two sub-lineages based on CRISPR diversity, showing different antibiotic resistance profile. These results demonstrate that CRISPR typing results have a good correspondence with bacterial phenotypes, and it will be a tremendously useful approach for elucidating inter-subtyping during molecular epidemiological investigations while interpreting the divergent evolution of Cronobacter. The presence of Cronobacter spp. in meat and meat product is a potential threat to human public health.

Identification and Characterization of Cronobacter Strains Isolated from Environmental Samples.

As an emerging food-borne pathogen, Cronobacter species are ubiquitous in the food and environment. In order to know the characteristics of Cronobacter spp. from the environment, we isolated Cronobacter spp. from soil and water, and then studied the molecular typing and antibiotic resistance characteristics of these isolates. In 2016, 141 soil and water samples were collected from farms and Riverside Park in Beijing. Isolates were identified by real-time PCR, 16s rRNA sequencing, and whole-genome sequencing. Molecular subtyping of these isolates was characterized by pulsed-field gel electrophoresis, multilocus sequence typing (MLST), and antibiotic susceptibility tests. Cronobacter species were classified based on fusA sequencing. Twenty-two samples (15.60%) contained Cronobacter spp., and four species were detected, i.e., C. dubliniensis (n = 10), C. sakazakii (n = 6), C. turicensis (n = 4), and C. malonaticus (n = 2). For MLST, 12 types (ST519-ST525, ST533-ST537) were newly identified, indicating high diversity. Most isolates (68.18%) showed resistance to cefazolin. Siccibacter turicensis and Cronobacter both with blue-green colonies on selective media should be respectively identified. Apparently, major Cronobacter species in soil and water samples differed from those in food. Molecular subtyping showed that the environment could not be excluded as a source of Cronobacter infection. The resistance to cefazolin of most isolates indicated natural resistance.

Occurrence of total coliforms, Escherichia coli and Cronobacter species in commercially available 20 l bottled drinking water sold in Rio de Janeiro State, Brazil.

Cronobacter infections of infants are commonly regarded as due to the ingestion of contaminated feed. The aim of this study was to determine the occurrence of Cronobacter, total coliforms and Escherichia coli in different brands of natural mineral waters as sold in 20 l returnable bottles in Rio de Janeiro, Brazil. The quantification of total coliforms and E. coli was performed by Most Probable Number. The detection of Cronobacter was as according to the ISO 22964:2017 and Bacteriological Analytical Manual/FDA. Molecular characterization of Cronobacter isolates was performed by real-time PCR and by multi-locus sequence typing. The antibiotic susceptibility profile was determined and biofilm production was evaluated in polystyrene microplates. Total coliforms and E. coli were detected in 13 (39·4%) and 2 (6·1%) of the 33 lots analysed respectively, and were considered unsatisfactory for human consumption according to Brazilian law. One (3·0%) lot showed contamination by C. malonaticus ST440 (Cronobacter MLST Databases accession no. ID 2646). The strain was susceptible to all (n = 13) antibiotics tested and only formed a weak biofilm. Since there is a high consumption of natural mineral waters by elderly and immunosuppressed persons, epidemiological surveillance agencies should be aware of the risk that these waters may represent for these groups. SIGNIFICANCE AND IMPACT OF THE STUDY: Cronobacter malonaticus ST440 was isolated from 20 l bottled drinking natural mineral waters sold in markets in Rio de Janeiro State, Brazil, and can be a potential threat to human health, particularly for neonates. Thirteen lots (39·4%) were unsatisfactory for human consumption due to the presence of total coliforms and/or Escherichia coli.

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 ß-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.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 ß-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.

Species identification and molecular characterization of Cronobacter spp. isolated from food imported over nine years into Beijing, China.

Cronobacter spp. are associated with serious infections in neonates with the clinical presentations of necrotizing enterocolitis, bacteraemia and meningitis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify 203 Cronobacter isolates from imported food during 2006-2015 with an optimized in-house database. The isolates were predominantly C. sakazakii (88.18%), followed by C. malonaticus (8.37%), C. muytjensii (1.48%), C. turicensis (0.99%) and C. dublinensis (0.99%). The result was totally consistent with that of fusA allele sequencing. 12.32% (25/203) of isolates gave inconsistent spectra following separate protein extractions. Sixty C. sakazakii isolates and 24 isolates from the other four species were chosen for multi-locus sequence type analyses (MLST) and PCR-serotyping. Thirty-one sequence types were identified. The common sequence types were ST1 (19/60) and ST4 (13/60) for C. sakazakii and ST7 (12/17) for C. malonaticus. The primary serotypes were Csak O:1 (30/60), Csak O:2 (25/60) and Cmal O:2 (16/17) for C. sakazakii and C. malonaticus isolates, respectively. In conclusion, appropriate in-house database could make MALDI-TOF MS method identifying Cronobacter spp. isolates to the species level. But the spectra data were not sufficiently consistent for subtyping, unlike MLST. The Cronobacter spp. isolates have a high diversity including recognized pathovars.

Molecular and phenotypical characterization of Cronobacter species isolated with high occurrence from oats and linseeds.

The aim of this study was to determine the prevalence Cronobacter from 30 samples of oats and 30 of linseeds commercially available in Brazil. The detection of Cronobacter was as according to the ISO 22964:2017. The isolates were characterized according to their phenotypically using Vitek 2.0 and antibiotic susceptibility profile. Molecular characterization was accomplished by real-time PCR targeting dnaG gene, PCR targeting rpoB gene, multiplex-PCR targeting cgcA gene and fusA allele sequencing. A total of 34 samples (56.7%) contained Cronobacter; 19 (63.3%) of linseeds and 15 (50.0%) of oats. The isolates were identified as C. sakazakii (n = 18, 52.9%), C. dublinensis (n = 7, 20.6%), C. turicensis (n = 6, 17.7%) and C. malonaticus (n = 3, 8.8%). Thirty-four Cronobacter isolates were assigned to 11 different fusA alleles of which 3 were new (169, 170 and 171). The PCR targeting rpoB gene and cgcA gene failed to identify 19 isolates. Seven (20.6%) strains showed resistance or intermediate/resistance to tetracycline, and one (2.9%) strain had intermediate resistance to piperacilin-tazobactam. The presence of Cronobacter in oats and linseeds indicate that these foods can be a potential threat to human health, particularly when preparing food for elderly or immunosuppressed persons. The incorrect use of this foods for feeding of neonates (<6 months) by careers should also be avoided.

Potential reservoirs and routes of Cronobacter transmission during cereal growing, processing and consumption.

Cronobacter are opportunistic bacterial pathogens of both infants and adults. We investigated the incidence and distribution of Cronobacter in 1245 samples of cereal and related environments. 39.1% (101/258) rice-related and 46.9% (98/209) wheat-related samples tested positive for Cronobacter, and the positive rate differed notably according to processing method. Cronobacter was found in rice and wheat plants at the tillering, filling and mature stages. Soil, water and swab samples from nearby milling plants were assayed, and results revealed that 6.3% (7/122) of water from paddy fields, 49.1% (28/57) and 62.1% (41/67) of swab samples from rice and wheat flour milling plants were Cronobacter positive. Pulsed-field gel electrophoresis (PFGE) subtyping indicated that some strains had a common profile, which suggested their persistence in the environment, potential transmission routes and cross-contamination in processing. Finally, we surveyed 18 families to evaluate potential risks. None of the families who primarily ate rice cooked with water tested positive for Cronobacter, though of 66.7% families (6/9) whose food staples were produced from wheat flour tested positive. Taken together, our results are important for understanding Cronobacter transmission and will aid in the development of additional control measures to reduce the risk of infection by these opportunistic pathogenic bacteria.

Cronobacter spp. in Common Breast Milk Substitutes, Bogotá, Colombia.

In Bogotá, Colombia, a large number of babies are fed with breast milk substitutes made from corn and plantain starch. We found 34.3% of tested samples to be contaminated with Cronobacter spp.; C. sakazakii was the most recovered species. Our findings underscore the risk for contamination of breast milk substitutes.

Use of biochemical miniaturized galleries, rRNA based lateral flow assay and Real Time PCR for Cronobacter spp. confirmation.

Identification of Cronobacter represent a major challenge for laboratories testing powdered infant formula (PIF). In the present study, two biochemical galleries and three molecular methods have been applied to confirm 276 Cronobacter spp. and non-Cronobacter isolates from different sources. Using the latest database of API 20 E and ID 32 E biochemical miniaturized kits, 53% and 78% of the isolates were identified respectively. From the available results, total accuracy for Cronobacter detection was in 97% (API 20 E) and 99% (ID 32 E). The three molecular methods were based on rRNA based lateral flow, Real Time PCR combined with either a hybridization or hydrolysis probe. For all three methods total accuracy was more than 99%. A pilot trial using Next Generation Sequencing (NGS) correctly identified 58 out of 66 isolates (88%) in DNA mixtures. The results indicate that the commercially available approaches such as ID 32 E, rRNA based lateral flow and Real Time PCR are all suitable for Cronobacter identification at the genus level. The NGS method may become a suitable alternative in the future, provided that the sequence database is improved.

Rapid detection of Cronobacter spp. in powdered infant formula by thermophilic helicase-dependent isothermal amplification combined with silica-coated magnetic particles separation.

Cronobacter spp. (previously Enterobacter sakazakii), an opportunistic food-borne pathogen, involved in fatal infections in neonates and infants. Contaminated powdered infant formula (PIF) was considered to be the uppermost infective resource. In the present study, a thermophilic helicase-dependent isothermal amplification (tHDA) based method combined with silica-coated magnetic nanoparticles (Si-MNPs) as a DNA separator for rapid and sensitive detection of Cronobacter has been developed. The whole detection process can be completed in <3 h, with a detection limit of 100 and 101 CFU/ml Cronobacter in pure culture and artificially contaminated PIF, respectively, with a great sensitivity (94%) and specificity (100%). Hence, this protocol might be useful for screening and monitoring the contamination of Cronobacter spp. in food industry, and helpful for avoiding the economic loss by retard of feedback of the contamination of pathogens in dairy products.

Contamination of Cronobacter spp. in Chinese Retail Spices.

Crononbacter spp. is an opportunistic foodborne pathogen that causes infections in neonates, infants, and immunocompromised adults. Although the contamination of spices with Cronobacter has been previously reported in some countries, there have been no studies on Cronobacter contamination in China. Therefore, this study aimed to investigate the prevalence of Cronobacter spp. in Chinese retail spices. Fifty-six packaged Chinese spices were collected from different markets, and 32 of these were found to be contaminated with Cronobacter. Five species were identified from the 54 isolates of the 32 positive samples: Cronobacter sakazakii (n = 35), Cronobacter muytjensii (n = 8), Cronobacter malonaticus (n = 6), Cronobacter turicensis (n = 3), and Cronobacter dublinensis (n = 2). Pulsed-field gel electrophoresis demonstrated high genetic diversity, as 53 PFGE profiles were revealed for the 54 isolates. Multilocus sequence typing analysis revealed 46 sequence types, and of these, 26 were newly identified. Most of the isolates were sensitive to antibiotics (n = 15), with the exception of cefazolin. This study revealed that the contamination of Chinese retail spices by Cronobacter spp. poses a potential risk to the consumer.

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.

Phenotypic characterization of pathogenic Cronobacter spp. strains.

BACKGROUND: Cronobacter species are Gram-negative opportunistic foodborne pathogens that may cause enterocolitis, bacteremia and meningitis in neonates and premature neonates. Lipopolysaccharide (LPS) serves as the major component of the outer membrane of cell, is a potential virulence factor for Cronobacter. METHODS: Given the potential importance of this molecule in infection and virulence, SDS-PAGE of LPS, MS and TLC characterization of phospholipids and phenotypic characterization of Cronobacter spp. strains were carried out. RESULT: The phospholipids from Cronobacter yielded four major peaks at m/z 719.9, 733.9, 747.9 and 773.9 in the spectrum. All Cronobacter showed O-antigen bands except C. muytjensii ATCC 51329. When Cronobacter defect O-antigen, the outer membrane permeability and cell surface hydrophobicities are increased. All Cronobacter are able to grow under pH 5.0 condition and able to grow under 6% NaCl concentration. C. dublinensis DSM 18705 has a higher infection rate to Caco-2 cells than other Cronobacter. CONCLUSION: Invasion of pathogens into a host cell is critical component to an infectious case. And C. dublinensis DSM 18705 has a higher infection rate to Caco-2 cells than other Cronobacter.

Confirmation and Identification of Salmonella spp., Cronobacter spp., and Other Gram-Negative Organisms by the Bruker MALDI Biotyper Method: Collaborative Study, First Action 2017.09.

The Bruker MALDI Biotyper® method utilizes matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS for the rapid and accurate identification and confirmation of Gram-negative bacteria from select media types. The alternative method was evaluated using nonselective and selective agars to identify Cronobacter spp., Salmonella spp., and select Gram-negative bacteria. Results obtained by the Bruker MALDI Biotyper were compared to the traditional biochemical methods as prescribed in the appropriate reference methods. Two collaborative studies were organized, one in the United States focusing on Cronobacter spp. and other Gram-negative bacteria, and one in Europe focusing on Salmonella spp. and other Gram-negative bacteria. Fourteen collaborators from seven laboratories located within the United States participated in the first collaborative study for Cronobacter spp. Fifteen collaborators from 15 service laboratories located within Europe participated in the second collaborative study for Salmonella spp. For each target organism (either Salmonella spp. or Cronobacter spp.), a total of 24 blind-coded isolates were evaluated. In each set of 24 organisms, there were 16 inclusivity organisms (Cronobacter spp. or Salmonella spp.) and 8 exclusivity organisms (closely related non-Cronobacter spp. and non-Salmonella spp. Gram-negative organisms). After testing was completed, the total percentage of correct identifications from each agar type for each strain was determined at a percentage of 100.0% to the genus level for the Cronobacter study and a percentage of 100.0% to the genus level for the Salmonella study. For both non-Cronobacter and non-Salmonella organisms, a percentage of 100.0% was correctly identified. The results indicated that the alternative method produced equivalent results when compared to the confirmatory procedures specified by each reference method.

Development of an isothermal amplification-based assay for the rapid detection of Cronobacter spp.

Cronobacter spp. is an opportunistic pathogen that is associated with rare but life-threatening neonatal infections resulting from the consumption of contaminated powdered infant formula milk (PIF). In the present study, we developed recombinase polymerase amplification (RPA) and real-time RPA for the detection of Cronobacter spp. in PIF for the first time by targeting the ompA gene. The specificity and sensitivity of the RPA and real-time RPA were validated and the practical applicability of these methods for the detection of Cronobacter spp. in artificially contaminated PIF samples was proved by comparing their reaction time, sensitivity, and efficacy with those of real-time PCR and the Chinese traditional method. The RPA and real-time RPA assays reduced the analysis time to less than 15 min and the results were as reliable as those of real-time PCR. Taken together, the RPA and real-time RPA assays served as fast, reliable, and sensitive techniques for the detection of Cronobacter spp.

Reconstituting the History of Cronobacter Evolution Driven by Differentiated CRISPR Activity.

Cronobacter strains harboring the CRISPR-Cas system are important foodborne pathogens causing serious neonatal infections. However, the specific role of the CRISPR-Cas system in bacterial evolution remains relatively unexplored. In this study, we investigated the impact of the CRISPR-Cas system on Cronobacter evolution and obtained 137 new whole-genome Cronobacter sequences by next-generation sequencing technology. Among the strains examined (n = 240), 90.6% (193/213) of prevalent species Cronobacter sakazakii, Cronobactermalonaticus, and Cronobacterdublinensis strains had intact CRISPR-Cas systems. Two rare species, Cronobactercondimenti (n = 2) and Cronobacteruniversalis (n = 6), lacked and preserved the CRISPR-Cas system at a low frequency (1/6), respectively. These results suggest that the presence of one CRISPR-Cas system is important for a Cronobacter species to maintain genome homeostasis for survival. The Cronobacter ancestral strain is likely to have harbored both subtype I-E and I-F CRISPR-Cas systems; during the long evolutionary process, subtype I-E was retained while subtype I-F selectively degenerated in Cronobacter species and was even lost by the major Cronobacter pathovars. Moreover, significantly higher CRISPR activity was observed in the plant-associated species Cdublinensis than in the virulence-related species C. sakazakii and Cmalonaticus Similar spacers of CRISPR arrays were rarely found among species, suggesting intensive change through adaptive acquisition and loss. Differentiated CRISPR activity appears to be the product of environmental selective pressure and might contribute to the bidirectional divergence and speciation of CronobacterIMPORTANCE This study reports the evolutionary history of Cronobacter under the selective pressure of the CRISPR-Cas system. One CRISPR-Cas system in Cronobacter is important for maintaining genome homeostasis, whereas two types of systems may be redundant and not conducive to acquiring beneficial DNA for environmental adaptation and pathogenicity. Differentiated CRISPR activity has contributed to the bidirectional divergence and genetic diversity of Cronobacter This perspective makes a significant contribution to the literature by providing new insights into CRISPR-Cas systems in general, while further expanding the roles of CRISPR beyond conferring adaptive immunity and demonstrating a link to adaptation and species divergence in a genus. Moreover, our study provides new insights into the balance between genome homeostasis and the uptake of beneficial DNA related to CRISPR-based activity in the evolution of Cronobacter.