Phylogeny and prediction of genetic similarity of Cronobacter and related taxa by multilocus sequence analysis (MLSA)

Bacterial species diversity of traditionally ripened sheep legs from the Faroe Islands (skerpikjøt)

Skerpikjøt is a traditionally ripened sheep leg product from the Faroe Islands, constituting a relatively underexplored microbial ecosystem. The objective of this study is to achieve a deeper understanding of the microbial composition of this artisanal product. Nine ripened hind legs, obtained from three different producers, were assessed regarding their bacterial communities and contents of biogenic amines, including both surface and core samples. Biogenic amine concentrations were generally low, although one sample had a somewhat elevated concentration of cadaverine. Bacterial diversity was investigated by culture-dependent and culture-independent techniques. Gram-positive catalase-positive cocci (GCC) constituted the most abundant group. Within this group, Staphylococcus equorum was the most prevailing species, followed by Kocuria sp., Mammaliicoccus vitulinus, and Staphylococcus saprophyticus. Lactic acid bacteria prevailed in only one sample and were mainly represented by Latilactobacillus curvatus. Enterobacterial communities were characterised by the prevalence of Serratia proteamaculans. Despite the majority of GCC, Clostridium putrefaciens was the most abundant bacterial species in some core samples. Taken together, the culture-dependent and culture-independent identification methods gave complementary results.

The Detection of Foodborne Pathogenic Bacteria in Seafood Using a Multiplex Polymerase Chain Reaction System

Multiplex polymerase chain reaction (PCR) assays are mainly used to simultaneously detect or identify multiple pathogenic microorganisms. To achieve high specificity for detecting foodborne pathogenic bacteria, specific primers need to be designed for the target strains. In this study, we designed and achieved a multiplex PCR system for detecting eight foodborne pathogenic bacteria using specific genes: toxS for Vibrio parahaemolyticus, virR for Listeria monocytogenes, recN for Cronobacter sakazakii, ipaH for Shigella flexneri, CarA for Pseudomonas putida, rfbE for Escherichia coli, vvhA for Vibrio vulnificus, and gyrB for Vibrio alginolyticus. The sensitivity of the single system in this study was found to be 20, 1.5, 15, 15, 13, 14, 17, and 1.8 pg for V. parahaemolyticus, L. monocytogenes, E. coli O157:H7, C. sakazakii, S. flexneri, P. putida, V. vulnificus, and V. alginolyticus, respectively. The minimum detection limit of the multiplex system reaches pg/μL detection level; in addition, the multiplex system exhibited good specificity and stability. Finally, the assays maintained good specificity and sensitivity of 10⁴ CFU/mL for most of the samples and we used 176 samples of eight aquatic foods, which were artificially contaminated to simulate the detection of real samples. In conclusion, the multiplex PCR method is stable, specific, sensitive, and time-efficient. Moreover, the method is well suited for contamination detection in these eight aquatic foods and can rapidly detect pathogenic microorganisms.

Molecular characterization of Escherichia coli isolated from milk samples with regard to virulence factors and antibiotic resistance

BACKGROUND AND AIM

Raw milk is considered an essential source of nutrition during all stages of human life because it offers a valuable supply of protein and minerals. Importantly, milk is considered a good media for the growth and contamination of many pathogenic bacteria, especially food-borne pathogens such as Escherichia coli. Thus, the objective of this study was to characterize E. coli and detect its virulence factors and antibiotic resistance from raw milk samples.

MATERIALS AND METHODS

Raw milk samples (n=100) were collected from different localities in Qena, Egypt, and investigated for the presence of E. coli using different biochemical tests, IMViC tests, serotyping to detect somatic antigen type, and molecularly by polymerase chain reaction (PCR) tests. The presence of different virulence and antimicrobial genes (hly, eae, stx1, stx2, blaTEM, tetA(A), and tetB genes) in E. coli isolates was evaluated using PCR.

RESULTS

The results demonstrated that 10 out of 100 milk samples were contaminated with E. coli. Depending on serology, the isolates were classified as O114 (one isolate), O27 (two isolates), O111 (one isolate), O125 (two isolates), and untypeable (five isolates) E. coli. The sequencing of partially amplified 16S rRNA of the untypeable isolates resulted in one isolate, which was initially misidentified as untypeable E. coli but later proved as Enterobacter hormaechei. Moreover, antibacterial susceptibility analysis revealed that nearly all isolates were resistant to more than 3 families of antibiotics, particularly to b-lactams, clindamycin, and rifampin. PCR results demonstrated that all E. coli isolates showed an accurate amplicon for the blaTEM and tetA(A) genes, four isolates harbored eae gene, other four harbored tetB gene, and only one isolate exhibited a positive stx2 gene.

CONCLUSION

Our study explored vital methods for identifying E. coli as a harmful pathogen of raw milk using 16S rRNA sequencing, phylogenetic analysis, and detection of virulence factors and antibiotic-resistant genes.

Jinshanibacter, a new genus of Budviciaceae: identification of Jinshanibacter zhutongyuii sp. nov. and Jinshanibacter xujianqingii sp. nov. isolated from cloacal content of snow finch (Montifringilla taczanowskii)

Four novel strains isolated from the cloacal contents of snow finches (Montifringilla taczanowskii) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458^T had the highest similarities of 96.9 and 96.4 % with Limnobaculum parvum HYN0051^T and Pragia fontium DSM 5563^T, while strain CF-1111^T shared the highest similarities of 96.4 and 96.1 % with Pantoea rodasii LMG 26273^T and Pectobacterium punjabense SS95^T. Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458^T and CF-917) and group Ⅱ (CF-1111^T and CF-509), and clustered independently in the vicinity of the genera Limnobaculum and Pragia. Summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c, 23.9 and 17.2 %, respectively), C_16 : 0 (21.8 and 22.1 %, respectively) and C_14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c, 12.3 %) was also a major fatty acid for strain CF-458^T while cyclo-C_17 : 0 (13.1%) was for strain CF-1111^T. Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458^T and CF-1111^T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family Budviciaceae are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458^T=CGMCC 1.16483^T=GDMCC 1.1586^T=JCM 33489^T) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111^T=CGMCC 1.16786^T=GDMCC 1.1587^T=JCM 33490^T), respectively.

Genetic diversity of Pantoea stewartii subspecies stewartii causing jackfruit-bronzing disease in Malaysia

Jackfruit-bronzing is caused by bacteria Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii), showing symptoms of yellowish-orange to reddish discolouration and rusty specks on pulps and rags of jackfruit. Twenty-eight pure bacterial strains were collected from four different jackfruit outbreak collection areas in Peninsular Malaysia (Jenderam, Maran, Muadzam Shah and Ipoh). Positive P. stewartii subsp. stewartii verification obtained in the study was based on the phenotypic, hypersensitivity, pathogenicity and molecular tests. Multilocus sequence analysis (MLSA) was performed using four housekeeping genes (gyrB, rpoB, atpD and infB) on all 28 bacterial strains. Single gyrB, rpoB, atpD and infB phylogenetic trees analyses revealed the bootstrap value of 99-100% between our bacterial strains with P. stewartii subsp. stewartii reference strains and P. stewartii subsp. indologenes reference strains. On the other hand, phylogenetic tree of the concatenated sequences of the four housekeeping genes revealed that our 28 bacterial strains were more closely related to P. stewartii subsp. stewartii (99% similarities) compared to its close relative P. stewartii subsp. indologenes, although sequence similarity between these two subspecies were up to 100%. All the strains collected from the four collection areas clustered together, pointing to no variation among the bacterial strains. This study improves our understanding and provided new insight on the genetic diversity of P. stewartii subsp. stewartii associated with jackfruit-bronzing in Malaysia.

Mapping the dominant microbial species diversity at expiration date of raw meat and processed meats from equine origin, an underexplored meat ecosystem, in the Belgian retail

Although equine meats and their derived smoked or fermented products are popular in some regions of the world, they only form a minor fraction of the global meat consumption. The latter may explain why their associated bacterial communities have not received much attention. In the present study, 69 different samples of equine meats and meat products were investigated. The samples consisted of raw meat from horses (17 samples) and zebra (7), as well as non-fermented but smoked (24) and fermented (21) horse meat products. After purchase, all samples were stored at 4 °C and analysed at expiration date. Besides an estimation of the total microbial counts, specific attention was paid to the identification of lactic acid bacteria (LAB) and catalase-positive cocci, in particular the group of coagulase-negative staphylococci (CNS), involved, due to their technological relevance in view of the elaboration of meat products. Samples that were loosely wrapped in butcher paper instead of vacuum- or modified-atmosphere packages were also screened for pseudomonads and enterobacterial species. In total, 1567 bacterial isolates were collected, subjected to (GTG)₅-PCR fingerprinting of genomic DNA, and identified by multiple gene sequencing (based on the 16S rRNA, pheS, rpoA, rpoB, and/or tuf genes). Overall, the bacterial species diversity consisted mostly of LAB but was contingent on the type of product. Raw meat was dominated by Carnobacterium divergens, Lactobacillus sakei, Lactococcus piscium, and Leuconostoc gelidum, with zebra meat being particularly rich in lactococci. Smoked and fermented horse meat products contained mostly Lb. sakei and, to a lesser degree, Lactobacillus curvatus. In addition, several catalase-positive cocci (mostly Staphylococcus equorum), Anoxybacillus sp., Brevibacterium sp., Brochothrix thermosphacta, and the enterobacterial species Hafnia alvei were found.

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.

Classification and fatty acid composition analysis of Cronobacter spp. isolated from powdered infant formula in China

This study aimed to classify a collection of Enterobacter sakazakii (E. sakazakii) strains previously identified from powdered infant formula (PIF) to species level by recN gene sequencing and biochemical testing to determine the distribution of Cronobacter species in China and investigate the strain diversity by cellular fatty acid (CFA) analysis. Of 24 E. sakazakii isolates, 23 were identified as C. sakazakii and one was C. malonaticus. The 23 C. sakazakii isolates showed the same CFA profiles. The C. malonaticus isolate was discriminated from the C. sakazakii isolates by the significant difference in the amounts of C_12:0, C_14:0, and C_{17:0 cyclo} acids. These results showed that C. sakazakii and C. malonaticus were the common Cronobacter species distributed in PIF in China and that the isolates of the two species exhibited different CFA profiles. These findings are of value for epidemiological investigations and provide an alternative method for confirming various Cronobacter spp.

Cronobacter spp

The Cronobacter group of pathogens, associated with severe and potentially life-threatening diseases, until recently were classified as a single species, Enterobacter sakazakii. The group was reclassified in 2007 into the genus Cronobacter as a member of the Enterobacteriaceae. This chapter outlines the history behind the epidemiology, analyzes how our understanding of these bacteria has evolved, and highlights the clinical significance the Cronobacter spp. have for neonatal and elderly patient populations and treatment of the associated infections.

Multilocus sequence analysis (MLSA) in prokaryotic taxonomy

To obtain a higher resolution of the phylogenetic relationships of species within a genus or genera within a family, multilocus sequence analysis (MLSA) is currently a widely used method. In MLSA studies, partial sequences of genes coding for proteins with conserved functions ('housekeeping genes') are used to generate phylogenetic trees and subsequently deduce phylogenies. However, MLSA is not only suggested as a phylogenetic tool to support and clarify the resolution of bacterial species with a higher resolution, as in 16S rRNA gene-based studies, but has also been discussed as a replacement for DNA-DNA hybridization (DDH) in species delineation. Nevertheless, despite the fact that MLSA has become an accepted and widely used method in prokaryotic taxonomy, no common generally accepted recommendations have been devised to date for either the whole area of microbial taxonomy or for taxa-specific applications of individual MLSA schemes. The different ways MLSA is performed can vary greatly for the selection of genes, their number, and the calculation method used when comparing the sequences obtained. Here, we provide an overview of the historical development of MLSA and critically review its current application in prokaryotic taxonomy by highlighting the advantages and disadvantages of the method's numerous variations. This provides a perspective for its future use in forthcoming genome-based genotypic taxonomic analyses.

Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae

Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships.

Genotypic and phenotypic characteristics of Cronobacter species, with particular attention to the newly reclassified species Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis

In 2013, Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis, were reclassified as Cronobacter helveticus, Cronobacter pulveris and Cronobacter zurichensis, respectively. Previously these species had been used as negative controls for some Cronobacter detection assays. This study examined cultural, biochemical and molecular Cronobacter detection and identification assays, with emphasis on the new species. Additionally, 32 Cronobacter genomes were examined for the presence of PCR target genes using the BLAST function of the online Cronobacter PubMLST facility. The results of the cultural methods varied and no single medium was able to correctly detect all Cronobacter spp. Since the supporting databases have not been updated to include the Cronobacter genus, Enterobacter sakazakii was returned for four strains of the newly reclassified species with ID32E and none with API 20E. PCR probes targeting rpoB and ompA could not correctly identify the new Cronobacter spp., due to primer specificity or absent target genes. As neonates have been identified as a high-risk group for infection, international standards require the absence of all Cronobacter species in powdered infant formula. However, many conventional detection methods cannot correctly identify the newly recognized species. Conversely, DNA sequence-based methods can adapt to taxonomic revisions and will likely become more common.

Phylogeny and classification of Dickeya based on multilocus sequence analysis

Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.

Pseudocitrobacter gen. nov., a novel genus of the Enterobacteriaceae with two new species Pseudocitrobacter faecalis sp. nov., and Pseudocitrobacter anthropi sp. nov, isolated from fecal samples from hospitalized patients in Pakistan

Four isolates of Gram-negative facultatively anaerobic bacteria, three of them producing NDM-1 carbapenemase, were isolated from hospitalized patients and outpatients attending two military hospitals in Rawalpindi, Pakistan, and studied for their taxonomic position. Initially the strains were phenotypically identified as Citrobacter species. Comparative analysis of 16S rRNA gene sequences then showed that the four strains shared >97%, but in no case >98.3%, 16S rRNA gene sequence similarities to members of the genera Citrobacter, Kluyvera, Pantoea, Enterobacter and Raoultella, but always formed a separate cluster in respective phylogenetic trees. Based on multilocus sequence analysis (MLSA) including partial recN, rpoA, thdF and rpoB gene sequence and respective amino acid sequence analysis it turned out that the strains also here always formed separate clusters. Based on further comparative analyses including DNA-DNA hybridizations, genomic fingerprint analysis using rep- and RAPD-PCRs and physiological tests, it is proposed to classify these four strains into the novel genus Pseudocitrobacter gen. nov. with a new species Pseudocitrobacter faecalis sp. nov. with strain 25 CIT(T) (=CCM 8479(T)=LMG 27751(T)) and Pseudocitrobacter anthropi sp. nov. with strain C138(T) (=CCM 8478(T)=LMG 27750(T)), as the type strains, respectively.

Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter

The taxonomy of Enterobacter has a complicated history, with several species transferred to and from this genus. Classification of strains is difficult owing to its polyphyletic nature, based on 16S rRNA gene sequences. It has been previously acknowledged that Enterobacter contains species which should be transferred to other genera. In an attempt to resolve the taxonomy of Enterobacter, MLSA based on partial sequencing of protein-encoding genes (gyrB, rpoB, infB and atpD) was performed on the type strains and reference strains of Enterobacter, Cronobacter and Serratia species, as well as members of the closely related genera Citrobacter, Klebsiella, Kluyvera, Leclercia, Mangrovibacter, Raoultella and Yokenella. Phylogenetic analyses of the concatenated nucleotide sequences revealed that Enterobacter can be divided into five strongly supported MLSA groups, suggesting that the species should be reclassified into five different genera. Further support for this was provided by a concatenated amino acid tree, phenotypic characteristics and fatty acid profiles, enabling differentiation of the MLSA groups. Three novel genera are proposed: Lelliottia gen. nov., Pluralibacter gen. nov. and Kosakonia gen. nov. and the following new combinations: Lelliottia nimipressuralis comb. nov., Lelliottia amnigena comb. nov., Pluralibacter gergoviae comb. nov., Pluralibacter pyrinus comb. nov., Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov., Kosakonia arachidis comb. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov. Additionally, the novel epithet Cronobacter zurichensis nom. nov. is proposed for the reclassification of Enterobacter turicensis into the genus Cronobacter, as Cronobacter turicensis (Iversen et al., 2008) is already in use.

Comparison of methods for the microbiological identification and profiling of Cronobacter species from ingredients used in the preparation of infant formula

Cronobacter spp. (formerly Enterobacter sakazakii) can be isolated from a wide range of foods and environments, and its association with neonatal infections has drawn considerable attention from regulatory authorities. The principle route of neonatal infection has been identified as the ingestion of contaminated infant formula. A number of methods have been developed to identify Cronobacter spp., however these were before the most recent (2012) taxonomic revision of the genus into seven species. In this study, phenotyping, protein profiling and molecular methods were used to identify Cronobacter strains which had been recently isolated from ingredients used in the preparation of infant formula. Pulsed field gel electrophoresis revealed that different Cronobacter strains had been recovered from the same food products. All isolates were identified as Cronobacter sakazakii according to four genus specific PCR-probes and protein profiling using MALDI-TOF analysis. However, 16S rDNA sequence analyses and fusA allele sequencing gave more accurate identification: four strains were C. sakazakii, one strain was Cronobacter malonaticus and the remaining strain was Cronobacter universalis. Multilocus sequence typing showed the strains were different sequence types. These results demonstrate the presence of different Cronobacter species in food ingredients used in the preparation of infant formula, and also the need for molecular identification and profiling methods to be revised according to taxonomic revisions.

Use of novel species-specific PCR primers targeted to DNA gyrase subunit B (gyrB) gene for species identification of the Cronobacter sakazakii and Cronobacter dublinensis

Cronobacter sakazakii and its phylogenetically closest species are considered to be an opportunistic pathogens associated with food-borne disease in neonates and infants. Neither phenotypic nor genotypic (16S ribosomal DNA sequence analysis) techniques can provide sufficient resolutions for accurately and rapidly identification of these species. The objective of this study was to develop species-specific PCR based on the gyrB gene sequence for direct species identification of the C. sakazakii and Cronobacter dublinensis within the C. sakazakii group. Two pair of species-specific primers were designed and used to specifically identify C. sakazakii and C. dublinensis, but none of the other C. sakazakii group strains. Our data indicate that the novel species-specific primers could be used to rapidly and accurately identify the species of C. sakazakii and C. dublinensis from C. sakazakii group by the PCR based assays.

Cronobacter species (formerly known as Enterobacter sakazakii) in powdered infant formula: a review of our current understanding of the biology of this bacterium

Cronobacter species (formerly known as Enterobacter sakazakii) are opportunistic pathogens that can cause necrotizing enterocolitis, bacteraemia and meningitis, predominantly in neonates. Infection in these vulnerable infants has been linked to the consumption of contaminated powdered infant formula (PIF). Considerable research has been undertaken on this organism in the past number of years which has enhanced our understanding of this neonatal pathogen leading to improvements in its control within the PIF production environment. The taxonomy of the organism resulted in the recognition of a new genus, Cronobacter, which consists of seven species. This paper presents an up-to-date review of our current knowledge of Cronobacter species. Taxonomy, genome sequencing, current detection protocols and epidemiology are all discussed. In addition, consideration is given to the control of this organism in the manufacturing environment, as a first step towards reducing the occurrence of this pathogen in PIF.

Genetic analysis of the Cronobacter sakazakii O4 to O7 O-antigen gene clusters and development of a PCR assay for identification of all C. sakazakii O serotypes

The Gram-negative bacterium Cronobacter sakazakii is an emerging food-borne pathogen that causes severe invasive infections in neonates. Variation in the O-antigen lipopolysaccharide in the outer membrane provides the basis for Gram-negative bacteria serotyping. The O-antigen serotyping scheme for C. sakazakii, which includes seven serotypes (O1 to O7), has been recently established, and the O-antigen gene clusters and specific primers for three C. sakazakii serotypes (O1, O2, and O3) have been characterized. In this study, the C. sakazakii O4, O5, O6, and O7 O-antigen gene clusters were sequenced, and gene functions were predicted on the basis of homology. C. sakazakii O4 shared a similar O-antigen gene cluster with Escherichia coli O103. The general features and anomalies of all seven C. sakazakii O-antigen gene clusters were evaluated and the relationship between O-antigen structures and their gene clusters were investigated. Serotype-specific genes for O4 to O7 were identified, and a molecular serotyping method for all C. sakazakii O serotypes, a multiplex PCR assay, was developed by screening against 136 strains of C. sakazakii and closely related species. The sensitivity of PCR-based serotyping method was determined to be 0.01 ng of genomic DNA and 10(3) CFU of each strain/ml. This study completes the elucidation of C. sakazakii O-antigen genetics and provides a molecular method suitable for the identification of C. sakazakii O1 to O7 strains.

Matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry, 16S rRNA gene sequencing, and API 32E for identification of Cronobacter spp.: a comparative study

Twenty-two isolates of the family Enterobacteriaceae, with focus on Cronobacter isolated from infant formula and the environment of milk powder plants, were comparatively identified using API 32E (bioMérieux, Marcy l'Etoile, France), 16S rRNA gene sequencing (Accugenix, Newark, USA), and matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry (MALDI-TOF MS; Mabritec, Riehen, Switzerland and AnagnosTec, Potsdam, Germany). With API 32E, 22% of the isolates were assigned to species, 64% were assigned to a genus, and 14% could not be discriminated at any taxonomic level. Both 16S rRNA gene sequencing and MALDI-TOF MS assigned 100% of the isolates to species, but the identifications based on MALDI-TOF MS results were more discriminating and unequivocal. Our data indicate that MALDI-TOF MS provides the most rapid and unambiguous identification of Cronobacter and closely related Enterobacteriaceae isolates.

Characterization of the lipopolysaccharide O-antigen of Cronobacter turicensis HPB3287 as a polysaccharide containing a 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic acid (legionaminic acid) residue

Cronobacter turicensis, previously known as Enterobacter sakazakii, is a Gram-negative opportunistic food-borne pathogen that has been reported as a cause of life-threatening neonatal infections. From chemical and physical analyses involving composition analysis, methylation, two-dimensional high-resolution nuclear magnetic resonance, and mass spectrometry methods, the antigenic O-polysaccharide in the smooth-type lipopolysaccharide of C. turicensis (strain HPB 3287) was determined to be a high molecular mass polymer of a repeating pentasaccharide unit composed of D-galactose, D-glucose, 2-acetamido-2-deoxy-D-galactose, and 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-galacto-non-2-ulosonic acid (legionaminic acid), in a molar ratio 2:1:1:1, and having the structure: [see formula in text].

PCR-RFLP analysis of the rpoB gene to distinguish the five species of Cronobacter

Members of the genus Cronobacter are opportunistic pathogens associated with life-threatening infections in immuno-compromised individuals. Polyphasic analysis has facilitated the classification of the novel genus Cronobacter containing five species. However, since this recent reclassification there are not many identification methods optimised for differentiation between the five Cronobacter species. This differentiation between the species is of importance as there are indications that the species may be diverse regarding their virulence. The aim of this study was to develop a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) protocol to differentiate between the five Cronobacter species. The rpoB gene of 49 Enterobacteriaceae strains, including 33 Cronobacter strains was amplified using conventional PCR, followed by digestion of these PCR products with restriction endonucleases MboI, HinP1I and Csp6I. The PCR-RFLP analysis with single digestions of each of the restriction endonucleases did not distinguish between all five Cronobacter species. This study describes the successful differentiation of the five Cronobacter species based on the amplification of the rpoB gene followed by the combined digestion with restriction endonucleases Csp6I and HinP1I. This PCR-RFLP assay is an accurate identification method that ensures rapid differentiation between the five species of Cronobacter.

Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species

D.R. Zeigler determined that the sequence identity of bacterial genomes can be predicted accurately using the sequence identities of a corresponding set of genes that meet certain criteria [32]. This three-gene model for comparing bacterial genome pairs requires the determination of the sequence identities for recN, thdF, and rpoA. This involves the generation of approximately 4.2kb of genomic DNA sequence from each organism to be compared, and also normally requires that oligonucleotide primers be designed for amplification and sequencing based on the sequences of closely related organisms. However, we have developed an analogous mathematical model for predicting the sequence identity of whole genomes based on the sequence identity of the 542-567 base pair chaperonin-60 universal target (cpn60 UT). The cpn60 UT is accessible in nearly all bacterial genomes with a single set of universal primers, and its length is such that it can be completely sequenced in one pair of overlapping sequencing reads via di-deoxy sequencing. These mathematical models were applied to a set of Thermoanaerobacter isolates from a wood chip compost pile and it was shown that both the one-gene cpn60 UT-based model and the three-gene model based on recN, rpoA, and thdF predicted that these isolates could be classified as Thermoanaerobacter thermohydrosulfuricus. Furthermore, it was found that the genomic prediction model using cpn60 UT gave similar results to whole-genome sequence alignments over a broad range of taxa, suggesting that this method may have general utility for screening isolates and predicting their taxonomic affiliations.

Comprehensive approaches to molecular biomarker discovery for detection and identification of Cronobacter spp. (Enterobacter sakazakii) and Salmonella spp

Cronobacter spp. (formerly Enterobacter sakazakii) and Salmonella spp. are increasingly implicated internationally as important microbiological contaminants in low-moisture food products, including powdered infant formula. Estimates indicate that 40 to 80% of infants infected with Cronobacter sakazakii and/or Salmonella in the United States may not survive the illness. A systematic approach, combining literature-based data mining, comparative genome analysis, and the direct sequencing of PCR products of specific biomarker genes, was used to construct an initial collection of genes to be targeted. These targeted genes, particularly genes encoding virulence factors and genes responsible for unique phenotypes, have the potential to function as biomarker genes for the identification and differentiation of Cronobacter spp. and Salmonella from other food-borne pathogens in low-moisture food products. In this paper, a total of 58 unique Salmonella gene clusters and 126 unique potential Cronobacter biomarkers and putative virulence factors were identified. A chitinase gene, a well-studied virulence factor in fungi, plants, and bacteria, was used to confirm this approach. We found that the chitinase gene has very low sequence variability and/or polymorphism among Cronobacter, Citrobacter, and Salmonella, while differing significantly in other food-borne pathogens, either by sequence blasting or experimental testing, including PCR amplification and direct sequencing. This computational analysis for Cronobacter and Salmonella biomarker identification and the preliminary laboratory studies are only a starting point; thus, PCR and array-based biomarker verification studies of these and other food-borne pathogens are currently being conducted.

Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly

The mosaic composition of the genomes of dsDNA tailed bacteriophages (Caudovirales) is well known. Observations of this mosaicism have generally come from comparisons of small numbers of often rather distantly related phages, and little is known about the frequency or detailed nature of the processes that generate this kind of diversity. Here we review and examine the mosaicism within fifty-seven clusters of virion assembly genes from bacteriophage P22 and its "close" relatives. We compare these orthologous gene clusters, discuss their surprising diversity and document horizontal exchange of genetic information between subgroups of the P22-like phages as well as between these phages and other phage types. We also point out apparent restrictions in the locations of mosaic sequence boundaries in this gene cluster. The relatively large sample size and the fact that phage P22 virion structure and assembly are exceptionally well understood make the conclusions especially informative and convincing.

Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates

Here, we report the complete and annotated genome sequence of Cronobacter turicensis, an opportunistic food-borne pathogen, which is known as a rare but important cause of life-threatening neonatal infections. Among all proteins of C. turicensis, 223 have been annotated as virulence- and disease-related proteins.

Rapid genus- and species-specific identification of Cronobacter spp. by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Cronobacter spp. are Gram-negative opportunistic food-borne pathogens and are known as rare but important causes of life-threatening neonatal infections. Rapid and reliable identification of Cronobacter species and their differentiation from phenotypically similar, nonpathogenic Enterobacter turicensis, Enterobacter helveticus, and Enterobacter pulveris have become increasingly important. We evaluated here the application of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid genus and species identification of the six Cronobacter species recognized so far. To this end, we developed a reference MS database library that includes 54 Cronobacter target strains as well as 17 nontarget strains. The strains provided reproducible and unique mass spectra profiles covering a wide molecular mass range (2,000 to 30,000 Da). Genus- and species-specific biomarker protein mass patterns were determined. The defined biomarker mass patterns (Spectral Archive and Microbial Identification System [SARAMIS] SuperSpectrum) were validated using 36 strains from various Cronobacter species as well as eight nontarget strains. For all strains the mass spectrometry-based identification scheme yielded identical results as with a PCR-based identification system. All strains were correctly identified, and no nontarget strain was misidentified as Cronobacter. Our study demonstrates that MALDI-TOF MS is a reliable and powerful tool for the rapid identification of Cronobacter strains to the genus and species level.

Comparison of virulence of three strains of Cronobacter sakazakii in neonatal CD-1 mice

Cronobacter sakazakii (Enterobacter sakazakii) is an emerging pathogen that has been isolated from powdered infant formula and associated with outbreaks of infection in infants in neonatal intensive care units. In a previous study, we observed that neonatal CD-1 mice are susceptible to C. sakazakii infection and that the pathogen invades brain, liver, and cecum tissues. The study objective was to compare the virulence of three strains of C. sakazakii in neonatal CD-1 mice. The strains tested were MNW2 (a food isolate), SK81 (a clinical isolate), and 3290 (a clinical isolate). Timed-pregnant CD-1 mice were allowed to give birth on gestation day 19 or 20. Neonatal mice were sexed and culled to 10 per litter, each having five males and five females. Neonates were orally gavaged with C. sakazakii strains MNW2, SK81, or 3290 at doses ranging from 10(2.8) to 10(10.5) CFU on postnatal day 3.5. Pups surviving to postnatal day 10.5 were euthanized, and brain, liver, and cecum tissues were excised. C. sakazakii was isolated from all three tissues in mice treated with C. sakazakii, regardless of strain. C. sakazakii strain 3290 was significantly more invasive in brains (42.1% of mice) than were strains MNW2 (6.7%) and SK81 (15.9%). Mortality was observed for all strains of C. sakazakii tested, with SK81 being significantly more lethal (5.6%) than MNW2 (1.2%) or 3290 (0.6%). Our findings suggest that invasiveness does not necessarily correlate with mortality among different strains of C. sakazakii, and the clinical isolates are more virulent than the food isolate.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes

BACKGROUND

The Cronobacter genus (Enterobacter sakazakii) has come to prominence due to its association with infant infections, and the ingestion of contaminated reconstituted infant formula. C. sakazakii and C. malonaticus are closely related, and are defined according their biotype. Due to the ubiquitous nature of the organism, and the high severity of infection for the immunocompromised, a multilocus sequence typing (MLST) scheme has been developed for the fast and reliable identification and discrimination of C. sakazakii and C. malonaticus strains. It was applied to 60 strains of C. sakazakii and 16 strains of C. malonaticus, including the index strains used to define the biotypes. The strains were from clinical and non-clinical sources between 1951 and 2008 in USA, Canada, Europe, New Zealand and the Far East.

RESULTS

This scheme uses 7 loci; atpD, fusA, glnS, gltB, gyrB, infB, and pps. There were 12 sequence types (ST) identified in C. sakazakii, and 3 in C. malonaticus. A third (22/60) of C. sakazakii strains were in ST4, which had almost equal numbers of clinical and infant formula isolates from 1951 to 2008. ST8 may represent a particularly virulent grouping of C. sakazakii as 7/8 strains were clinical in origin which had been isolated between 1977 - 2006, from four countries. C. malonaticus divided into three STs. The previous Cronobacter biotyping scheme did not clearly correspond with STs nor with species.

CONCLUSION

In conclusion, MLST is a more robust means of identifying and discriminating between C. sakazakii and C. malonaticus than biotyping. The MLST database for these organisms is available online at http://pubmlst.org/cronobacter/.

Development and evaluation of rpoB based PCR systems to differentiate the six proposed species within the genus Cronobacter

Although there are various PCR based methods described in the literature to detect the genus Cronobacter, none of these methods is able to differentiate the six proposed species within this genus. A species differentiation is important for epidemiological studies. Moreover, the different species show differences in sensitivity to chemical agents and antibiotics. Here we report for the first time different rpoB based PCR systems which enable the identification to species level of strains previously confirmed to belong to the genus Cronobacter. Different primer pairs based on the rpoB sequences of the six Cronobacter species type strains were designed. Thereafter, 57 target and non-target strains, previously described in the Cronobacter taxonomy paper, were included for the specificity evaluation. C. turicensis, C. muytjensii, C. dublinensis and C. genomospecies 1 can be reliably identified by the proposed single primer pairs. Only target strains showed a correctly sized amplification product, whereas no amplification product was obtained for all non-target strains used in this study (100% specificity). However, as the rpoB gene sequences of C. sakazakii and C. malonaticus are closely related, a two step procedure is necessary. We therefore recommend a two-step procedure in which the primer pairs Cmalf/Cmalr are used in a follow up PCR on strains that are found to be positive in the amplification with the C. sakazakii specific primers Csakf/Csakr.