Insights into the Emergent Bacterial Pathogen Cronobacter spp., Generated by Multilocus Sequence Typing and Analysis

Insights into virulence factors determining the pathogenicity of Cronobacter sakazakii

Cronobacter sakazakii is an opportunistic pathogen associated with outbreaks of life-threatening necrotizing enterocolitis, meningitis and sepsis in neonates and infants. The pathogen possesses an array of virulence factors which aid in tissue adhesion, invasion and host cell injury. Although the identification and validation of C. sakazakii virulence factors has been hindered by availability of suitable neonatal animal model, various studies has reported outer membrane protein A (ompA) as a potential virulence marker. Various other plasmid associated genes such as filamentous hemagglutinin (fhaBC), Cronobacter plasminogen activator (cpa) and genes responsible for iron acquisition (eitCBAD and iucABD/iutA) have been reported in different strains of C. sakazakii. Besides these proposed virulence factors, several biophysical growth factors such as formation of biofilms and resistance to various environmental stresses also contributes to the pathogenic potential of this pathogen. This review provides an update on virulence determinants associated with the pathogenesis of C. sakazakii. The potential reservoirs of the pathogen, mode of transmission and epidemiology are also discussed.

Multilocus sequence typing analysis of Cronobacter spp. isolated from China

Multilocus sequence typing (MLST) has proven to be an effective approach for the subtyping isolates of the Cronobacter genus and to exhibit a high level of discrimination between isolates. In this study, 151 Cronobacter strains were isolated from different sources and provinces across China from 2010 to 2012 and analyzed by MLST. Their sequence type profiles were compared with strains from other countries which were widely geographically and temporally distributed. Out of 151 strains in this study, the majority of strains were Cronobacter sakazakii (70.9 %), C. malonaticus (15.9 %), C. dublinensis (10.6 %), C. turicensis (2.0 %), and C. muytjensii (0.7 %). The strains were divided into 85 sequence types (STs), among which only 17 had previously been reported in other countries. The 85 identified STs for the Cronobacter genus were grouped into 14 clonal complexes and 47 singletons according to eBURST algorithm. The Cronobacter isolated from China showed a high diversity when they were subtyped using the MLST method. When compared to the Cronobacter PubMLST database, some sequence types of strains cultured from food and/or water in this study were also the same with strains isolated from patients in other countries as reported previously. This result showed the potential hazard of strains contaminating water and weaning food from China.

Prevalence, molecular characterization, and antibiotic susceptibility of Cronobacter spp. in Chinese ready-to-eat foods

Cronobacter spp. are foodborne pathogens that cause rare but life-threatening diseases in neonates and infants; they can also cause disease in adults. Cronobacter spp. contamination of ready-to-eat (RTE) foods has been reported previously. However, to date, the prevalence and contamination levels of these bacteria in RTE foods in China have not yet been determined. Therefore, the aim of this study was to investigate the prevalence of Cronobacter spp. in RTE foods marketed in China. Two-hundred and eighty RTE food samples were collected from different producers and retailers and analyzed using quantitative methods. The isolates obtained were identified to the species level based on fusA sequences, and were subtyped using a PCR-based serotyping technique. Selected isolates were further characterized by multilocus sequence typing (MLST) and antimicrobial sensitivity determination. Of 280 samples tested, 52 (18.6%) were positive for Cronobacter spp. The contamination levels were less than 110 MPN/g for 78.8% (41/52) of the samples. The results of the O-antigen serotyping for 111 isolates showed that Cronobacter sakazakii serogroup O2 (28 isolates) was the most prevalent serotype. MLST analyses produced 41 sequence types (STs), including 20 novel STs. ST8 was the most prevalent ST (9 isolates) followed by ST4 (5 isolates). Antimicrobial sensitivity testing showed that 84.5% and 46.5% of the isolates were resistant to penicillin G and cephalothin, respectively; in contrast, all of the tested isolates were susceptible to cefotaxime, ciprofloxacin, tetracycline, and nalidixic acid. To the best of our knowledge, this is the first report on Cronobacter spp. prevalence in RTE foods in China, and the findings of our study nonetheless suggested that Cronobacter spp. contamination of Chinese RTE foods poses a potential risk for the consumer. Thus, the study highlights the significance of developing more effective control strategies during the manufacturing process.

Description of Siccibacter colletis sp. nov., a novel species isolated from plant material, and emended description of Siccibacter turicensis

A re-evaluation of the taxonomic position of two strains, 1383(T) and 2249, isolated from poppy seeds and tea leaves, which had been identified as Siccibacter turicensis (formerly Cronobacter zurichensis ), was carried out. The analysis included phenotypic characterization, 16S rRNA gene sequencing, multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, fusA, glnS, gyrB and infB; 2034 bp) and ribosomal MLSA (53 loci; 22 511 bp). 16S rRNA gene sequence analysis and MLSA showed that the strains formed an independent phylogenetic lineage, with Siccibacter turicensis LMG 23730(T) as the closest neighbour. Average nucleotide identity analysis and phenotypic analysis confirmed that these strains represent a novel species, for which the name Siccibacter colletis sp. nov. is proposed. The type strain is 1383(T) ( = NCTC 14934(T) = CECT 8567(T) = LMG 28204(T)). An emended description of Siccibacter turicensis is also provided.

Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri

Four Xanthomonas species are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype of X. gardneri, possible regional differentiation in X. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events between X. euvesicatoria and X. perforans. Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.

Cronobacter sakazakii: stress survival and virulence potential in an opportunistic foodborne pathogen

A characteristic feature of the opportunistic foodborne pathogen Cronobacter sakazakii is its ability to survive in extremely arid environments, such as powdered infant formula, making it a dangerous opportunistic pathogen of individuals of all age groups, especially infants and neonates. Herein, we provide a brief overview of the pathogen; clinical manifestations, environmental reservoirs and our current understanding of stress response mechanisms and virulence factors which allow it to cause disease.

Cronobacter Species Contamination of Powdered Infant Formula and the Implications for Neonatal Health

Cronobacter is a class of Enterobacteriaceae that cause infections in neonates, especially those born prematurely. Over 90% of these infections have been linked epidemiologically to powdered infant formula (PIF). Contamination of PIF can occur at manufacture, reconstitution, or storage of reconstituted product. Intrinsic properties that enable Cronobacter to cause disease include resistance to heat, ultraviolet radiation, oxygen radicals, stomach acids, and pasteurization; an ability to utilize sialic acid (a nutrition additive to PIF that facilitates the organism's growth and survival), and an exceptional affinity for biofilms in enteral feeding tubes. As part of ongoing endeavors to reduce the incidence of neonatal PIF-associated Cronobacter infections, the World Health Organization and the US Food and Drug Administration have established guidelines for PIF production, preparation for infant feeding, and storage of reconstituted product.

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis

BACKGROUND

Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the organism. This paper presents the application of Next Generation Sequencing (NGS) to Cronobacter which has led to the establishment of the Cronobacter PubMLST genome and sequence definition database (http://pubmlst.org/cronobacter/) containing over 1000 isolates with metadata along with the recognition of specific clonal lineages linked to neonatal meningitis and adult infections

RESULTS

Whole genome sequencing and multilocus sequence typing (MLST) has supports the formal recognition of the genus Cronobacter composed of seven species to replace the former single species Enterobacter sakazakii. Applying the 7-loci MLST scheme to 1007 strains revealed 298 definable sequence types, yet only C. sakazakii clonal complex 4 (CC4) was principally associated with neonatal meningitis. This clonal lineage has been confirmed using ribosomal-MLST (51-loci) and whole genome-MLST (1865 loci) to analyse 107 whole genomes via the Cronobacter PubMLST database. This database has enabled the retrospective analysis of historic cases and outbreaks following re-identification of those strains.

CONCLUSIONS

The Cronobacter PubMLST database offers a central, open access, reliable sequence-based repository for researchers. It has the capacity to create new analysis schemes 'on the fly', and to integrate metadata (source, geographic distribution, clinical presentation). It is also expandable and adaptable to changes in taxonomy, and able to support the development of reliable detection methods of use to industry and regulatory authorities. Therefore it meets the WHO (2004) request for the establishment of a typing scheme for this emergent bacterial pathogen. Whole genome sequencing has additionally shown a range of potential virulence and environmental fitness traits which may account for the association of C. sakazakii CC4 pathogenicity, and propensity for neonatal CNS.

Draft Genome Sequence of Cronobacter sakazakii Clonal Complex 45 Strain HPB5174, Isolated from a Powdered Infant Formula Facility in Ireland

Cronobacter sakazakii is a food-borne pathogenic bacterium that may cause severe illness in neonates and the elderly. We present the genome sequence of a rare strain (ST40, CC45), commonly found in multiple food processing facilities and in powdered infant formula and only indicted in a single clinical case.

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.

Analysis of the role of the Cronobacter sakazakii ProP homologues in osmotolerance

Bacteria respond to elevated osmolality by the accumulation of a range of low molecular weight molecules, known as compatible solutes (owing to their compatibility with the cells' normal physiology at high internal concentrations). The neonatal pathogen Cronobacter sakazakii is uniquely osmotolerant, surviving in powdered infant formula (PIF) which typically has a water activity (aw) of 0.2 - inhospitable to most micro-organisms. Mortality rates of up to 80% in infected infants have been recorded making C. sakazakii a serious cause for concern. In silico analysis of the C. sakazakii BAA-894 genome revealed seven copies of the osmolyte uptake system ProP. Herein, we test the physiological role of each of these homologues following heterologous expression against an osmosensitive Escherichia coli host.

Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility

Outbreaks of human infection linked to the powdered infant formula (PIF) food chain and associated with the bacterium Cronobacter, are of concern to public health. These bacteria are regarded as opportunistic pathogens linked to life-threatening infections predominantly in neonates, with an under developed immune system. Monitoring the microbiological ecology of PIF production sites is an important step in attempting to limit the risk of contamination in the finished food product. Cronobacter species, like other microorganisms can adapt to the production environment. These organisms are known for their desiccation tolerance, a phenotype that can aid their survival in the production site and PIF itself. In evaluating the genome data currently available for Cronobacter species, no sequence information has been published describing a Cronobacter sakazakii isolate found to persist in a PIF production facility. Here we report on the complete genome sequence of one such isolate, Cronobacter sakazakii SP291 along with its phenotypic characteristics. The genome of C. sakazakii SP291 consists of a 4.3-Mb chromosome (56.9% GC) and three plasmids, denoted as pSP291-1, [118.1-kb (57.2% GC)], pSP291-2, [52.1-kb (49.2% GC)], and pSP291-3, [4.4-kb (54.0% GC)]. When C. sakazakii SP291 was compared to the reference C. sakazakii ATCC BAA-894, which is also of PIF origin, the annotated genome data identified two interesting functional categories, comprising of genes related to the bacterial stress response and resistance to antimicrobial and toxic compounds. Using a phenotypic microarray (PM), we provided a full metabolic profile comparing C. sakazakii SP291 and the previously sequenced C. sakazakii ATCC BAA-894. These data extend our understanding of the genome of this important neonatal pathogen and provides further insights into the genotypes associated with features that can contribute to its persistence in the PIF environment.

Screening for Cronobacter species in powdered and reconstituted infant formulas and from equipment used in formula preparation in maternity hospitals

BACKGROUND/AIMS

Cronobacter spp. have been identified as being of considerable risk to neonates. The occurrence of organisms in infant formulas is therefore of considerable interest.

METHODS

The occurrence of Cronobacter spp. in infant feeds (formulas and fortified cow's milk) was determined using most probable number (MPN) analysis, and from formula preparation utensils. Ninety-nine samples were analyzed, of which 42 were unopened cans of powdered infant formula (PIF), 25 reconstituted infant formulas in feeding bottles, 27 utensils used in the preparation of infant formula and 5 samples of fortified cow's milk. Presumptive Cronobacter spp. isolates were identified using the 7 allele multilocus sequence typing (MLST) scheme.

RESULTS

C. sakazakii, C. malonaticus and C. muytjensii were recovered from PIF. Although the incidence of Cronobacter in PIF was 29% (12/42), the level was low with an average of 0.54 MPN/100 g. According to MLST profiling, C. sakazakii was the most frequently isolated Cronobacter species, and C. sakazakii ST4 (associated with neonatal meningitis) was recovered from 2/42 PIF samples at 0.51 and 0.92 MPN/100 g.

CONCLUSIONS

Cronobacter spp. can be isolated from PIF and therefore strict hygienic practices during PIF preparation are important to minimize neonate exposure and reduce the risk of severe infections.