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. Applyingthe 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

Genotypic and phenotypic characteristics of Cronobacter species, with particular attention to the newly reclassified species C. helveticus, C. pulveris, and C. zurichensis [forthcoming]

In 2013, Enterobacter helveticus, E. pulveris and E. turicensis, were reclassified as Cronobacter helveticus, C. pulveris and C. 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 BIGSdb 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

CRISPR–cas loci profiling of Cronobacter sakazakii pathovars

Aim: Cronobacter sakazakii sequence types 1, 4, 8 and 12 are associated with outbreaks of neonatal meningitis and necrotizing enterocolitis infections. However clonality results in strains which are indistinguishable using conventional methods. This study investigated the use of clustered regularly interspaced short palindromic repeats (CRISPR)–cas loci profiling for epidemiological investigations. Materials & methods: Seventy whole genomes of C. sakazakii strains from four clonal complexes which were widely distributed temporally, geographically and origin of source were profiled. Results & conclusion: All strains encoded the same type I-E subtype CRISPR–cas system with a total of 12 different CRISPR spacer arrays. This study demonstrated the greater discriminatory power of CRISPR spacer array profiling compared with multilocus sequence typing, which will be of use in source attribution during Cronobacter outbreak investigations

Comparative study of Cronobacter identification according to phenotyping methods

Background: Microbiological criteria applied to powdered infant formula (PIF) require the absence of all Cronobacter spp. Consequently, misidentification of isolates from finished products can lead to significant financial losses for manufacturers and could increase the risk of neonatal infection. Biochemical identification of suspect isolates using commercially available test panels is recommended for use by PIF manufacturers by both the US FDA and ISO standard methods for Cronobacter species; however, phenotyping can be unreliable, particularly for a genus such as Cronobacter where the taxonomy has been subject to frequent changes. This study compared the predicted identification by commonly used phenotyping kits (API20E and ID32E) for over 240 strains of Cronobacter from diverse sources, which had been identified using DNA sequence analysis. In 2015, the databases associated with the API20E and ID32E biochemical test panels were updated, including the recognition of the Cronobacter genus. Thus, the identifications from multiple versions the databases were compared to each other and toidentifications based on DNA sequencing methods. Results: Using previous versions of the API20E database, 90.0% of strains (216/240) resulted in a match for the species identification; however, version 5.0 produced matches for only 82.3% of strains (237/288). Similarly, the update to version 4.0 in the ID32E database caused the percentage of matches to drop from 88.9% (240/270) to 43.2% (139/322). A smaller study showed that the Vitek GN system identified all 14 strains, belonging all seven Cronobacter species, as members of the 'C. sakazakii group', but also attributed three strains of Franconibacter helveticus and F. pulveris to this group. In silco analysis of a PCR-based method targeting ompA predicted that amplification would only occur with Cronobacter species and this method may be a feasible alternative to biochemical phenotyping. Conclusions: These results indicate that commercially available biochemical test panels are not sufficiently reliable for speciation of Cronobacter isolates. Although DNA-sequence based methods would be the more reliable approach; however, this is not currently feasible for many food microbiology laboratories. Instead, a previously published PCR-based method targeting ompA is suggested as an alternative for identification of Cronobacter species based on in silico analysis

Draft Genome Sequence of anEnterobacterSpecies Associated with Illnesses and Powdered Infant Formula

This is the first report of the draft genome sequence of an Enterobacter species that may have been transmitted from powdered infant formula (PIF) to infants, resulting in illness. Enterobacter spp. are currently permitted in PIF, but the transmission of this strain indicates that the microbiological criteria for PIF may need revision

Multilocus sequence typing of Cronobacter spp. from powdered infant formula and milk powder production factories

This study applied the Cronobacter spp. multilocus sequence typing (MLST) scheme to three strain collections, then known as Enterobacter sakazakii, which had been isolated between 1988 and 2009 from 14 countries. The results revealed the predominance (85%) of C. 29 sakazakii (72 strains) in all three collections. The remaining strains were C. turicensis (10%), C. malonaticus (4%), and C. muytjensii (1%). No strains of C. dublinensis, C. universalis or C. condimenti were identified. Twenty-one out of seventy two C. sakazakii strains were in the clinically significant ST4 clonal complex, and were found in all three strain collections. These results confirm C. sakazakii ST4 is one of the predominant clonal complexes over the past 20 years in several parts of the world. Further understanding of the ecosystem and sources of the organism may be used for the development of improved intervention strategies in the dairy industry

Adherence to and Invasion of Human Intestinal Cells by Arcobacter Species and Their Virulence Genotypes

The genus Arcobacter is composed of 17 species which have been isolated from various sources. Of particular interest are A. butzleri, A. cryaerophilus, and A. skirrowii, as these have been associated with human cases of diarrhea, the probable transmissionrroutes being through the ingestion of contaminated drinking water and food. To date, only limited studies of virulence traits in this genus have been undertaken. The present study used 60 Arcobacter strains isolated from different sources, representing 16 of the 17 species of the genus, to investigate their ability to adhere to and invade the human intestinal cell line Caco-2. In addition, the presence of five putative virulence genes (ciaB, cadF, cj1349, hecA, and irgA) was screened for in these strains by PCR. All Arcobacter species except A. bivalviorum and Arcobacter sp. strain W63 adhered to Caco-2 cells, and most species (10/16) were invasive. The most invasive species were A. skirrowii, A. cryaerophilus, A. butzleri, and A. defluvii. All invasive strains were positive for ciaB (encoding a putative invasion protein). Other putative virulence genes were present in other species, i.e., A. butzleri (cadF, cj1349, irgA, and hecA), A. trophiarum (cj1349), A. ellisii (cj1349), and A. defluvii (irgA). No virulence genes were detected in strains which showed little or no invasion of Caco-2 cells. These results indicate that many Arcobacter species are potential pathogens of humans and animals

Desiccation survival of Acinetobacter spp. in infant formula

Acinetobacter spp. are included under category B in the FAO-WHO list of organisms of concern for neonatal health following the consumption of powdered infant formula. However, the ability of Acinetobacter spp. to maintain their viability in desiccated infant formula over a storage period consistent with the shelf-life of commercially available powdered infant formula (2 years) has not been demonstrated. In this study, 9 clinical and food isolates of A. baumannii, A. calcoaceticus, and Acinetobacter genomosp. 3 were desiccated in infant formula and then reconstituted at designated time points. Bacterial viability was followed for a maximum period of 24 months or until the strain became undetectable (<5 x 102 cfu/ml). For comparative purposes, one Enterobacter hormaechei and two Enterobacter cloacae strains were also monitored for their desiccation survival. The seven clinical and food strains remained cultivable for the whole duration of the study and showed biphasic survival curves. The initial drop in viable count was up to 3.5 log10 cfu/ml within 18 h of desiccation exposure. By the end of the study, the reduction in viability was between 3.6 and 4.8 log10 cfu/ml. In contrast the A. baumanii and A. calcoaceticus species type strains only persisted for 6 and 9 months, respectively, possibly due to laboratory adaptation. The E. cloacae and E. hormaecehei strains were undetectable after 12 and 17 months, respectively. The persistence of Acinetobacter spp. strains in desiccated powdered infant formula, supports the FAO-WHO designation of this organism as a risk to neonatal health

International survey of Cronobacter sakazakii and other Cronobacter spp. in follow up formulas and infant food

A coordinated survey for Cronobacter and related organisms in powdered infant formula, follow up formula and infant foods was undertaken by 8 laboratories in 7 countries in recognition of and in response to the data needs identified in an FAO/WHO call for data in order to develop global risk management guidance for these products. The products (domestic and imported) were purchased from the local market and were categorised according to their principle ingredients. A total of 290 products were analysed using a standardised procedure of pre-enrichment in 225 ml Buffered Peptone Water (BPW), followed by enrichment in Enterobacteriaceae Enrichment (EE) broth, plating on the chromogenic Cronobacter Druggan–Forsythe–Iversen (DFI) agar and presumptive identification with ID 32 E. Presumptive Cronobacter isolates were identified using 16S rRNA gene sequence analysis. Aerobic plate counts (APC) of the products were also determined on nutrient agar. Fourteen samples had APC > 105 cfu/g, 3 of which contained probiotic cultures. C. sakazakii was isolated from 27 products; 3/91 (3%) follow up formulas (as defined by Codex Alimentarius Commission), and 24/199 (12%) infant foods and drinks. Hence C. sakazakii was less prevalent in follow up formula than other foods given to infants over the same age range. A range of other bacteria were also isolated from follow up formulas, including Acinetobacter baumannii, Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, and Serratia ficaria. There was significant variation in the reconstitution instructions for follow up formulas. These included using water at temperatures which would enable bacterial growth. Additionally, the definition of follow up formula varied between countries

The speciation and genotyping of Cronobacter isolates from hospitalised patients

The World Health Organization (WHO) has recognised all Cronobacter species as human pathogens. Among premature neonates and immunocompromised infants, these infections can be life-threatening, with clinical presentations of septicaemia, meningitis and necrotising enterocolitis. The neurological sequelae can be permanent and the mortality rate as high as 40 – 80 %. Despite the highlighted issues of neonatal infections, the majority of Cronobacter infections are in the elderly population suffering from serious underlying disease or malignancy and include wound and urinary tract infections, osteomyelitis, bacteraemia and septicaemia. However, no age profiling studies have speciated or genotyped the Cronobacter isolates. A clinical collection of 51 Cronobacter strains from two hospitals were speciated and genotyped using 7-loci multilocus sequence typing (MLST), rpoB gene sequence analysis, O-antigen typing and pulsed- field gel electrophoresis (PFGE). The isolates were predominated by C. sakazakii sequence type 4 (63 %, 32/51) and C. malonaticus sequence type 7 (33 %, 17/51). These had been isolated from throat and sputum samples of all age groups, as well as recal and faecal swabs. There was no apparent relatedness between the age of the patient and the Cronobacter species isolated. Despite the high clonality of Cronobacter , PFGE profiles differentiated strains across the sequence types into 15 pulsotypes. There was almost complete agreement between O-antigen typing and rpoB gene sequence analysis and MLST profiling. This study shows the value of applying MLST to bacterial population studies with strains from two patient cohorts, combined with PFGE for further discrimination of strains