Comparative Genomic Characterization of the Highly Persistent and Potentially Virulent Cronobacter sakazakii ST83, CC65 Strain H322 and Other ST83 Strains

Abstract

Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product. The presence of this strain in the production environment was traced back more than 4 years. Whole genome sequencing (WGS) of this strain together with four more ST83 strains (PIF production environment-associated) confirmed a high degree of sequence homology among four of the five strains. Phylogenetic analysis using microarray (MA) and WGS data showed that the ST83 strains were highly phylogenetically related and MA showed that between 5 and 38 genes differed from one another in these strains. All strains possessed the pESA3-like virulence plasmid and one strain possessed a pESA2-like plasmid. In addition, a pCS1-like plasmid was also found. In order to assess the potential in vivo pathogenicity of the ST83 strains, each strain was subjected to infection studies using the recently developed zebrafish embryo model. Our results showed a high (90–100%) zebrafish mortality rate for all of these strains, suggesting a high risk for infections and illness in neonates potentially exposed to PIF contaminated with ST83 C. sakazakii strains. In summary, virulent ST83, CC65, serotype CsakO:7 strains, though rarely found intrinsically in PIF, can persist within a PIF manufacturing facility for years and potentially pose significant quality assurance challenges to the PIF manufacturing industry.

Prevalence, Molecular Characterization, and Antibiotic Susceptibility of Cronobacter sakazakii Isolates from Powdered Infant Formula Collected from Chinese Retail Markets

“…Meanwhile, C. sakazakii isolates belonging to ST4 had a stronger ability to resistance to desiccation than ST1, ST8, ST12, ST21, ST64, ST201, and ST258, which may be one of reasons that ST4 was the main sequence type recovered from PIF (Fei et al, 2017 ). C. sakazakii ST83 is another major sequence type with a strong capacity to resistance to desiccation in PIF factories (Chase et al, 2017 ). C. sakazakii ST1 is reported to be a major sequence type of strains from PIF, while C. sakazakii ST8 strains are primarily isolated from clinical sources (Sonbol et al, 2013 ).…”

“…Meanwhile, C. sakazakii serotype O2 and O1 were the main O-antigen serotypes, which had been confirmed to be particularly predominant in clinical cases by Blažková et al ( 2015 ). C. sakazakii ST83 and C. sakazakii O7 strains can survive in PIF and PIF processing environment for several years, and infect neonates with a high risk (Chase et al, 2017 ). Our result indicated there was a correlation between O-antigen serotype O7 and ST 83, which was consistent with the finding of Mueller et al ( 2013 ).…”

Advancements in Microarray Utility for Detection and Tracking of Foodborne Microbes in the Genomic Era

“…Currently, DNA microarray technology is widely used for the investigation of foodborne pathogenic and environmental isolates [4,15,19,21] for source attribution, phylogeny, serotyping [16,19,22,23] and for sequence typing (ST) analysis [24]. For instance, during the last decade, scientists at the Center of Food Safety and Applied Nutrition (CFSAN), FDA in conjunction with Affymetrix, Inc., have developed several microarray assays [25] for the investigation of genetic diversity and phylogenetic relatedness of Escherichia coli O157:H7 [23,26], STEC [22,27], Salmonella [19], Listeria monocytogenes [21], Cronobacter [28][29][30] and enteric viruses [15,17].…”

First Detection of Augmentin and Colistin Resistant <i>Cronobacter Sakazakii</i> from a Pharmaceutical Wastewater in South-Western Nigeria

“…Meanwhile, C. sakazakii isolates belonging to ST4 had a stronger ability to resistance to desiccation than ST1, ST8, ST12, ST21, ST64, ST201, and ST258, which may be one of reasons that ST4 was the main sequence type recovered from PIF [15]. C. sakazakii ST83 is another major sequence type with a strong capacity to resistance to desiccation in PIF factories [16]. C. sakazakii ST1 is reported to be a major sequence type of strains from PIF, while C. sakazakii ST8 strains are primarily isolated from clinical sources [17].…”