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

Emerging of Multidrug-Resistant Cronobacter sakazakii Isolated from Infant Supplementary Food in China

Cronobacter is a foodborne pathogen associated with severe infections in restricted populations and particularly with high mortality in neonates and infants. The prevalence and antimicrobial resistance (AMR) phenotype of Cronobacter cultured from powdered infant formula and supplementary food were studied. The virulence factors, AMR genes, and genomic environments of the multidrug-resistant isolates were further studied. A total of 1,055 Cronobacter isolates were recovered from 12,105 samples of powdered infant formula and supplementary food collected from 29 provinces between 2018 and 2019 in China. Among these, 1,048 isolates were from infant supplementary food and 7 were from powdered infant formula. Regarding antimicrobial resistance susceptibility, 11 (1.0%) isolates were resistant and two showed resistance to four antimicrobials (ampicillin [AMP], tetracycline [TET], sulfamethoxazole-trimethoprim [SXT], and chloramphenicol [CHL]), defined as MDR. These two MDR isolates were subsequently identified as Cronobacter sakazakii sequence type 4 (ST4) (C. sakazakii Crono-589) and ST40 (C. sakazakii Crono-684). Both MDR isolates contain 11 types of virulence genes and 7 AMR genes on their genomes. Meanwhile, the IncFIB plasmids of both MDR C. sakazakii isolates also harbored 2 types of virulence genes. Results of the genomic comparative analysis indicated that food-associated C. sakazakii could acquire antimicrobial resistance determinants through horizontal gene transfer (HGT). IMPORTANCE As a foodborne pathogen, Cronobacter can cause serious infections in restricted populations and lead to death or chronic sequelae. Although a number of investigations showed that Cronobacter isolates are susceptible to most antimicrobial agents, MDR Cronobacter isolates, isolated mainly from clinical cases but occasionally from foods, have been reported in recent years. In this study, we successfully identified two MDR Cronobacter sakazakii isolates from infant foods based on nationwide surveillance and genome sequencing in China. Genomic analysis revealed that these two MDR C. sakazakii strains acquired resistance genes from other species via different evolution and transmission routes. It is important to monitor MDR C. sakazakii isolates in infant foods, and appropriate control measures should be taken to reduce the contamination with and transmission of this MDR bacterium.

The Secretion of Toxins and Other Exoproteins of Cronobacter: Role in Virulence, Adaption, and Persistence

: Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capable of causing both intestinal and systemic human disease. This review describes common virulence themes shared among the seven Cronobacter species and describes multiple exoproteins secreted by Cronobacter, many of which are bacterial toxins that may play a role in human disease. The review will particularly concentrate on the virulence factors secreted by C. sakazakii, C. malonaticus, and C. turicensis, which are the primary human pathogens of interest. It has been discovered that various species-specific virulence factors adversely affect a wide range of eukaryotic cell processes including protein synthesis, cell division, and ion secretion. Many of these factors are toxins which have been shown to also modulate the host immune response. These factors are encoded on a variety of mobile genetic elements such as plasmids and transposons; this genomic plasticity implies ongoing re-assortment of virulence factor genes which has complicated our efforts to categorize Cronobacter into sharply defined genomic pathotypes.

Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error

Background

The influences that different programs and conditions have on error rates of single-nucleotide polymorphism (SNP) analyses are poorly understood. Using Illumina short-read sequence data generated from Listeria monocytogenes strain HPB5622, we assessed the performance of four SNP callers (BCFtools, FreeBayes, UnifiedGenotyper, VarScan) under a variety of conditions, including: (1) a range of sequencing coverages; (2) use of four popular reference-guided assemblers (Burrows-Wheeler Aligner, Novoalign, MOSAIK, SMALT); (3) with and without read quality trimming and filtering; and (4) use of different reference sequences.

Results

At 8-fold coverage the proportions of true positive calls ranged from 0.22 to 25.00 % when reads were aligned to a nearly identical reference (0.000096 % distant). Calls made when reads were aligned to a non-identical reference (0.85 % distant) were from 92.54 to 98.88 % accurate. At 79-fold coverage accuracies ranged from 3.95 to 20.00 % with the nearly identical reference and 93.80–98.75 % with the non-identical reference. Read preprocessing significantly changed the numbers of false positive calls made, from a 65.24 % decrease to a 54.55 % increase.

Conclusions

The combinations of reference-guided sequence assemblers and SNP callers greatly influenced not only the numbers of true and false positive sites but also the proportions of true positive calls relative to the total numbers of calls made. Furthermore, the efficacy of different assembler and caller combinations changed dramatically with the different conditions tested. Researchers should consider whether identifying the greatest numbers of true positive sites, reducing the numbers of false positive calls, or achieving the highest accuracies are desired.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-1689-4) contains supplementary material, which is available to authorized users.

Genome Sequence of Listeria monocytogenes Strain HPB5415, Collected during a 2008 Listeriosis Outbreak in Canada

Listeria monocytogenes strain HPB5415-isolated from deli meat-was found in 2008 to have the same pulsed-field gel electrophoresis patterns as a clinical strain (08-5923). However, whether nucleotide differences (single nucleotide polymorphisms [SNPs]) exist between their genomes was not determined. We sequenced the L. monocytogenes strain HPB5415 genome and identified 52 SNPs relative to strain 08-5923.

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.

Draft Whole-Genome Sequences of 14 Vibrio parahaemolyticus Clinical Isolates with an Ambiguous K Serogroup

Vibrio parahaemolyticus is a bacterial pathogen responsible for mild to severe gastroenteritis, wound infections, and septicemia resulting from the ingestion or handling of raw or undercooked contaminated seafood. Here, we report the draft whole-genome sequences and annotations of 14 Canadian V. parahaemolyticus clinical isolates that were serologically identified as K group II using polyvalent antisera but were not specifically K serogrouped using monovalent antisera.

Draft Genome Sequences of Four Vibrio parahaemolyticus Isolates from Clinical Cases in Canada

Vibrio parahaemolyticus is a leading cause of bacterial gastroenteritis following ingestion of contaminated seafood. This report presents the draft genome sequences of four clinical strains of V. parahaemolyticus isolated in Canada. All four strains lack traditional pathogenic markers and possess uniquely individual characteristics identified using other typing criteria.