Clusters of Salmonella Enteritidis cases were identified by the Minnesota Department of Health using both pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) single nucleotide polymorphism analysis from 1 January 2015 through 31 December 2017. The median turnaround time for obtaining WGS results was 11 days longer than for PFGE (12 vs. 1 day). WGS analysis more than doubled the number of clusters compared to PFGE analysis, but reduced the total number of cases included in clusters by 34%. The median cluster size was two cases for WGS compared to four for PFGE, and the median duration of WGS clusters was 27 days shorter than PFGE clusters. While the percentage of PFGE clusters with a confirmed source (46%) was higher than WGS clusters (32%), a higher percentage of cases in clusters that were confirmed as outbreaks reported the vehicle or exposure of interest for WGS (78%) than PFGE (46%). WGS cluster size was a significant predictor of an outbreak source being confirmed. WGS data have enhanced S. Enteritidis cluster investigations in Minnesota by improving the specificity of cluster case definitions and has become an integral part of the S. Enteritidis surveillance process.

Salmonella is a leading cause of foodborne outbreaks in Taiwan. On 27 April 2018, a salmonellosis outbreak among customers of a restaurant was reported to the Taiwan CDC. We investigated the outbreak to identify infection sources and prevent further transmission. We interviewed ill customers and their dining companions. We conducted a case-control study to identify foods associated with the illness. Case-patients were those who had diarrhoea within 72 h after eating at the restaurant during 16–27 April 2018. Specimens, food samples and environmental samples were collected and tested for enteric pathogens. Salmonella isolates were analysed with pulse-field gel electrophoresis and whole-genome sequencing. We inspected the restaurant sanitation and reviewed kitchen surveillance camera recordings. We identified 47 case-patients, including one decedent. Compared with 44 controls, case-patients were more likely to have had a French toast sandwich (OR: 102.4; 95% CI: 18.7–952.3). Salmonella Enteritidis isolates from 16 case-patients shared an indistinguishable genotype. Camera recordings revealed eggshell contamination, long holding time at room temperature and use of leftovers during implicated food preparation. Recommendations for restaurant egg-containing food preparation are to use pasteurised egg products and ensure a high enough cooking temperature and long enough cooking time to prevent Salmonella contamination.

We determined the molecular epidemiology of Bordetella pertussis isolates to evaluate its potential impact on pertussis reemergence in a population of Mexico. Symptomatic and asymptomatic cases were included. Pertussis infection was confirmed by culture and real-time polymerase chain reaction (PCR). Selected B. pertussis isolates were further analysed; i.e. clonality was analysed by pulsed-field gel electrophoresis (PFGE) and ptxP-ptxA, prn, fim2 and fim3 typing was performed by PCR and sequencing. Out of 11 864 analysed samples, 687 (5.8%) were positive for pertussis, with 244 (36%) confirmed by both culture and PCR whereas 115 (17%) were positive only by culture and 328 (48%) were positive only by PCR. One predominant clone (clone A, n = 62/113; 55%) and three major subtypes (A1, A2 and A3) were identified by PFGE. All 113 selected isolates had the allelic combination ptxP3-ptxA1. The predominant clone A and the three major subtypes (A1, A2 and A3) corresponded to the emerging genotypes ptxP3-ptxA1-prn2-fim2-1-fim3-2 and ptxP3-ptxA1-prn2-fim2-1-fim3-1. In conclusion, the presence of an endemic clone and three predominant subtypes belonging to the genotypes ptxP3-ptxA1-prn2-fim2-1-fim3-2 and ptxP3-ptxA1-prn2-fim2-1-fim3-1 were detected. This finding supports the global spread/expansion reported for these outbreaks associated genotypes.

Sampling approaches following the dairy chain, including microbiological hygiene status of critical processing steps and physicochemical parameters, contribute to our understanding of how Staphylococcus aureus contamination risks can be minimised. Such a sampling approach was adopted in this study, together with rapid culture-independent quantification of Staph. aureus to supplement standard microbiological methods. A regional cheese production chain, involving 18 farms, was sampled on two separate occasions. Overall, 51·4% of bulk milk samples were found to be Staph. aureus positive, most of them (34·3%) at the limit of culture-based detection. Staph. aureus positive samples >100 cfu/ml were recorded in 17·1% of bulk milk samples collected mainly during the sampling in November. A higher number of Staph. aureus positive bulk milk samples (94·3%) were detected after applying the culture-independent approach. A concentration effect of Staph. aureus was observed during curd processing. Staph. aureus were not consistently detectable with cultural methods during the late ripening phase, but >100 Staph. aureus cell equivalents (CE)/ml or g were quantifiable by the culture-independent approach until the end of ripening. Enterotoxin gene PCR and pulsed-field gel electrophoresis (PFGE) typing provided evidence that livestock adapted strains of Staph. aureus mostly dominate the post processing level and substantiates the belief that animal hygiene plays a pivotal role in minimising the risk of Staph. aureus associated contamination in cheese making. Therefore, the actual data strongly support the need for additional sampling activities and recording of physicochemical parameters during semi-hard cheese-making and cheese ripening, to estimate the risk of Staph. aureus contamination before consumption.

Strain characteristics of 51 Shigella sonnei isolates obtained from children seeking medical care (MC) and 48 isolates recovered during a prospective diarrhoea birth cohort (BC) study were compared. Biochemical characterization and antibiotic susceptibility testing determined that all S. sonnei isolates were biotype g and multidrug-resistant. Plasmid profiling identified 15 closely related patterns and XbaI pulsed-field gel electrophoresis confirmed the high degree of genetic similarity between isolates. All S. sonnei isolates harboured ipaH and class II integrase genes and 84·3 and 80% of the MC and BC isolates, respectively carried the sen gene. Neither the class I integrase nor the set gene was detected. Our results indicate that S. sonnei isolates associated with severe diarrhoea were indistinguishable from those associated with mild diarrhoea. Additional genetic tests with greater discrimination might offer an opportunity to determine genetic differences within the globally disseminating biotype g clone.