Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand.

Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.

Use of the EntericBio Gastro Panel II in a diagnostic microbiology laboratory: challenges and opportunities.

We sought to verify the performance of the EntericBio real-time Gastro Panel 2 (GP2; Serosep, Ireland) assay targeting Salmonella, Shigella, Campylobacter, verotoxin producing E. coli (VTEC), Giardia, and Cryptosporidium in a high-throughput diagnostic laboratory. Following a technical verification period where 237 faecal samples were tested in parallel, guided culture and discrepancy analysis were performed. A total of 13,223 faecal samples were screened by the GP2 assay. During technical verification, sensitivity, specificity, negative and positive predictive value of the GP2 assay compared with conventional methods were 100% (83-100%), 98% (96.7-98.2%), 100% (98.5-100%), and 82.6% (69-83%), respectively. With guided culture, specificity (99.4-100%) and positive predictive value (15-100%) varied by target. Challenges with interpretation of results, particularly for VTEC, Shigella and Salmonella, are discussed.

Genomic Insights into a Sustained National Outbreak of Yersinia pseudotuberculosis.

In 2014, a sustained outbreak of yersiniosis due to Yersinia pseudotuberculosis occurred across all major cities in New Zealand (NZ), with a total of 220 laboratory-confirmed cases, representing one of the largest ever reported outbreaks of Y. pseudotuberculosis. Here, we performed whole genome sequencing of outbreak-associated isolates to produce the largest population analysis to date of Y. pseudotuberculosis, giving us unprecedented capacity to understand the emergence and evolution of the outbreak clone. Multivariate analysis incorporating our genomic and clinical epidemiological data strongly suggested a single point-source contamination of the food chain, with subsequent nationwide distribution of contaminated produce. We additionally uncovered significant diversity in key determinants of virulence, which we speculate may help explain the high morbidity linked to this outbreak.

Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015.

In 2013, an unusual increase in the number of Salmonella enterica serotype Paratyphi A (Salmonella Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations did not identify a common source of exposure. To analyse the population structure and genetic diversity of these Salmonella Paratyphi A isolates, we used whole-genome sequencing on 65 isolates collected from 1999 to 2014: 55 from infections acquired in Cambodia and 10 from infections acquired in other countries in Asia, Africa and Europe. Short-read sequences from 80 published genomes from around the world and from 13 published genomes associated with an outbreak in China were also included. Pulsed-field gel electrophoresis (PFGE) was performed on a subset of isolates. Genomic analyses were found to provide much more accurate information for tracking the individual strains than PFGE. All but 2 of the 36 isolates acquired in Cambodia during 2013-2014 belonged to the same clade, C5, of lineage C. This clade has been isolated in Cambodia since at least 1999. The Chinese outbreak isolates belonged to a different clade (C4) and were resistant to nalidixic acid, whereas the Cambodian outbreak isolates displayed pan-susceptibility to antibiotics. Since 2014, the total number of cases has decreased, but there has been an increase in the frequency with which nalidixic acid-resistant C5 isolates are isolated. The frequency of these isolates should be monitored over time, because they display decreased susceptibility to ciprofloxacin, the first-choice antibiotic for treating paratyphoid fever.

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

PFGE for Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) and non-O157 STEC.

This chapter describes the procedure of generating pulsed-field gel electrophoresis (PFGE) profiles (DNA fingerprints) of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) and non-O157 STEC strains within 48 h, based on the standardized laboratory protocol developed by the Centers for Disease Control and Prevention, USA. The protocol describes the preparation of agarose plugs containing STEC O157 and non-O157 STEC cells, the digestion of bacterial DNA in the plugs using restriction endonuclease enzymes, and the electrophoresis conditions to generate the characteristic PFGE profiles of STEC O157 and non-O157 STEC isolates.

An outbreak of multiple serotypes of salmonella in New Zealand linked to consumption of contaminated tahini imported from Turkey.

A widespread salmonellosis outbreak linked to consumption of hummus made from contaminated tahini imported from Turkey occurred in New Zealand in November 2012. This article summarizes the outbreak detection, investigation, and control. The New Zealand Enteric Reference Laboratory alerted public health units regarding a cluster of 11 persons with Salmonella Montevideo infection identified from different regions of the North Island of New Zealand. A multiagency outbreak investigation commenced to determine the source of illness and prevent further transmission. Salmonellosis is a notifiable disease in New Zealand. Outbreak cases were identified through routine salmonellosis notifications, and interviewed using a standardized questionnaire to identify common exposures. Clinical and food isolates were initially characterized by serotyping and then further typed by pulsed-field gel electrophoresis (PFGE). PFGE profiles were sent to PulseNet and international alerts were posted. The scope of the investigation widened to include persons with either Salmonella Maastricht and Salmonella Mbandaka infection following detection of these serotypes in tahini epidemiologically linked to laboratory-confirmed cases. All three of the tahini-associated serotypes were detected in people who had consumed tahini, and these were found to have PFGE profiles indistinguishable from the tahini isolates. Twenty-seven salmonellosis cases infected with at least one of the three tahini-associated Salmonella serotypes were detected between September 1 and December 31, 2012; of these, 16 (59%) cases (12 with Salmonella Montevideo, 3 with Salmonella Mbandaka, and 1 with Salmonella Maastricht infection) had PFGE patterns indistinguishable from the outbreak profile. The investigation led to a trade withdrawal and consumer recall for tahini sesame paste from the consignment and products containing this tahini. The outbreak ceased following the recall. The importer of the implicated tahini was reminded of his duties as a food importer, including ensuring appropriate product testing. Changes to New Zealand legislation strengthened food safety responsibilities of food importers.

Parallel independent evolution of pathogenicity within the genus Yersinia.

The genus Yersinia has been used as a model system to study pathogen evolution. Using whole-genome sequencing of all Yersinia species, we delineate the gene complement of the whole genus and define patterns of virulence evolution. Multiple distinct ecological specializations appear to have split pathogenic strains from environmental, nonpathogenic lineages. This split demonstrates that contrary to hypotheses that all pathogenic Yersinia species share a recent common pathogenic ancestor, they have evolved independently but followed parallel evolutionary paths in acquiring the same virulence determinants as well as becoming progressively more limited metabolically. Shared virulence determinants are limited to the virulence plasmid pYV and the attachment invasion locus ail. These acquisitions, together with genomic variations in metabolic pathways, have resulted in the parallel emergence of related pathogens displaying an increasingly specialized lifestyle with a spectrum of virulence potential, an emerging theme in the evolution of other important human pathogens.

A prospective case-control and molecular epidemiological study of human cases of Shiga toxin-producing Escherichia coli in New Zealand.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) O157:H7 and related non-O157 STEC strains are enteric pathogens of public health concern worldwide, causing life-threatening diseases. Cattle are considered the principal hosts and have been shown to be a source of infection for both foodborne and environmental outbreaks in humans. The aims of this study were to investigate risk factors associated with sporadic STEC infections in humans in New Zealand and to provide epidemiological information about the source and exposure pathways. METHODS: During a national prospective case-control study from July 2011 to July 2012, any confirmed case of STEC infection notified to regional public health units, together with a random selection of controls intended to be representative of the national demography, were interviewed for risk factor evaluation. Isolates from each case were genotyped using pulsed-field gel electrophoresis (PFGE) and Shiga toxin-encoding bacteriophage insertion (SBI) typing. RESULTS: Questionnaire data from 113 eligible cases and 506 controls were analysed using multivariate logistic regression. Statistically significant animal and environmental risk factors for human STEC infections were identified, notably 'Cattle livestock present in meshblock' (the smallest geographical unit) (odds ratio 1.89, 95% CI 1.04-3.42), 'Contact with animal manure' (OR 2.09, 95% CI 1.12-3.90), and 'Contact with recreational waters' (OR 2.95, 95% CI 1.30-6.70). No food-associated risk factors were identified as sources of STEC infection. E. coli O157:H7 caused 100/113 (88.5%) of clinical STEC infections in this study, and 97/100 isolates were available for molecular analysis. PFGE profiles of isolates revealed three distinctive clusters of genotypes, and these were strongly correlated with SBI type. The variable 'Island of residence' (North or South Island of New Zealand) was significantly associated with PFGE genotype (p = 0.012). CONCLUSIONS: Our findings implicate environmental and animal contact, but not food, as significant exposure pathways for sporadic STEC infections in humans in New Zealand. Risk factors associated with beef and dairy cattle suggest that ruminants are the most important sources of STEC infection. Notably, outbreaks of STEC infections are rare in New Zealand and this further suggests that food is not a significant exposure pathway.

An outbreak of Salmonella Typhimurium phage type 42 associated with the consumption of raw flour.

A cluster of salmonellosis cases caused by Salmonella Typhimurium phage type 42 (STM42) emerged in New Zealand in October 2008. STM42 isolates from a wheat-based poultry feed raw material (broll; i.e., product containing wheat flour and particles of grain) had been identified in the 2 months prior to this cluster. Initial investigations indicated that eating uncooked baking mixture was associated with illness. A case-control study was conducted to test the hypothesis that there was an association between STM42 cases and consumption of raw flour or other baking ingredients. Salmonella isolates from human and non-human sources were compared using pulsed-field gel electrophoresis (PFGE) and multiple-locus variable number tandem repeat analysis (MLVA). Environmental investigations included testing flour and other baking ingredients from case homes, unopened bags of flour purchased from retail stores, and inspection of an implicated flour mill. A case-control study of 39 cases and 66 controls found cases had 4.5 times the odds of consuming uncooked baking mixture as controls (95% confidence interval [CI] 1.6-12.5, p-value 0.001). Examination of individual baking ingredients found that, after adjusting for eggs, flour had an odds ratio (OR) of 5.7 (95% CI 1.1-29.1, p-value 0.035). After adjusting for flour, eggs had an OR of 0.8 (95% CI 0.2-3.4, p-value 0.762). PFGE patterns were identical for all STM42 isolates tested; however, MLVA distinguished isolates that were epidemiologically linked to the cluster. STM42 was recovered from flour taken from four cases' homes, two unopened packs purchased from retail stores and packs from three batches of retrieved (recalled) product. This outbreak was associated with the consumption of uncooked baking mixture containing flour contaminated with STM42. The implicated flour mill initiated a voluntary withdrawal from sale of all batches of flour thought to be contaminated. Media releases informed the public about implicated flour brands and the risks of consuming uncooked baking mixture.

Zoocin A facilitates the entry of antisense constructs into Streptococcus mutans.

The use of antisense oligodeoxyribonucleotides (asODNs) to inhibit gene function has proven to be an extremely powerful tool for establishing gene-function relationships. Diffusion limitations imposed by the thick peptidoglycan layer of Gram-positive bacteria have proven difficult to overcome for permeability of asODNs. Typically, introduction of the asODN is achieved by cloning the antisense sequence into a vector downstream of an inducible promoter and transforming this construct into the cell of interest. In this study, we report that the use of the streptococcolytic enzyme zoocin A facilitated entry of phosphorothioate oligodeoxyribonucleotides (PS-ODNs) into Streptococcus mutans, such that the degree of phenotypic response (cell growth inhibition) observed was sequence specific and correlated with the amount of zoocin A (R(2) =0.9919) or PS-ODN (R(2) =0.9928) used. Quantitative reverse transcriptase PCR was used to demonstrate that only the expression of the target gene against which the PS-ODN was designed was affected. We believe that the use of an appropriate bacteriolytic enzyme to facilitate entry of asODNs into bacterial cells provides a method that will be generally useful in the study of gene regulation in Gram-positive bacteria.

An outbreak of Salmonella typhimurium phage type 1 associated with watermelon in Gisborne, January 2009.

AIM: To investigate an increase in Salmonella typhimurium phage type 1 (STM1) cases identified in the Gisborne region (eastern North Island, New Zealand) in January 2009. METHODS: Initial investigations found that ham and watermelon were both consumed by a high proportion of cases. A case control study was conducted to determine if there was an association between cases of STM1 in Gisborne and consumption of ham or watermelon. Environmental investigations were conducted and included testing of ham and watermelon samples, as well as trace back of suppliers of these foods. RESULTS: The case control study included 15 cases and 40 controls and found that cases were seven times more likely to have eaten watermelon compared with controls (p=0.026). Cases were one and a half times more likely to have eaten ham compared with controls (p=0.620). Pulsed field gel electrophoresis analysis determined that cases were caused by indistinguishable STM1 isolates. Salmonella was not recovered from any food samples. Trace back found watermelons were purchased from roadside stalls and came from one grower. CONCLUSIONS: This outbreak was associated with watermelon consumption from a grower in the Gisborne region. The outbreak was most likely controlled by the implementation of chlorine washing of watermelons at the grower's pack house.

Characterization of monolaurin resistance in Enterococcus faecalis.

There is increasing concern regarding the presence of vancomycin-resistant enterococci in domestically farmed animals, which may act as reservoirs and vehicles of transmission for drug-resistant enterococci to humans, resulting in serious infections. In order to assess the potential for the use of monolaurin as a food preservative, it is important to understand both its target and potential mechanisms of resistance. A Tn917 mutant library of Enterococcus faecalis AR01/DGVS was screened for resistance (MIC, >100 microg/ml) to monolaurin. Three mutants were identified as resistant to monolaurin and were designated DGRM2, DGRM5, and DGRM12. The gene interrupted in all three mutants was identified as traB, which encodes an E. faecalis pheromone shutdown protein and whose complementation in trans restored monolaurin sensitivity in all three mutants. DGRM2 was selected for further characterization. E. faecalis DGRM2 showed increased resistance to gentamicin and chloramphenicol (inhibitors of protein synthesis), while no difference in the MIC was observed with the cell wall-active antibiotics penicillin and vancomycin. E. faecalis AR01/DGVS and DGRM2 were shown to have similar rates (30% cell lysis after 4 h) of cell autolytic activity when activated by monolaurin. Differences in cell surface hydrophobicity were observed between the wild type and the mutant, with the cell surface of the parent strain being significantly more hydrophobic. Analysis of the cell wall structure of DGRM2 by transmission electron microscopy revealed an increase in the apparent cell wall thickness and contraction of its cytoplasm. Taken together, these results suggest that the increased resistance of DGRM2 was due to a change in cell surface hydrophobicity, consequently limiting the diffusion of monolaurin to a potential target in the cytoplasmic membrane and/or cytoplasm of E. faecalis.

Targeting of streptococci by zoocin A.

Zoocin A is a domain-structured peptidoglycan hydrolase produced by Streptococcus equi ssp. zooepidemicus 4881. [(14)C]-zoocin A was used to measure the amount of zoocin A bound to the surface of cells and to purified peptidoglycan. The sensitivity of various streptococci to zoocin A correlated with the amount of zoocin A bound (R(2)=0.8609). Peptidoglycan purified from Streptococcus oralis and Streptococcus rattus were able to bind zoocin A but remained resistant to hydrolysis. All Streptococcus pyogenes strains were extremely sensitive to zoocin A with minimum inhibition concentrations of 31.5 ng mL(-1) or less, suggesting that zoocin A may have potential for use as an enzybiotic.

The streptococcolytic enzyme zoocin A is a penicillin-binding protein.

Zoocin A is a streptococcolytic enzyme produced by Streptococcus equi subsp. zooepidemicus 4881 that has an unknown site of action on the peptidoglycans of susceptible organisms. Analysis of a mutant strain in which the genes for zoocin A and resistance to zoocin A were inactivated revealed that this strain was more susceptible to beta-lactam antibiotics than the parental organism. Purified zoocin A had weak beta-lactamase activity, bound radioactive penicillin covalently, and its streptococcolytic activity was inhibited by penicillin. Thus, zoocin A is a penicillin-binding protein and presumably is a D-alanyl endopeptidase.

Development of a laboratory scale clean-in-place system to test the effectiveness of "natural" antimicrobials against dairy biofilms.

A laboratory scale system, partially reproducing dairy plant conditions, was developed to quantify the effectiveness of chlorine and alternative sanitizers in reducing the number of viable bacteria attached to stainless steel surfaces. Stainless steel tubes fouled in a continuous flow reactor were exposed to a standard clean-in-place regime (water rinse, 1% sodium hydroxide at 70 degrees C for 10 min, water rinse, 0.8% nitric acid at 70 degrees C for 10 min, water rinse) followed by exposure to either chlorine (200 ppm) or combinations of nisin (500 ppm), lauricidin (100 ppm), and the lactoperoxidase system (LPS) (200 ppm) for 10 min or 2, 4, 8, 18, or 24 h. There was significant variation in the effectiveness of the alkaline-acid wash steps in reducing cell numbers (log reduction between 0 and 2). Following a 10-min treatment, none of the sanitizers significantly reduced the number of attached cells. Two hours of exposure to chlorine, nisin + the LPS, or lauricidin + the LPS achieved 2.8, 2.2, and 1.6 log reductions, respectively. Exposure times > 2 h did not further decrease the number of viable bacteria attached to the stainless steel. The effectiveness of combinations of nisin, lauricidin, and the LPS was similar to that of chlorine (P > 0.05), and these sanitizers could be used to decontaminate the surfaces of small-volume or critical hard-to-clean milk processing equipment.