Neutral genomic microevolution of a recently emerged pathogen, salmonella enterica serovar agona

Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks

Role of subtyping in detecting Salmonella cross contamination in the laboratory

<p>Abstract</p> <p>Background</p> <p>With the exception of <it>M. tuberculosis</it>, little has been published on the problems of cross-contamination in bacteriology laboratories. We performed a retrospective analysis of subtyping data from the National <it>Salmonella </it>Reference Laboratory (Ireland) from 2000–2007 to identify likely incidents of laboratory cross contamination.</p> <p>Methods</p> <p>Serotyping and antimicrobial susceptibility testing was performed on all <it>Salmonella </it>isolates received in the NSRL. Phage typing was performed on all <it>S</it>. Typhimurium and <it>S</it>. Enteritidis isolates while multi-locus variance analysis (MLVA) was performed on selected <it>S</it>. Typhimurium isolates. Pulsed field gel electrophoresis (PFGE) using the PulseNet standard protocol was performed on selected isolates of various serovars.</p> <p>Results</p> <p>Twenty-three incidents involving fifty-six isolates were identified as likely to represent cross contamination. The probable sources of contamination identified were the laboratory positive control isolate (n = 13), other test isolates (n = 9) or proficiency test samples (n = 1).</p> <p>Conclusion</p> <p>The scale of laboratory cross-contamination in bacteriology is most likely under recognized. Testing laboratories should be aware of the potential for cross-contamination, regularly review protocols to minimize its occurrence and consider it as a possibility when unexpected results are obtained.</p

Colonisation with ESBL-producing and carbapenemase-producing Enterobacteriaceae, vancomycin-resistant enterococci, and meticillin-resistant Staphylococcus aureus in a long-term care facility over one year.

BACKGROUND: This study examined colonisation with and characteristics of antimicrobial-resistant organisms among residents of a long-term care facility (LTCF) over one year, including strain persistence and molecular diversity among isolates of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. METHODS: Sixty-four residents of a LTCF were recruited (51 at baseline, 13 during the year). Data on dependency levels, hospitalisations, and antimicrobial prescribing were collected. Nasal and rectal swabs and catheter urine specimens were examined quarterly, using chromogenic agars, for ESBL-producing Enterobacteriaceae, carbapenemase-producing Enterobacteriaceae (CPE), vancomycin-resistant enterococci (VRE), and meticillin-resistant S. aureus (MRSA). All ESBL-producing E. coli (ESBL-EC) were characterised by pulsed-field gel electrophoresis (PFGE) and PCR to assess for sequence type (ST) ST131, its resistance-associated H30 and H30-Rx subclones, and blaCTX-M, blaTEM, blaSHV, and blaOXA-1. RESULTS: The overall number of residents colonised, by organism, was as follows: ESBL-EC, 35 (55%); MRSA, 17 (27%); ESBL-producing K. pneumoniae (ESBL-KP), 5 (8%); VRE, 2 (3%) and CPE, 0 (0%). All 98 ESBL-EC isolates were H30-Rx ST131, with bla CTX-M-group 1. By PFGE, a group of 91 ESBL-EC (from 33 participants) had ≥85% similar profiles and resembled UK epidemic strain A/ international pulsotype PFGE812. Sequential ESBL-EC from individual residents were closely related. Six ESBL-KP isolates, from five participants, had bla CTX-M-group 1 and by PFGE were closely related. Colonisation with ESBL and MRSA was associated with location within the LTCF and previous exposure to antimicrobials. CONCLUSIONS: Among LTCF residents, colonisation with ESBL-EC and MRSA was common. All ESBL-EC were H30-Rx ST131, consistent with clonal dissemination

Temporal and spatial distribution of human cryptosporidiosis in the west of Ireland 2004-2007

<p>Abstract</p> <p>Background</p> <p>Cryptosporidiosis is increasingly recognised as a cause of gastrointestinal infection in Ireland and has been implicated in several outbreaks. This study aimed to investigate the spatial and temporal distribution of human cryptosporidiosis in the west of Ireland in order to identify high risk seasons and areas and to compare Classically Calculated (CC) and Empirical Bayesian (EB) incidence rates. Two spatial scales of analysis were used with a view to identifying the best one in assessing geographical patterns of infection. Global Moran's I and Local Moran's I tests of autocorrelation were used to test for evidence of global and local spatial clustering.</p> <p>Results</p> <p>There were statistically significant seasonal patterns of cryptosporidiosis with peaks in spring and an increasing temporal trend. Significant (p < 0.05) global spatial clustering was observed in CC rates at the Electoral Division (ED) level but not in EB rates at the same level. Despite variations in disease, ED level was found to provide the most accurate account of distribution of cryptosporidiosis in the West of Ireland but required spatial EB smoothing of cases. There were a number of areas identified with significant local clustering of cryptosporidiosis rates.</p> <p>Conclusion</p> <p>This study identified spatial and temporal patterns in cryptosporidiosis distribution. The study also showed benefit in performing spatial analyses at more than one spatial scale to assess geographical patterns in disease distribution and that smoothing of disease rates for mapping in small areas enhances visualisation of spatial patterns. These findings are relevant in guiding policy decisions on disease control strategies.</p

Draft genome sequences of 25 Listeria monocytogenes isolates associated with human clinical Listeriosis in Ireland

Listeria monocytogenes is a Gram-positive opportunistic pathogen that is the causative agent of listeriosis. Here, we report the draft genome sequences of 25 L. monocytogenes strains isolated from patients with clinical listeriosis in the Republic of Ireland between 2013 and 201

Molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli

ABSTRACT Objectives: E. coli O25b-ST131 has disseminated worldwide in hospitals and the community. The objective of this study was to determine the extent to which E. coli O25b-ST131 accounts for extended-spectrum beta-lactamase (ESBL)-producing E. coli from clinical samples from all sources in this region. Methods: Between January and June 2010 ESBL-producing E. coli were collected from 94 routine samples including 47 from residents of 25 nursing homes, 15 categorized as hospital acquired and 32 others. PCR was performed for detection of bla CTX-M , bla OXA-1 , bla TEM , bla SHV and for the identification of members of the E. coli O25b:ST131 clonal group. PFGE was carried out using XbaI in accordance with PulseNet protocols. Results: The majority (97%) of isolates harbored a bla CTX-M gene. E. coli O25b-ST131 accounted for 87% of all ESBLproducing E. coli and for 96% of isolates from nursing home residents. Sonuç: E. coli O25b-ST131 klonal grubu bakımevi kaynaklı olanlarda daha belirgin olmak üzere toplanan ESBL üreten E. coli suşları arasında baskındı. Conclusion Anahtar kelimeler: Escherichia coli, O25b-ST131, Direnç, Sağlık hizmeti, Bakımevi Ludden C

A multi-country outbreak of Salmonella newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing:October 2011 to January 2012

In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate. A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate. In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil. Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe. Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection, to support public health interventions in global food markets

A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012

In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate. A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate. In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil. Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe. Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection, to support public health interventions in global food markets

Chlamydia Screening in Ireland: a pilot study of opportunistic screening for genital Chlamydia trachomatis infection in Ireland (2007-2009). Economic evaluation

Economic Evaluation The aim of the economic evaluation was to examine the cost effectiveness of the two screening models tested in the Chlamydia Screening in Ireland Pilot (CSIP) study: (a) Clinical Setting screening, and (b) ’Pee-in-a-pot’ periodic screening in third level institution/college settings. The methodological approach comprised of a dynamic transmission model paired with an economic model. In both analyses, screening was compared to a control strategy of no organised screening, that is existing care in Ireland. A public health system or provider perspective was adopted with respect to costs. The analysis considered the cost of screening to the health service, and the costs of infection and complications, not any additional costs reported by young people in accepting a chlamydia screening test. Health outcomes were assessed in terms of major outcomes (MOs) averted and quality adjusted life years (QALYs) gained. The costs of Clinical Setting screening were presented in terms of the cost per offer (€26 ), the cost per negative case (€66), the cost per positive case (€152), and the cost per partner notified and treated (€74). The costs of ’Pee-in-a-pot’ screening were presented in terms of the cost per negative case (€39), the cost per positive case (€125), and the cost per partner notified and treated (€74). In both analyses, screening was estimated to result in fewer major outcomes, fewer QALYs lost, and higher healthcare costs compared to the control strategy. The incremental cost effectiveness analyses indicated that screening in the Clinical Setting would result in an incremental cost per MO averted of €6,093 and an incremental cost per QALY gained of €94,717. ’Pee-in-a-pot’ screening was estimated to result in incremental cost effectiveness ratios of €2,294 per MO averted and €34,486 per QALY gained respectively. In Ireland, there is no fixed and generally agreed cost effectiveness threshold below which health care technologies would be considered by policy makers to be costeffective. Nonetheless, on the basis of other technologies that are currently funded, it is not likely that screening delivered in the Clinical Setting, given an incremental cost per QALY in the region of the €94,717 found in this study, would be considered cost effective. ’Pee-in-a-pot’ screening in third level institution/college settings may be considered cost effective if a cost effectiveness threshold in the region of €45,000 per QALY gained is used. This is open to question, however, given the current economic climate and its resulting impact in terms of imposing further constraints on future healthcare budgets. It is also important to note that this strategy would have minimal in impact in reducing overall chlamydia prevalence in the population, if not supported by general population screening and prevention strategy