https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(13)60687-X.pdf

Chronic kidney disease: global dimension and perspectives

Dangerous, antibiotic resistant bacteria have been observed with increasing frequency over the past several decades. In this review the factors that have been linked to this phenomenon are addressed. Profiles of bacterial species that are deemed to be particularly concerning at the present time are illustrated. Factors including economic impact, intrinsic and acquired drug resistance, morbidity and mortality rates, and means of infection are taken into account. Synchronously with the waxing of bacterial resistance there has been waning antibiotic development. The approaches that scientists are employing in the pursuit of new antibacterial agents are briefly described. The standings of established antibiotic classes as well as potentially emerging classes are assessed with an emphasis on molecules that have been clinically approved or are in advanced stages of development. Historical perspectives, mechanisms of action and resistance, spectrum of activity, and preeminent members of each class are discussed.

Antibiotics and Bacterial Resistance in the 21st Century

Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. The MiSeq had the highest throughput per run (1.6 Gb/run, 60 Mb/h) and lowest error rates. The 454 GS Junior generated the longest reads (up to 600 bases) and most contiguous assemblies but had the lowest throughput (70 Mb/run, 9 Mb/h). Run in 100-bp mode, the Ion Torrent PGM had the highest throughput (80–100 Mb/h). Unlike the MiSeq, the Ion Torrent PGM and 454 GS Junior both produced homopolymer-associated indel errors (1.5 and 0.38 errors per 100 bases, respectively).

Performance comparison of benchtop high-throughput sequencing platforms

Current methods for screening Enterohemorrhagic Escherichia coli (EHEC) O157 and non-O157 in beef enrichments typically rely on the molecular detection of stx, eae, and serogroup-specific wzx or wzy gene fragments. As these genetic markers can also be found in some non-EHEC strains, a number of “false positive” results are obtained. Here, we explore the suitability of five novel molecular markers, espK, espV, ureD, Z2098, and CRISPRO26:H11 as candidates for a more accurate screening of EHEC strains of greater clinical significance in industrialized countries. Of the 1739 beef enrichments tested, 180 were positive for both stx and eae genes. Ninety (50%) of these tested negative for espK, espV, ureD, and Z2098, but 12 out of these negative samples were positive for the CRISPRO26:H11 gene marker specific for a newly emerging virulent EHEC O26:H11 French clone. We show that screening for stx, eae, espK, and espV, in association with the CRISPRO26:H11 marker is a better approach to narrow down the EHEC screening step in beef enrichments. The number of potentially positive samples was reduced by 48.88% by means of this alternative strategy compared to the European and American reference methods, thus substantially improving the discriminatory power of EHEC screening systems. This approach is in line with the EFSA (European Food Safety Authority) opinion on pathogenic STEC published in 2013.

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Revisiting the STEC Testing Approach: Using espK and espV to Make Enterohemorrhagic Escherichia coli (EHEC) Detection More Reliable in Beef.

Illness and death from diseases caused by contaminated food are a constant threat to public health and a significant impediment to socio-economic development worldwide. To measure the global and regional burden of foodborne disease (FBD), the World Health Organization (WHO) established the Foodborne Disease Burden Epidemiology Reference Group (FERG), which here reports their first estimates of the incidence, mortality, and disease burden due to 31 foodborne hazards. We find that the global burden of FBD is comparable to those of the major infectious diseases, HIV/AIDS, malaria and tuberculosis. The most frequent causes of foodborne illness were diarrheal disease agents, particularly norovirus and Campylobacter spp. Diarrheal disease agents, especially non-typhoidal Salmonella enterica, were also responsible for the majority of deaths due to FBD. Other major causes of FBD deaths were Salmonella Typhi, Taenia solium and hepatitis A virus. The global burden of FBD caused by the 31 hazards in 2010 was 33 million Disability Adjusted Life Years (DALYs); children under five years old bore 40% of this burden. The 14 subregions, defined on the basis of child and adult mortality, had considerably different burdens of FBD, with the greatest falling on the subregions in Africa, followed by the subregions in South-East Asia and the Eastern Mediterranean D subregion. Some hazards, such as non-typhoidal S. enterica, were important causes of FBD in all regions of the world, whereas others, such as certain parasitic helminths, were highly localised. Thus, the burden of FBD is borne particularly by children under five years old-although they represent only 9% of the global population-and people living in low-income regions of the world. These estimates are conservative, i.e., underestimates rather than overestimates; further studies are needed to address the data gaps and limitations of the study. Nevertheless, all stakeholders can contribute to improvements in food safety throughout the food chain by incorporating these estimates into policy development at national and international levels.

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World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010

Background We describe an outbreak of gastroenteritis and the hemolytic–uremic syndrome caused by Shiga-toxin–producing Escherichia coli in Germany in May, June, and July, 2011. The consumption of sprouts was identified as the most likely vehicle of infection. Methods We analyzed data from reports in Germany of Shiga-toxin–producing E. coli gastro enteritis and the hemolytic–uremic syndrome and clinical information on patients presenting to Hamburg University Medical Center (HUMC). An outbreak case was defined as a reported case of the hemolytic–uremic syndrome or of gastroenteritis in a patient infected by Shiga-toxin–producing E. coli, serogroup O104 or serogroup unknown, with an onset of disease during the period from May 1 through July 4, 2011, in Germany. Results A total of 3816 cases (including 54 deaths) were reported in Germany, 845 of which (22%) involved the hemolytic–uremic syndrome. The outbreak was centered in northern Germany and peaked around May 21 to 22. Most of the patients in whom the hemolytic–uremic syndrome developed were adults (88%; median age, 42 years), and women were overrepresented (68%). The estimated median incubation period was 8 days, with a median of 5 days from the onset of diarrhea to the development of the hemolytic–uremic syndrome. Among 59 patients prospectively followed at HUMC, the hemolytic–uremic syndrome developed in 12 (20%), with no significant differences according to sex or reported initial symptoms and signs. The outbreak strain was typed as an enteroaggregative Shiga-toxin–producing E. coli O104:H4, producing extended-spectrum beta-lactamase. Conclusions In this outbreak, caused by an unusual E. coli strain, cases of the hemolytic–uremic syndrome occurred predominantly in adults, with a preponderance of cases occur ring in women. The hemolytic–uremic syndrome developed in more than 20% of the identified cases.

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Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany

Since early May 2011, an increased incidence of haemolytic uraemic syndrome (HUS) and bloody diarrhoea related to infections with Shiga toxin-producing Escherichia coli (STEC) has been observed in Germany, with most cases in the north of the country. Cases reported from other European countries had travelled to this area. First results of a case–control study conducted in Hamburg suggest an association between the occurrence of disease and the consumption of raw tomatoes, cucumber and leaf salad.

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Large and ongoing outbreak of haemolytic uraemic syndrome, Germany, May 2011

In the context of a large outbreak of Shiga toxin–producing Escherichia coli O104:H4 in Germany, we quantified the timeliness of the German surveillance system for hemolytic uremic syndrome and Shiga toxin–producing E. coli notifiable diseases during 2003–2011. Although reporting occurred faster than required by law, potential for improvement exists at all levels of the information chain.

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Timeliness of Surveillance during Outbreak of Shiga Toxin–producing Escherichia coli Infection, Germany, 2011

Infection with sorbitol-fermenting Shiga toxin-producing Escherichia coli O157:H- (sf STEC O157:H-) is rare, but emerging in Europe. The pathogen is typically isolated from paediatric patients with life-threatening haemolytic uraemic syndrome (HUS). It is unclear whether this observation primarily reflects the pathogen's virulence or its complex laboratory diagnosis, not routinely conducted in diarrhoeal patients. In summer 2009, four boys living in the same suburb in Germany developed diarrhoea-associated HUS: three were infected by sf STEC O157:H- and one died. We conducted two analytical epidemiological studies, an extensive search for diarrhoeal cases in potentially exposed groups, and an environmental investigation. Outbreak cases were residents of the suburb diagnosed with HUS, sf STEC O157:H- infection, or both between 24 July 2009 and 25 August 2009. Overall, we ascertained eight cases with a median age of 4 years (range: from 8 months to 9 years). Stool screening of 220 persons led to the identification of only four additional cases: two asymptomatic carriers and two diarrhoeal cases. HUS was strongly associated with visiting a local playground in July, particularly on 16th July (odds ratio = 42.7, P = 0.002). No other commonality, including food, was identified, and all environmental samples (n = 24) were negative. In this localized non-foodborne outbreak, the place of likely infection was a local playground. Sf STEC O157:H- infection apparently limits itself rarely to diarrhoeal illness and progresses frequently to HUS. Therefore, detection of and response to this hypervirulent pathogen primarily relies on HUS surveillance.

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Desperately Seeking Diarrhoea: Outbreak of Haemolytic Uraemic Syndrome Caused by Emerging Sorbitol- Fermenting Shiga Toxin- Producing Escherichia coli O157:H-, Germany, 2009

Anke Spode

Papers

Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany

Large and ongoing outbreak of haemolytic uraemic syndrome, Germany, May 2011

Timeliness of Surveillance during Outbreak of Shiga Toxin–producing Escherichia coli Infection, Germany, 2011

Desperately Seeking Diarrhoea: Outbreak of Haemolytic Uraemic Syndrome Caused by Emerging Sorbitol- Fermenting Shiga Toxin- Producing Escherichia coli O157:H-, Germany, 2009