The first attempt of an active integrated laboratory-based Salmonella surveillance programme in the north-eastern region of Nigeria.

Aim: To identify the sources of Salmonella contamination, distribution, prevalence and antimicrobial susceptibility patterns, which have significant impact on public and animal health, and international trade.

Methods And Results: A total of 1888 samples were collected by stratified random sampling from 2009 to 2011 from cattle, camels, poultry, fish, vegetables and humans. All identified Salmonella isolates were serotyped and tested for antimicrobial susceptibility by MIC determinations.

Nutritional status and systemic inflammatory activity of colorectal patients on symbiotic supplementation.

Background: Nutritional depletion in patients with advanced colorectal cancer, even with adequate weight, may be associated with co-morbidity factors such as: reduction of immunity, increased rate of infections, impaired cicatrization and muscle weakness. Immunomodulating diets have recently been used as a nutritional approach to cancer patients. Prebiotics, probiotics and symbiotics (a mixture of the first two) have been studied.

Low-level laser reduces the production of TNF-α, IFN-γ, and IL-10 induced by OVA.

Delayed, or type IV, hypersensitivity reactions are a useful model to study the effects of new substances on the immune system. In this study, the experimental model of the delayed type hypersensitivity (DTH) reaction to ovalbumin (OVA) was used to evaluate the immunomodulating effects of low-level laser therapy (LLLT), which is used as an adjuvant therapy in medicine, dentistry, and physical therapy because of its potential anti-inflammatory and analgesic effects observed in several studies. The effects of LLLT (λ 780 nm, 0.

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

Background: The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs).

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing.

Objectives: Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics.

External quality assurance system (EQAS) for identification of mastitis pathogens in Denmark from 2006 to 2011.

Bovine mastitis is the most common and costly dairy cattle disease. Mastitis is most frequently caused by bacterial species, and to ensure optimal treatment and control strategies, proper quality assured diagnosis and identification of the causative agent is important. With the aim to assess the capacity to isolate and identify mastitis pathogens at veterinary clinics, an external quality assurance system (EQAS) was annually (from 2006 to 2011) provided for the identification of mastitis pathogens.

Voluntary ban on cephalosporin use in Danish pig production has effectively reduced extended-spectrum cephalosporinase-producing Escherichia coli in slaughter pigs.

Objectives: To measure the effect of a voluntary ban on cephalosporin usage in the Danish pig production on the prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in pigs and pork.

Methods: Data on cephalosporin consumption were obtained from the VetStat database. For detection of ESC-producing E.

Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.

Background: Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful for creating better phylogenies, for determination of molecular clocks and for improved typing techniques.

Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.

The rapid advancement of genome technologies holds great promise for improving the quality and speed of clinical and public health laboratory investigations and for decreasing their cost. The latest generation of genome DNA sequencers can provide highly detailed and robust information on disease-causing microbes, and in the near future these technologies will be suitable for routine use in national, regional, and global public health laboratories. With additional improvements in instrumentation, these next- or third-generation sequencers are likely to replace conventional culture-based and molecular typing methods to provide point-of-care clinical diagnosis and other essential information for quicker and better treatment of patients.

Extremely drug-resistant Salmonella enterica serovar Senftenberg infections in patients in Zambia.

Two cases of extremely drug-resistant Salmonella enterica serovar Senftenberg isolated from patients in Zambia were investigated by utilizing MIC determinations and whole-genome sequencing. The isolates were resistant to, and harbored genes toward, nine drug classes, including fluoroquinolones and extended-spectrum cephalosporins, contained two plasmid replicons, and differed by 93 single-nucleotide polymorphisms.

[Waist circumference measured before the 12th week of pregnancy: correlation with serum leptin levels].

Purpose: To evaluate the correlation between maternal waist circumference measured before the 12th week of gestation and serum leptin levels during pregnancy, as well as to compare the leptin levels of women with and without abdominal obesity diagnosed in early pregnancy.

Methods: Prospective study including 40 pregnant women receiving low-risk prenatal care, older than 20 years, nonsmokers, with singleton pregnancies and without chronic disease. Waist circumference was measured before the 12th week and serum leptin levels were measured between the 9th and 12th, 25th and 28th and 34th and 37th weeks of gestation.

Identification of acquired antimicrobial resistance genes.

Objectives: Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available in routine diagnostic laboratories and is anticipated to substitute traditional methods for resistance gene identification. Thus, the current challenge is to extract the relevant information from the large amount of generated data.

In vitro susceptibility testing of fluoroquinolone activity against Salmonella: recent changes to CLSI standards.

Fluoroquinolone (FQ) resistance in Salmonella enterica is a significant clinical concern. Recognition of resistance by the clinical laboratory is complicated by the multiple FQ resistance mechanisms found in Salmonella. The Clinical Laboratory Standards Institute (CLSI) recently addressed this issue by revising the ciprofloxacin break points for Salmonella species.

Expansion of a plasmid classification system for Gram-positive bacteria and determination of the diversity of plasmids in Staphylococcus aureus strains of human, animal, and food origins.

An expansion of a previously described plasmid classification was performed and used to reveal the plasmid content of a collection of 92 Staphylococcus aureus strains of different origins. rep genes of other genera were detected in Staphylococcus. S1 pulsed-field gel electrophoresis (PFGE) hybridizations were performed with 18 representative S.

SCCmec Type IX Element in Methicillin Resistant Staphylococcusaureusspa Type t337 (CC9) Isolated from Pigs and Pork in Thailand.

Methicillin resistant Staphylococcusaureus (MRSA) have emerged among livestock in several countries. In this study, we describe the results of a screening performed in pigs and raw pork samples in Thailand. Ten pork samples and 15 nasal swabs from pigs were collected from 2 markets and 1 pig farm in the Samuth Songkhram province in Thailand.

Genomic variation in Salmonella enterica core genes for epidemiological typing.

Background: Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology.

Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock.

Unlabelled: Since its discovery in the early 2000s, methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often associated with livestock exposure. We applied whole-genome sequence typing to characterize a diverse collection of CC398 isolates (n = 89), including MRSA and methicillin-susceptible S. aureus (MSSA) from animals and humans spanning 19 countries and four continents.

Antimicrobial-resistant Shigella infections from Iran: an overlooked problem?

Objectives: In this study, we wanted to assess the level of antimicrobial resistance, the presence of genes encoding resistance to cephalosporins and plasmid-mediated quinolone resistance (PMQR), and genetic relatedness among Shigella isolates obtained from Iranian patients.

Methods: A total of 44 Shigella isolates were collected from Iranian patients admitted to Milad Hospital, Tehran, Iran, during 2008-10. Of these, 37 were serotyped and characterized by MIC determination.

Antimicrobial resistance in Salmonella spp. recovered from patients admitted to six different hospitals in Tehran, Iran from 2007 to 2008.

The objective of this study was to assess the genotypic diversity associated with antimicrobial susceptibility of Salmonella serovars isolated from patients arriving with diarrhoea to six hospitals of Tehran, Iran. During 2007-2008, a cross-sectional convenience study was performed. Stool samples were screened for the presence of Salmonella, serotyped, tested for antimicrobial susceptibility using disk diffusion and examined for the presence of relevant resistance genes and integrons by PCR.

Study of methicillin resistant Staphylococcus aureus (MRSA) in Danish pigs at slaughter and in imported retail meat reveals a novel MRSA type in slaughter pigs.

Methicillin-resistant Staphylococcus aureus (MRSA), especially CC398, have emerged in livestock worldwide. We investigated the occurrence of MRSA in pigs at slaughter and in retail meat. During 2009, nasal swabs (n=789) were taken from pigs at slaughter.

Multilocus sequence typing of total-genome-sequenced bacteria.

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories.

Prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in Danish slaughter pigs and retail meat identified by selective enrichment and association with cephalosporin usage.

Objectives: To investigate the prevalence of extended-spectrum cephalosporinase (ESC)-producing Escherichia coli in pigs at slaughter and retail meat, and possible associations with the consumption of third- and fourth-generation cephalosporins.

Methods: During 2009, faecal samples from Danish pigs (n=786) were collected at slaughter, and 866 meat samples [Danish: pork (153), broiler meat (121) and beef (142); and imported: pork (173), broiler meat (193) and beef (84)] were randomly collected in retail stores and outlets. E.

Characterization of isolates of Salmonella enterica serovar Stanley, a serovar endemic to Asia and associated with travel.

Salmonella enterica serovar Stanley (S. Stanley) is a common serovar in Southeast Asia and was the second most common serovar implicated in human salmonellosis in Thailand in the years 2002 to 2007. In contrast, this serovar is relatively uncommon in Europe.