Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis.

Streptococcus pyogenes causes 700 million human infections annually worldwide, yet, despite a century of intensive effort, there is no licensed vaccine against this bacterium. Although a number of large-scale genomic studies of bacterial pathogens have been published, the relationships among the genome, transcriptome, and virulence in large bacterial populations remain poorly understood. We sequenced the genomes of 2,101 emm28 S. pyogenes invasive strains, from which we selected 492 phylogenetically diverse strains for transcriptome analysis and 50 strains for virulence assessment. Data integration provided a novel understanding of the virulence mechanisms of this model organism. Genome-wide association study, expression quantitative trait loci analysis, machine learning, and isogenic mutant strains identified and confirmed a one-nucleotide indel in an intergenic region that significantly alters global transcript profiles and ultimately virulence. The integrative strategy that we used is generally applicable to any microbe and may lead to new therapeutics for many human pathogens.

Streptococcus pneumoniae: Antimicrobial Resistance and Serotypes of Strains Carried by Children and Causing Invasive Disease in the Faroe Islands.

Knowledge about pneumococcal carriage, antibacterial resistance, serotype prevalence, and prevalence of invasive pneumococcal disease (IPD) after introduction of pneumococcal conjugate vaccines (PCVs) is lacking in the Faroe Islands. PCV-7 was introduced in 2008 and PCV-13 in 2010. The aim was to obtain knowledge on serotypes and antimicrobial resistance in pneumococci from carriage in children attending day-care centers (DCCs) and invasive isolates. Nasopharyngeal swabs were collected from 607 healthy children attending DCCs in the Faroe Islands in January to March in 2009, 2010, and 2011. Pneumococci were cultured selectively, tested for antibacterial susceptibility, and serotyped. Data from IPD isolates from 1974 to 2016 from the Department of Microbiology, National Hospital of the Faroe Islands, and typed and stored at Staten Serum Institute were also analyzed. Of the 607 screened children, 45% were pneumococcal carriers, 50% in 2009, 40% in 2010, and 42% in 2011. Antibiotic resistance in pneumococci was rare both in carriers and patients. Five penicillin nonsusceptible pneumococci were found in carriers (1.8%) and one among the invasive isolates (1.7%). The most common serotypes in carriage were 6B and 6A in 2009, serotype 3 and 6C in 2010, and serotype 11 and 6C in 2011. Serotype 6B was not found in 2011. The most common serotypes among IPD were 7F and 3. Pneumococcal carriage prevalence in healthy children attending DCCs in the Faroe Islands was low and antibacterial resistance was rare, compared with Iceland. The results suggest a possible serotype shift, reduction in antibacterial use, and PCV-7/13 serotype decrease in IPD after the introduction of pneumococcal vaccinations in children.

Antibacterial Susceptibilities of Escherichia coli from Community-Acquired Urinary Tract Infections in the Faroe Islands, Associations with Antibacterial Sales, and Comparison with Iceland and Denmark.

Currently, data on Escherichia coli antibacterial susceptibilities in the Faroe Islands are lacking. The aim was to investigate the antibacterial susceptibilities of E. coli from patients with community-acquired urinary tract infections in the Faroe Islands, correlate with antibacterial sales, and compare with Iceland and Denmark. From 2009 to 2010 and in 2012, 12 general practitioners from the Faroe Islands were recruited to provide urine samples from patients. Antibacterial susceptibilities were determined by disc diffusion testing according to the Clinical and Laboratory Standards Institute methods and criteria. Logistic regression (quasibinomial) of the antibacterial resistance proportions versus mean sales during the period of 2008-2011 was used to determine association. Nonsusceptibility to at least 1 of the 14 antibacterial drugs investigated was found in 54% of the E. coli isolates and was most common to ampicillin (46%), followed by sulfamethoxazole (39%), trimethoprim (27%), trimethoprim/sulfamethoxazole (27%), and <10% to the remaining 10 antibiotics. The resistance prevalence did not change significantly with time. From logistic regression modeling, we find significant associations between antibacterial mean sales and antibacterial resistances. For the resistances in the Faroe Islands compared with data from Denmark and Iceland, we infer two groups of resistances indicating different responses-one steep and one gradual-to antibacterial sales. For these two groups, we find ß1 = 4.77 (Std. Error = 0.624, p-value = 0.002) and ß1 = 0.26 (Std. Error = 0.020, p-value = 4e-7) for the steep and gradual groups, respectively. This knowledge can potentially be used to predict and control the future increase in E. coli resistance with antibacterial sales.

Antibacterial resistance in Streptococcus pyogenes (GAS) from healthy carriers and tonsillitis patients and association with antibacterial sale in the Faroe Islands.

The aim of this study was to investigate the antibacterial resistance of Streptococcus pyogenes (GAS), and correlate the findings with the sales of erythromycin and tetracycline. General practitioners in the Faroe Islands were recruited to send oropharyngeal swabs. From an ongoing pneumococcal study, nasopharyngeal swabs were sampled from healthy children 0-7 years of age. Erythromycin susceptibility data from Iceland were obtained from the reference laboratory at the Landspitali University Hospital. Susceptibility testing in the Faroe Islands and Iceland was performed according to CLSI methods and criteria. The resistance rate to erythromycin and tetracycline found in patients in the Faroe Islands in 2009/2010 was 6% and 30% respectively. Tetracycline resistance in patients declined significantly from 2009 to 2010 (37-10%, p-value = 0.006 < 0.05) and differed significantly between age groups (p-value = 0.03 < 0.05). In Iceland, there was a peak in erythromycin resistance in 2008 (44%) and a substantial decrease in 2009 (5%). Although the prevalence of erythromycin and tetracycline resistance in the Faroe Islands and Iceland may be associated with antimicrobial use, sudden changes can occur with the introduction of new resistant clones.

Antibacterial use in the Faroe Islands, Iceland, and Denmark 1999-2011.

BACKGROUND: The Faroe Islands, Iceland, and Denmark are neighbouring Nordic countries with great ethnic, cultural, and political similarities and are relatively homogeneous. Important information about prescribing practices can be obtained by comparing the antibacterial use in these countries. The objective was to describe, compare, and analyse the use of systemic antibacterial agents in these countries during the y 1999-2011. METHODS: Data were obtained from the Faroe Islands, Iceland, and Denmark on systemic antibacterial use and expressed in defined daily dosages (DDD). Prescription data were also obtained for specific age groups. RESULTS: The total antibacterial use for the y 1999-2011 varied markedly between the 3 countries, with a mean use of 21.8 DDD/1000 inhabitants/day (DID) in Iceland, 17.7 in the Faroe Islands, and 16.3 in Denmark. The total use remained fairly constant over the years in the Faroe Islands and Iceland, whereas in Denmark it increased gradually from 13.5 DID in 1999 to 19.5 DID in 2011. The higher use in Iceland can be explained by much higher consumption of tetracyclines. There was also considerable variation in the use of individual penicillins and macrolides between the countries. CONCLUSIONS: Despite the great ethnic and cultural similarities of these 3 countries, we found marked differences in total antibacterial use and important differences in the use of individual antibacterials.

Laboratory and in-use assessment of methicillin-resistant Staphylococcus aureus contamination of ergonomic computer keyboards for ward use.

BACKGROUND: An ideal computer keyboard for clinical use would be easily cleanable and cleaned by staff, meet acceptable levels of usability, and not attract hospital bacteria. METHODS: In vitro studies were performed to demonstrate bacterial transfer between keyboard surfaces and gloves. This was followed by a usability study and a controlled trial of keyboard contamination in an intensive care unit both with and without an alarm to indicate the need for cleaning. Eight cleanable keyboards were placed at random beds and compared with standard keyboards. RESULTS: Bacteria were most easily removed from a flat silicone-coated surface. The total viable count on flat keyboards with an alarm was lower than that on standard or other cleanable keyboards (median, 19 colony-forming units [cfu] (interquartile range, 7 to 40 cfu), n = 34; 65 cfu (33 to 140 cfu), n = 50; and 40 cfu (21 to 57 cfu), n = 80). Compliance with hand hygiene before touching the standard keyboard was 27%, but the alarmed keyboard was cleaned on 87% of occasions on which the alarm was triggered. The usability study found the flat profile of the cleanable keyboard did not interfere with routine use, except for touch-typing. CONCLUSION: The flat keyboard with an alarm is easy to clean, and it use is associated with better cleaning compliance.