Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

Background: Enterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results. Results: The genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene. Conclusions: The sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control

Diversity of Staphylococcus aureus Isolates in European Wildlife

Staphylococcus aureus is a well-known colonizer and cause of infection among animals and it has been described from numerous domestic and wild animal species. The aim of the present study was to investigate the molecular epidemiology of S. aureus in a convenience sample of European wildlife and to review what previously has been observed in the subject field. 124 S. aureus isolates were collected from wildlife in Germany, Austria and Sweden; they were characterized by DNA microarray hybridization and, for isolates with novel hybridization patterns, by multilocus sequence typing (MLST). The isolates were assigned to 29 clonal complexes and singleton sequence types (CC1, CC5, CC6, CC7, CC8, CC9, CC12, CC15, CC22, CC25, CC30, CC49, CC59, CC88, CC97, CC130, CC133, CC398, ST425, CC599, CC692, CC707, ST890, CC1956, ST2425, CC2671, ST2691, CC2767 and ST2963), some of which (ST2425, ST2691, ST2963) were not described previously. Resistance rates in wildlife strains were rather low and mecA-MRSA isolates were rare (n = 6). mecC-MRSA (n = 8) were identified from a fox, a fallow deer, hares and hedgehogs. The common cattle- associated lineages CC479 and CC705 were not detected in wildlife in the present study while, in contrast, a third common cattle lineage, CC97, was found to be common among cervids. No Staphylococcus argenteus or Staphylococcus schweitzeri-like isolates were found. Systematic studies are required to monitor the possible transmission of human- and livestock- associated S. aureus/MRSA to wildlife and vice versa as well as the possible transmission, by unprotected contact to animals. The prevalence of S. aureus/MRSA in wildlife as well as its population structures in different wildlife host species warrants further investigation

Mupirocin-resistant Staphylococcus aureus in Africa: a systematic review and meta-analysis

Background Mupirocin is widely used for nasal decolonization of Staphylococcus aureus to prevent subsequent staphylococcal infection in patients and healthcare personnel. However, the prolonged and unrestricted use has led to the emergence of mupirocin-resistant (mupR) S. aureus. The aim of this systematic review was to investigate the prevalence, phenotypic and molecular characteristics, and geographic spread of mupR S. aureus in Africa. Methods We examined five electronic databases (EBSCOhost, Google Scholar, ISI Web of Science, MEDLINE, and Scopus) for relevant English articles on screening for mupR S. aureus from various samples in Africa. In addition, we performed random effects meta-analysis of proportions to determine the pooled prevalence of mupR S. aureus in Africa. The search was conducted until 3 August 2016. Results We identified 43 eligible studies of which 11 (26%) were obtained only through Google Scholar. Most of the eligible studies (28/43; 65%) were conducted in Nigeria (10/43; 23%), Egypt (7/43; 16%), South Africa (6/43; 14%) and Tunisia (5/43; 12%). Overall, screening for mupR S. aureus was described in only 12 of 54 (22%) African countries. The disk diffusion method was the widely used technique (67%; 29/43) for the detection of mupR S. aureus in Africa. The mupA-positive S. aureus isolates were identified in five studies conducted in Egypt (n = 2), South Africa (n = 2), and Nigeria (n = 1). Low-level resistance (LmupR) and high-level resistance (HmupR) were both reported in six human studies from South Africa (n = 3), Egypt (n = 2) and Libya (n = 1). Data on mupR-MRSA was available in 11 studies from five countries, including Egypt, Ghana, Libya, Nigeria and South Africa. The pooled prevalence (based on 11 human studies) of mupR S. aureus in Africa was 14% (95% CI =6.8 to 23.2%). The proportion of mupA-positive S. aureus in Africa ranged between 0.5 and 8%. Furthermore, the frequency of S. aureus isolates that exhibited LmupR, HmupR and mupR-MRSA in Africa were 4 and 47%, 0.5 and 38%, 5 and 50%, respectively. Conclusions The prevalence of mupR S. aureus in Africa (14%) is worrisome and there is a need for data on administration and use of mupirocin. The disk diffusion method which is widely utilized in Africa could be an important method for the screening and identification of mupR S. aureus. Moreover, we advocate for surveillance studies with appropriate guidelines for screening mupR S. aureus in Africa

A charge-pump 60kV modulator for the ISOLDE target extraction voltage

The ISOLDE facility at CERN provides radioactive ion beams to a number of experimental stations. These ions are produced by a metal target, floating at 60 kV, which is impacted by a 1.4 GeV high intensity proton beam. The ions are then accelerated by a grounded extraction electrode to 60 keV, before transport to the experimental area. During proton beam impact extremely high ionisation of the volume around the target gives rise to significant leakage current which results in loss of charge on the effective target capacitance of approximately 6 nF. If short life-time isotopes are to be studied, the 60 kV must be re-established within a maximum of 10 ms. Recharging the target capacitance to 60 kV and to the required stability of better than 10-4 precludes a direct charging system and an alternative method of re-establishing the 60 kV is used. The present system [1], in operation since 1991, employs a resonant circuit which is triggered 35 µs prior to beam impact. This circuit transfers the charge on the effective target capacitance to a buffer capacitor and reduces the target voltage to zero; the resonance then restores the target voltage to within a few percent of its nominal value within a further 200 µs. Finally the high precision 60 kV d.c. power supply brings the target voltage back to the required ±0.6 V tolerance within a total of 6 ms. In recent years, new types of ion sources (neutron converter targets) have been developed which present ever increasing ionisation loads with the result that it is becoming impossible to respect the maximum 10ms voltage recovery time. Future increases in beam energy to 2 GeV and higher intensity beams will further aggravate the situation. To mitigate the problem new circuit topologies have been conceived and developed. One promising development is a ''Charge pump modulator''. In this circuit a 400 nF buffer capacitor and the target capacitance are charged to 60 kV by a low power, high precision d.c. power supply (HVPS). Immediately prior to beam impact the HVPS is disconnected from the target and buffer capacitors using a 90 kV rated semiconductor switch. During beam impact the target capacitance is rapidly discharged to ~54 kV after which the buffer capacitor, which is partially isolated from the beam impact ionisation by virtue of a series-connected 3.3 kΩ resistor, begins to re-establish voltage on the target. After 1ms a feedback loop controlling an auxiliary high voltage amplifier, which applies a voltage in series with the buffer capacitor, is switched in. This additional voltage brings the target voltage back to the required ± 0.6 V tolerance within 5 ms. Finally, when the target has recovered sufficient high impedance, the feedback loop is opened and the HVPS is re-connected to the target to maintain the stable 60 kV voltage

Clonal lineages detected amongst tetracyclineresistant meticillin-resistant Staphylococcus aureus isolates of a Tunisian hospital, with detection of lineage ST398

Tetracycline resistance has been postulated as a potential phenotypic marker of livestockassociated lineage ST398 amongst meticillin-resistant Staphylococcus aureus (MRSA) clinical isolates in some European hospitals. The objective of this study was to determine if this marker could also be applied to Maghrebian countries. In total, 99 MRSA isolates were collected in a Tunisian hospital during January 2011October 2012, and 24 tetracycline-resistant MRSA isolates of this collection were characterized. All isolates were tested for antimicrobial resistance phenotypes and genotypes, molecular typing, and virulence genes. Multilocus sequence typing showed that the majority of the isolates (19/24) belonged to clonal complex CC8 (ST247, n512 isolates; ST239, n56isolates; ST241, n51 isolate). The remaining isolates belonged to CC398 (ST398, n51 isolate), CC5 (ST5 and ST641, n52 isolates), and CC80 (ST728, n52 isolates). Spa typing discriminated MRSA in eight spa types: t052 (n512 isolates), t037 (n55 isolates), t044 (n52 isolates), and t899, t129, t311, t1744 and the new t14712 (n51 isolate each). Three agr groups were found amongst the studied isolates: agr group I (n520 isolates), agr group II (n52) and agr group III (n52 isolates). We report the detection of one MRSA ST398t899 isolate in the nasal sample of a farmer patient in Tunisia, representing the first report of ST398 in humans in Africa. Tetracycline resistance seems not to be a good phenotypic marker for MRSA ST398 strains in Tunisia, where CC8 was the most prevalent lineage. Continuous efforts to understand the changing epidemiology of this micro-organism are necessary not only for appropriate antimicrobial treatment and effective infection control, but also to monitor its evolution. © 2015 The Authors

High diversity of genetic lineages and virulence genes in nasal Staphylococcus aureus isolates from donkeys destined to food consumption in Tunisia with predominance of the ruminant associated CC133 lineage

Background: The objective of this study was to determine the genetic lineages and the incidence of antibiotic resistance and virulence determinants of nasal Staphylococcus aureus isolates of healthy donkeys destined to food consumption in Tunisia.Results: Nasal swabs of 100 donkeys obtained in a large slaughterhouse in 2010 were inoculated in specific media for S. aureus and methicillin-resistant S. aureus (MRSA) recovery. S. aureus was obtained in 50% of the samples, being all of isolates methicillin-susceptible (MSSA). Genetic lineages, toxin gene profile, and antibiotic resistance mechanisms were determined in recovered isolates. Twenty-five different spa-types were detected among the 50 MSSA with 9 novel spa-types. S. aureus isolates were ascribed to agr type I (37 isolates), III (7), II (4), and IV (2). Sixteen different sequence-types (STs) were revealed by MLST, with seven new ones. STs belonging to clonal clomplex CC133 were majority. The gene tst was detected in 6 isolates and the gene etb in one isolate. Different combinations of enterotoxin, leukocidin and haemolysin genes were identified among S. aureus isolates. The egc-cluster-like and an incomplete egc-cluster-like were detected. Isolates resistant to penicillin, erythromycin, fusidic acid, streptomycin, ciprofloxacin, clindamycin, tetracycline, or chloramphenicol were found and the genes blaZ, erm(A), erm(C), tet(M), fusC were identified.Conclusions: The nares of donkeys frequently harbor MSSA. They could be reservoirs of the ruminant-associated CC133 lineage and of toxin genes encoding TSST-1 and other virulence traits with potential implications in public health. CC133 seems to have a broader host distribution than expected. © 2012 Gharsa et al.; licensee BioMed Central Ltd