Genetic Characterization of Carbapenem-Resistant Enterobacteriaceae and the Spread of Carbapenem-Resistant Klebsiella pneumonia ST340 at a University Hospital in Thailand

Carbapenem-resistant Enterobacteriaceae (CRE) has increasingly spread worldwide in the past decade. The prevalence and characteristics of CRE in Thailand are unknown. In this study, we conducted a 2-year surveillance of CRE among 12,741 clinical isolates of Enterobacteriaceae at the largest university hospital in Thailand with molecular characterization of beta-lactamase (bla) genes, including carbapenemase genes. The CRE prevalence was 1.4%. bla _KPC-13 and bla _IMP-14a were the only carbapenemase genes detected among these CRE isolates. bla _KPC-13 gene was found in a single isolate of Escherichia coli, Enterobacter cloacae and Citrobacter freundii, and bla _IMP-14a was found in four isolates of Klebsiella pneumoniae. Carbapenem-resistant K. pneumoniae (CRKP) isolates were resistant to multiple carbapenems at a higher ratio than other CRE species, and thus were further characterized for resistance phenotypes, bla genotypes and molecular epidemiology. Most CRKP isolates harboured multiple bla genes, especially those related to extended-spectrum beta-lactamases. Seven CRKP isolates were resistant to all tested carbapenems, and showed decreased ompK35 and/or ompK36 porin gene expression. Molecular typing of CRKP based on pulsed-field gel electrophoresis (PFGE) demonstrated several unrelated clones. Multilocus sequence typing (MLST) was partially concordant with PFGE results and revealed that ST340, a member of drug-resistant K. pneumoniae clonal complex 258, was the most predominant clone, followed by ST48, ST11 and ST273. The novel ST1645 was identified from this study. ST340 has neither been shown to be predominated among CRKP from other studies, nor been reported in Thailand. Therefore, it emphases a critical concern to monitor and control the spread of CRKP.     

Prevalence and Characterization of Carbapenem-Resistant Enterobacteriaceae Isolated from Mulago National Referral Hospital,Uganda

Introduction

Carbapenemases have increasingly been reported in enterobacteriaceae worldwide. Most carbapenemases are plasmid encoded hence resistance can easily spread. Carbapenem-resistant enterobacteriaceae are reported to cause mortality in up to 50% of patients who acquire bloodstream infections. We set out to determine the burden of carbapenem resistance as well as establish genes encoding for carbapenemases in enterobacteriaceae clinical isolates obtained from Mulago National Referral Hospital, Uganda.

Methods

This was a cross-sectional study with a total of 196 clinical isolates previously collected from pus swabs, urine, blood, sputum, tracheal aspirates, cervical swabs, endomentrial aspirates, rectal swabs, Vaginal swabs, ear swabs, products of conception, wound biopsy and amniotic fluid. All isolates were subjected to phenotypic carbapenemase screening using Boronic acid-based inhibition, Modified Hodge and EDTA double combined disk test. In addition, all the isolates were subjected to PCR assay to confirm presence of carbapenemase encoding genes.

Results

The study found carbapenemase prevalence of 22.4% (44/196) in the isolates using phenotypic tests, with the genotypic prevalence slightly higher at 28.6% (56/196). Over all, the most prevalent gene was blaVIM (21,10.7%), followed by blaOXA-48 (19, 9.7%), blaIMP (12, 6.1%), blaKPC (10, 5.1%) and blaNDM-1 (5, 2.6%). Among 56 isolates positive for 67 carbapenemase encoding genes, Klebsiella pneumonia was the species with the highest number (52.2%). Most 32/67(47.7%) of these resistance genes were in bacteria isolated from pus swabs.

Conclusion

There is a high prevalence of carbapenemases and carbapenem-resistance encoding genes among third generation cephalosporins resistant Enterobacteriaceae in Uganda, indicating a danger of limited treatment options in this setting in the near future.     

Mitochondrial DNA structure in the Arabian Peninsula

Background  

Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.     

Clinical Significance of Community- and Healthcare-Acquired Carbapenem-Resistant Enterobacteriaceae Isolates

This study was conducted to investigate the clinical significance, manifestations, microbiological characteristics and outcomes of carbapenem-resistant Enterobacteriaceae (CRE) isolates, and compare the clinical features of community- and healthcare-acquired CRE isolates. A total of 78 patients were identified to have CRE. Klebsiella pneumoniae was the most common pathogens (n = 42, 53.8%), followed by Enterobacter cloacae (n = 24, 30.8%), and Escherichia coli (n = 11, 14.1%). Most of the patients acquired CRE from healthcare settings (n = 55, 70.5%), and other cases got CRE from community settings (n = 23, 29.5%). Nine cases (11.5%) were classified as CRE colonization. Among the remaining 69 cases of CRE infections, pneumonia (n = 28, 40.6%) was the most common type of infections, followed by urinary tract infection (n = 24, 34.8%), and intra-abdominal infection (n = 16, 23.2%). The patients acquired CRE from community settings were more likely to be elderly, female, and had more urinary tract infections than from healthcare settings. In contrast, the patients acquired CRE from healthcare settings had more intra-abdominal infections, intra-abdominal surgery, and presence of indwelling device than from community settings. In conclusion, community-acquired CRE are not rare, and their associated clinical presentations are different from healthcare-acquired CRE.     

First dinosaur tracks from the Arabian Peninsula

Background

The evolutionary history of Mesozoic terrestrial vertebrates from the Arabian Peninsula is virtually unknown. Despite vast exposures of rocky outcrops, only a handful of fossils have yet been described from the region. Here we report a multi-taxon dinosaur track assemblage near Madar village, 47 km north of Sana''a, Republic of Yemen. This represents the first dinosaur tracksite from the Arabian Peninsula, and the only multi-taxon dinosaur ichnosite in the Middle East.

Methodology/Findings

Measurements were taken directly from trackway impressions, following standard ichnological conventions. The presence of bipedal trackmakers is evidenced by a long series of pes imprints preserving smoothly rounded posterior margins, no evidence of a hallux, bluntly rounded digit tips and digital divarication angles characteristic of ornithopod dinosaurs. Nearby, eleven parallel quadrupedal trackways document a sauropod herd that included large and small individuals traveling together. Based on the morphology of manus impressions along with a narrow-gauged stance, the quadrupedal trackways were made by non-titanosauriform neosauropods. Additional isolated tracks and trackways of sauropod and ornithopod dinosaurs are preserved nearby.

Conclusions/Significance

Taken together, these discoveries present the most evocative window to date into the evolutionary history of dinosaurs of the Arabian Peninsula. Given the limited Mesozoic terrestrial record from the region, this discovery is of both temporal and geographic significance, and massive exposures of similarly-aged outcrops nearby offer great promise for future discoveries.     

On the nature of sickle-cell disease in the Arabian Peninsula

Summary The sickle-cell gene contributes substantially to the presentation of anaemia in certain areas of the Arabian Peninsula. However, the clinical presentation of the homozygous state of Hb S is less severe than that observed in other ethnic groups, such as American negroes. In the present paper, biosynthesis studies performed on reticulocytes from heterozygotes and homozygotes for the Hb S give further indications of the mild nature of sickle-cell disease in Arabia. Comparison of two affected families, from Saudi Arabia and Jordan, showed that clinical manifestation of the disease is mirrored by the biochemical and haematological findings in affected individuals. The results are discussed in terms of the effect of co-existing thalassaemia and/or iron deficiency with Hb S. It is suggested that both genetic and acquired conditions play a role in the clinical features of the disease. The mechanisms responsible for regulation of -chain synthesis by iron (haem) deficiency are discussed.     

Geographical distribution and chorology of grasses in the Arabian Peninsula

Arid regions of Saudi Arabia occupy most of the area of the Arabian Peninsula. These areas are at the meeting position of plants from Mediterranean, Irano-Turanian, Saharo-Arabian, and Sudanian phytogegraphical regions. Geomorphology of the area reveals a wide diversity of landforms including coastal lines, desert plains, and high mountains. Grasses are well represented in the flora of Saudi Arabia and form an appropriate group for studying the relation of grass distribution, chorology, and photosynthetic pathways. In this paper, geographical distribution of C₃ and C₄ grasses was studied in an area extending between latitude 17°N and latitude 31°N. Two regions were recognized in the study area, namely; a (relatively) cold region north of latitude 24°N with ample winter rainfall, and a hot region south of latitude 24°N with scarce summer rainfall. Work involved field observations and collection of grass species in the study area. Work also depended on published carbon discrimination values of grasses and biochemical analysis of C₄ species subtypes. Climatic conditions in the study area vary considerably, and the distribution of grass species was found to follow patterns that reveal adaptive advantages of different photosynthetic pathways. Grass species in the cold northern region with ample winter rainfall are generally C₃ grasses belonging mainly to Mediterranean/Irano-Turanean chorotypes. C₃ grass species found in the southern hot region were recorded at high altitudes of southern mountains characterized by low temperatures. Grass species recorded at low altitudes in the south hot region with scarce summer rainfall were mainly C₄ grasses belonging to Tropical and Saharo-Arabian-Sudanean chorotypes. Pronounced spatial variations of temperature profoundly control the geographical distribution of C₃ and C₄ grasses. Low temperatures in the northern cold region and at high altitudes of the southern hot region limit the occurrence of C₄ grasses and shift the ecological balance in favor of C₃ grasses. Results are discussed in terms of heat sensitivity of the CO₂ carboxylating enzyme of C₃ grasses and high temperature optima for CO₂ assimilation of C₄ grasses. Results are also discussed in comparison with geographical distribution of grasses in other parts of the world.     

Removal of Carbapenem-Resistant Enterobacteriaceae (CRE) from Blood by Heparin-Functional Hemoperfusion Media

Bloodstream infections due to Carbapenem-Resistant Enterobacteriaceae (CRE) are becoming more frequent and are associated with a high mortality. At present, combination antimicrobial therapy yields the best outcomes, but treatment options are limited. Many bacteria utilize heparan sulfate to bind to human cells. We studied the ability of a biomimetic device composed of polyethylene beads with endpoint-attached heparin to bind both sensitive and (CRE) E. coli and Klebsiella pneumoniae from spiked blood samples. Greater than 90% of susceptible, E. coli, CRE E. coli and CRE Klebsiella were removed by the beads. Future studies in human bacteremia with this technology are planned.     

Autochthonous Chikungunya Transmission and Extreme Climate Events in Southern France

BackgroundExtreme precipitation events are increasing as a result of ongoing global warming, but controversy surrounds the relationship between flooding and mosquito-borne diseases. A common view among the scientific community and public health officers is that heavy rainfalls have a flushing effect on breeding sites, which negatively affects vector populations, thereby diminishing disease transmission. During 2014 in Montpellier, France, there were at least 11 autochthonous cases of chikungunya caused by the invasive tiger mosquito Aedes albopictus in the vicinity of an imported case. We show that an extreme rainfall event increased and extended the abundance of the disease vector Ae. albopictus, hence the period of autochthonous transmission of chikungunya.Conclusions/SignificanceOur empirical data suggests that heavy rainfall events did increase the risk of arbovirus transmission in Southern France in 2014 by favouring a rapid rise in abundance of vector mosquitoes. Further studies should now confirm these results in different ecological contexts, so that the impact of global change and extreme climatic events on mosquito population dynamics and the risk of disease transmission can be adequately understood.     

Population genetics of four heavily exploited shark species around the Arabian Peninsula

The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.     

New records of rodents, bats and insectivores from the Arabian Peninsula

Recent collections from diverse parts of the Arabian Peninsula include a number of new geographical records of Arabian rodents, bats and insectivores of systematic interest and providing new distributional knowledge. The material is listed systematically and discussed.     

Fungal Contamination of Non-Renewable Groundwater in the Arabian Peninsula: Assessing the Harmfulness to Humans

Most of the studies about the groundwater quality have been focused on chemical and bacterial contamination. However, fungal contamination of drinking water has been suggested as an underestimated problem. We studied 20 wells in the Arabian Peninsula, identified their fungal contamination and assessed the potential harmfulness of the fungi to humans. We identified 28 fungal species, many of them commonly known to occur in drinking water. To assess the potential role of fungi in water, we selected 15 species for a bioassay with a model bacterium Bacillus subtilis. All fungal species inhibited the growth of B. subtilis, thus showing antibacterial activity. These fungi were interpreted to secrete toxins and thus, be possibly harmful to humans. Nine of the species retained their antibacterial activity in a boiling treatment. Therefore, they cannot be disinfected by boiling. This study raises new aspects and questions about the harmfulness of the fungal contamination in drinking water to humans.     

Genetic structure of Arabian Peninsula dromedary camels revealed three geographic groups

Dromedary camels (Camelus dromedarius) are widespread in the desert and semi-desert areas of Africa, the Arabian Peninsula, some parts of southwest Asia and Australia. In the Arabian Peninsula, these well-adapted species have been classified based on their ecology into Desert camels, found mainly in the north and center of the Peninsula, Mountain camels, distributed along the west and south of the Peninsula, and Beach camels, populating the west to southwest of the Peninsula. Here, we aimed to investigate the genetic relationship between 386 camels corresponding to 12 dromedary populations from different geographical locations and ecology in the Arabian Peninsula with the genotyping of 17 microsatellite loci. No significant deviation was observed in heterozygosity, allelic richness, Fis (inbreeding coefficient) among the studied populations had a mean value of 0.5849, 4.808 and 0.04, respectively. A mean Fst (fixation index) value of 0.0304 was calculated for the various populations with the highest value obtained between racing Omani and Awarik camel populations (0.079). Both the neighbor-joining phylogenetic tree and the STRUCTURE analysis divided the populations into three different groups corresponding to their Arabian Peninsula geographic location (North, Central and West, South-West, and South-East of the Arabian Peninsula), rather than their ecological classification, with a high level of genetic admixture and gene flow among them. Investigating the genetic relationship of dromedary populations in the Arabian Peninsula can be considered as the first milestone to conserve this well-adapted species. The results obtained here need to be further validated using whole genome sequencing data.     

The ant genus Carebara Westwood in the Arabian Peninsula (Hymenoptera,Formicidae)

The ant genus Carebara of the Arabian Peninsula is revised. Carebara abuhurayri Sharaf & Aldawood, 2011 is synonymized under Carebara arabica Collingwood & van Harten, 2001. Carebara arabica is redescribed and a Neotype is fixed based on a specimen collected from southwestern Kingdom of Saudi Arabia. A new species, C. fayrouzae sp. n. is described from Saudi Arabia based on queens, major and minor workers. Keys to major and minor workers of the two Arabian Carebara species are given.     

Realizing algae value chains in arid environments: an Arabian Peninsula perspective

Algae are a promising feedstock for the sustainable production of feed, fuels, and chemicals. Especially in arid regions such as the Arabian Peninsula, algae could play a significant role in enhancing food security, economic diversification, and decarbonization. Within this context, the regional potential of algae commercialization is discussed, exploring opportunities and challenges across technical, societal, and political aspects. Climate, availability of process inputs, and funding opportunities are identified as essential strengths that increase the global competitiveness of regional algae production. Implementation challenges include climate change, securing human resources, and the vital transitioning from research to commercial scales. With balanced management, however, the region’s efforts could be the push that is necessary for algal technologies to take off globally.     

Tuberculosis Transmission among Immigrants and Autochthonous Populations of the Eastern Province of Saudi Arabia

Background

Eastern province of Saudi Arabia is an industrial zone with large immigrant population and high level of tuberculosis case notification among immigrants. The impact of immigration and current trends of tuberculosis transmission among immigrants and autochthonous population in the region had not been investigated so far using molecular tools.

Methodology

During 2009- 2011, a total of 524 Mycobacterium tuberculosis isolates were collected from the central tuberculosis reference laboratory, representing an estimated 79.2% of the culture-positive tuberculosis cases over the study period in the province. These isolates were genotyped by using 24 locus-based MIRU-VNTR typing and spoligotyping followed by first line drug susceptibility testing. The molecular clustering profiles and phylogenetic diversity of isolates were determined and compared to the geographical origins of the patients.

Principle Findings

Genotyping showed an overall predominance of Delhi/CAS (29.4%), EAI (23.8%) and Ghana (13.3%) lineages, with slightly higher proportions of Delhi/CAS among autochthonous population (33.3 %) and EAI (30.9%) among immigrants. Rate of any drug resistance was 20.2% with 2.5% of multi-drug resistance. Strain cluster analysis indicated 42 clusters comprising 210 isolates, resulting in a calculated recent transmission index of 32.1%. Overall shared cluster ratio was 78.6% while 75.8% were shared between autochthonous population and immigrant population with a predominance of immigrants from South east Asia (40.7%). In contrast, cross national transmission within the immigrant population was limited (24.2%). Younger age (15-30- p value-0.043, 16-45, p value 0.030), Saudi nationality (p value-0.004) and South East Asian origin (p value-0.011) were identified as significant predisposing factors for molecular strain clustering.

Conclusions

The high proportion of molecular clusters shared among the autochthonous and immigrant populations suggests a high permeability of tuberculosis transmission between both populations in the province. These results prompt for the need to strengthen the current tuberculosis control strategies and surveillance programs.     

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographical features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two‐band anemonefish Amphiprion bicinctus across its entire geographical range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both isolation by distance (IBD) and isolation by environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic–eutrophic gradient at around 16–20?N in the Red Sea. The other agrees with a historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of interspecific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.