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Staphylococcus aureus is a clinically important bacteria with high antimicrobial resistance (AMR) challenge globally. The emergence of methicillin-resistant Staphylococcus aureus (MRSA) clones with unique sequence types have been identified in the community showing evidence that the epidemiology of MRSA globally is changing and requires continual surveillance. We utilized whole genome sequencing to characterize two community acquired-MRSA (CA-MRSA) strains isolated from wound swabs from community-onset infections in two health facilities in Kenya. The two strains belonged to multilocus sequence type (MLST) sequence type (ST) 7460, and ST 7635. The resistance genes detected showed that the novel STs are carriers of clinically relevant resistance genes. Linezolid and mupirocin resistance was observed, yet mupirocin is not commonly used in the country. Mutations within resistance genes were also detected and the pathogenicity toward the human host matched various pathogenic global S. aureus families, e.g., S. aureus subsp. aureus USA300. Multidrug efflux transporters, important in antimicrobial resistance including restriction enzymes type I and type IV were detected. Plasmids identified showed similarities with the plasmids in other clinically significant non-staphylococcal species, such as Pseudomonas aeruginosa, Escherichia coli, Morganella morganii, and Enterococcus faecium. Both STs belong to clonal complex 8 (CC8) which is the most successful MRSA clone in Kenya. Spa type t30 to which ST 7635 belongs has not been reported in the country. The results of this study further highlight the need for epidemiological studies to reveal circulating strains and antimicrobial resistance spread between hospitals and the community. The genomic research highlights resistance to anti-staphylococcal broad-spectrum antimicrobials not used frequently in the country, jeopardizing successful MRSA treatment since most health facilities do not perform genotypic resistance tests for routine patient management. Preliminary insights into unidentified STs of CA-MRSA in Kenya show the need for molecular epidemiological surveillance studies to further understand the diversity of S. aureus in Africa.

Background: The burden of Helicobacter pylori infection (HPI) in Africa remains high with varying levels of prevalence among children and adults reported in different regions of the continent. Persistent and uneradicated HPI could result in gastric cancer, although less severe pathological outcomes have been reported among Africans – the so-called “African enigma.” Summary: Analysis of endoscopic findings of the upper gastrointestinal tract demonstrates similarities with that of patients from the West. Thus, it could be asserted that the true picture of HPI in Africa is yet to be unveiled due to several challenges including inadequate health-care system, lack of treatment guidelines and standardized protocol for diagnosis, and lack of data. This review explores the prevalence, diagnosis, treatment, and health-care system in Africa as it relates to HPI, thus providing an update and highlighting the need for an African HPI guideline. Key Messages: There is high prevalence of Helicobacter pylori infection (HPI) in Africa with an increasing burden of antibiotic resistance. Various methods including invasive and noninvasive methods are deployed in the diagnosis of HPI in Africa. There is a need for consensus on diagnosis and treatment of HPI in Africa.

Wastewater treatment plants and solid dump sites act as potential reservoirs of highly resistant bacterial strains. This study presents information on the patterns of antimicrobial resistance among pathogenic bacteria in the sewage treatment plants and solid dump site in Nairobi County, Kenya. We employed standard microbiological methods to isolate and identify bacteria from these selected sites. Members of Escherichia, Klebsiella, Serratia, Shigella, Pseudomonas, Citrobacter spp, Enterobacter, Salmonella, Staphylococcus, Bacillus, Yersinia, Vibro cholera, Providencia, Morganella and Proteus spp were isolated. Escherichia and Klebsiella recorded the highest occurrence at 13.9% and 10.3% in wastewater. Shigella, Serratia Citrobacterfreundii, Pseudomonas, Staphylococcus, Escherichia and Klebsiella recorded the highest level of occurrence at 15.1%, 14.1%, 12%, 11%, 10.4%, 10.3%, and 8.3% in dumpsite respectively. Drug sensitivity using the Disc diffusion method showed that Ampicillin, Ceftazidime, Cefotaxime, Amoxicillin, and Cefepime had the highest levels of inactivity at (68.5%, 89.5%), (64.2%, 87%), (54.5%, 80.2%), (52%, 74%) and (49.1%, 72.4%) respectively while Levofloxacin and Gentamicin showed the smallest level of antibiotic resistance at (4.8%, 4.7%) and (4.2%, 2.6%) in both sites. Members of Escherichia, Klebsiella, Proteus vulgaris, Salmonella, Pseudomonas, Shigella and Serratia showed the highest level of ESBLs production at 28.9%, 18.4%, 15.8%, 10.5%, 7.9%, 7.9%, 7.9% and 7.9% in the wastewater whereas Shigella, Escherichia, Serratia, Pseudomonas, Klebsiella, and Proteus vulgaris showed the highest level ESBLs production at 45.5%, 10.9%, 9.1%, 9.1%, 7.3% and 7.3% from the dump site. All the antibiotics tested except for Gentamicin, Chloramphenicol and Ciprofloxacin differed significantly in terms of resistance levels (p < 0.05). The study concluded that, wastewater treatment plant and dump sites bear heavy burdens of potentially virulent resistant bacterial strains which may constitute major public health hazards to scavengers and those living near these sites. There is need therefore to educate people on the use of appropriate protective materials and the settlement patterns of individuals and communities near these sites.

The burden of Helicobacter pylori infection (HPI) in Africa remains high with varying levels of prevalence among children and adults reported in different regions of the continent. Persistent and uneradicated HPI could result in gastric cancer, although less severe pathological outcomes have been reported among Africans - the so-called "African enigma."Analysis of endoscopic findings of the upper gastrointestinal tract demonstrates similarities with that of patients from the West. Thus, it could be asserted that the true picture of HPI in Africa is yet to be unveiled due to several challenges including inadequate health-care system, lack of treatment guidelines and standardized protocol for diagnosis, and lack of data. This review explores the prevalence, diagnosis, treatment, and health-care system in Africa as it relates to HPI, thus providing an update and highlighting the need for an African HPI guideline.There is high prevalence of Helicobacter pylori infection (HPI) in Africa with an increasing burden of antibiotic resistance. Various methods including invasive and noninvasive methods are deployed in the diagnosis of HPI in Africa. There is a need for consensus on diagnosis and treatment of HPI in Africa.

Additional file 10: Summary data compiled for the statistical analysis of clinical endpoints: Table S11. Summary of outcome variables for the clinical data set. Table S12. Summary of explanatory variables for the clinical data set. Statistical analyses examining differences in clinical outcome between the Klebsiella groups and species: Table S13. Odds ratio estimates from the generalized linear mixed-effects model (GLMM) for all cause death within 30 days from diagnosis. Table S14. Odds ratio estimates from the generalized linear mixed-effects model (GLMM) for ICU admission. Table S15. Hazard ratio estimates from cause-specific hazards Cox proportional hazards model for time to death within hospital after diagnosis with hospital discharge as competing event. Table S16. Estimates of the multiplicative effects from the Poisson generalized linear mixed-effects model (GLMM) for the number of medical disciplines involved. Table S17. Odds ratio estimates from the generalized linear mixed-effects model (GLMM) for the mentioning of the infection in the patient letter.

Additional file 9: Odds ratio estimates comparing Klebsiella groups and species for resistance to different antibiotic classes: Table S7. Penicillins with beta-lactamase Inhibitors. Table S8. 3rd-generation cephalosporins. Table S9. 4th-generation cephalosporins. Table S10. Aminoglycosides.

Additional file 3. Supplementary methods for: Measurement of primary metabolites. Fatty acid analysis. Statistical analysis of clinical outcome data.

In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology., Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.

Background: Sepsis is the leading cause of maternal death in sub-Saharan Africa (SSA), a region that sees some of the highest rates of maternal death and morbidity in the world. As one of the most ...

Streptococcus agalactiae is a leading cause of morbidity and mortality among neonates and causes severe infections in pregnant women and nonpregnant predisposed adults, in addition to various animal species worldwide. Still, information on the population structure of S. agalactiae and the geographical distribution of different clones is limited. Further data are urgently needed to identify particularly successful clones and obtain insights into possible routes of transmission within one host species and across species borders. We aimed to determine the population structure and virulence gene profiles of S. agalactiae strains from a diverse set of sources and geographical origins. To this end, 373 S. agalactiae isolates obtained from humans and animals from five different continents were typed by DNA microarray profiling. A total of 242 different S. agalactiae strains were identified and further analyzed. Particularly successful clonal lineages, hybridization patterns, and strains were identified that were spread across different continents and/or were present in more than one host species. In particular, several strains were detected in both humans and cattle, and several canine strains were also detected in samples from human, bovine, and porcine hosts. The findings of our study suggest that although S. agalactiae is well adapted to various hosts including humans, cattle, dogs, rodents, and fish, interspecies transmission is possible and occurs between humans and cows, dogs, and rabbits. The virulence and resistance gene profiles presented enable new insights into interspecies transmission and make a crucial contribution to the identification of suitable targets for therapeutic agents and vaccines.

Graphical abstract, Highlights • Hospital-acquired infections (HAIs) are associated with significant morbidity and mortality across the globe. • Resources outlining infection prevention and control (IPC) practices are in existence, but there are many barriers to IPC implementation in low- and middle-income countries (LMICs). • Further studies are required to evaluate simplified approaches adapted to the needs of LMICs in order to guide IPC in practice., Summary Hospital-acquired infections (HAIs) are a major concern to healthcare systems around the world. They are associated with significant morbidity and mortality, in addition to increased hospitalization costs. Recent outbreaks, including those caused by the Middle East respiratory syndrome coronavirus and Ebola virus, have highlighted the importance of infection control. Moreover, HAIs, especially those caused by multidrug-resistant Gram-negative rods, have become a top global priority. Although adequate approaches and guidelines have been in existence for many years and have often proven effective in some countries, the implementation of such approaches in low- and middle-income countries (LMICs) is often restricted due to limited resources and underdeveloped infrastructure. While evidence-based infection prevention and control (IPC) principles and practices are universal, studies are needed to evaluate simplified approaches that can be better adapted to LMIC needs, in order to guide IPC in practice. A group of experts from around the world attended a workshop held at the 17th International Congress on Infectious Diseases in Hyderabad, India in March 2016, to discuss the existing IPC practices in LMICs, and how best these can be improved within the local context.

Objectives: With increasing global interest in hospital antimicrobial stewardship (AMS) programmes, there is a strong demand for core elements of AMS to be clearly defined on the basis of principles of effectiveness and affordability. To date, efforts to identify such core elements have been limited to Europe, Australia, and North America. The aim of this study was to develop a set of core elements and their related checklist items for AMS programmes that should be present in all hospitals worldwide, regardless of resource availability. Methods: A literature review was performed by searching Medline and relevant websites to retrieve a list of core elements and items that could have global relevance. These core elements and items were evaluated by an international group of AMS experts using a structured modified Delphi consensus procedure, using two-phased online in-depth questionnaires. Results: The literature review identified seven core elements and their related 29 checklist items from 48 references. Fifteen experts from 13 countries in six continents participated in the consensus procedure. Ultimately, all seven core elements were retained, as well as 28 of the initial checklist items plus one that was newly suggested, all with >= 80% agreement; 20 elements and items were rephrased. Conclusions: This consensus on core elements for hospital AMS programmes is relevant to both high- and low-to-middle-income countries and could facilitate the development of national AMS stewardship guidelines and adoption by healthcare settings worldwide. (C) 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.