The causes of antibiotic resistance are complex and include human behaviour at many levels of society; the consequences aff ect everybody in the world. Similarities with climate change are evident. Many eff orts have been made to describe the many diff erent facets of antibiotic resistance and the interventions needed to meet the challenge. However, coordinated action is largely absent, especially at the political level, both nationally and internationally. Antibiotics paved the way for unprecedented medical and societal developments, and are today indispensible in all health systems. Achievements in modern medicine, such as major surgery, organ transplantation, treatment of preterm babies, and cancer chemotherapy, which we today take for granted, would not be possible without access to eff ective treatment for bacterial infections. Within just a few years, we might be faced with dire setbacks, medically, socially, and economically, unless real and unprecedented global coordinated actions are immediately taken. Here, we describe the global situation of antibiotic resistance, its major causes and consequences, and identify key areas in which action is urgently needed.

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Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains a serious global health concern. Since their emergence in the mid-1970s multi-drug resistant (MDR) S. Typhi now dominate drug sensitive equivalents in many regions. MDR in S. Typhi is almost exclusively conferred by self-transmissible IncHI1 plasmids carrying a suite of antimicrobial resistance genes. We identified over 300 single nucleotide polymorphisms (SNPs) within conserved regions of the IncHI1 plasmid, and genotyped both plasmid and chromosomal SNPs in over 450 S. Typhi dating back to 1958. Prior to 1995, a variety of IncHI1 plasmid types were detected in distinct S. Typhi haplotypes. Highly similar plasmids were detected in co-circulating S. Typhi haplotypes, indicative of plasmid transfer. In contrast, from 1995 onwards, 98% of MDR S. Typhi were plasmid sequence type 6 (PST6) and S. Typhi haplotype H58, indicating recent global spread of a dominant MDR clone. To investigate whether PST6 conferred a selective advantage compared to other IncHI1 plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 plasmids in a common S. Typhi host. The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.

Summary Background Antimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance. Methods 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli , our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock. Findings E coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485 samples), which varied between taxa and by foraging traits. Multiple isolates were resistant to one agent from at least seven antimicrobial classes tested for, and a single isolate was resistant to all antibiotics tested for in the study. The phenotypic diversity of antimicrobial-resistant E coli in wildlife was lower than in livestock, humans, and the environment. Within household compounds, statistical models identified two interfaces for exchange of antimicrobial resistance: between both rodents, humans and their rubbish, and seed-eating birds, humans and their rubbish; and between seed-eating birds, cattle, and bovine manure. Interpretation Urban wildlife carry a high burden of clinically relevant antimicrobial-resistant E coli in Nairobi, exhibiting resistance to drugs considered ...

Objectives: To determine the quantity and quality of bacterial and fungi on money coins and to identify those that could pose a public health risk. Design: Random sampling of coins from subjects within predetermined categories. Setting: Westlands division of Nairobi Metropolitan province. Subjects: Twenty-shilling coin samples were collected from matatu (a common commuter vehicle in Kenya) taxi conductors, greengrocers, shoe shiners, butchers, food kiosk/restaurant attendants, grocery shops attendants, roast maize vendors and school children. Forty coin samples were analysed for both the total viable content and the types of bacterial and fungal organisms. Results: Average bacterial content on the coins ranged from 2.3xl0 3 to 25.5x10 3 and fungi content from 11 to 377 colony forming units. The following potentially pathogenic bacteria were among those isolated: Escherichia coli, Klebsiella, Serratia, Enterobacter, Salmonella, Acinetobacter, Enterococci, Staphylococcus and Bacillus cereus. In addition, this is the first report of potentially pathogenic fungal isolation from money coins. Penicillium spp, Aspergillus niger, Fusarium, Rhizopus, Altenaria spp, Candida spp and Cryptococcus were isolated. Conclusion: Money coins harbour potentially pathogenic bacteria and fungi that may pose a public health risk. Hand hygiene is therefore strongly recommended, especially for those who simultaneously handle food and money.

Antibiogram patterns and chromosomal DNA typing were used to compare 151 non-typhoidal Salmonella spp. (NTS) isolated from patients and 78 from animals, environmental or food specimens obtained within or near the homes of patients with invasive salmonellosis. The majority of NTS from humans (137; 90.7%) were Salmonella enterica serotype Typhimurium (S. Typhimurium) and S. Enteritidis. Chicken specimens and feeds produced (24; 52.2%) S. Enteritidis, while S. Agona was the predominant (20; 77%) serovar among pigs and dairy cows. The majority (97; 64.2%) of NTS from humans were multidrug resistant, while NTS from cows, pigs, beef carcass swabs and sewers were fully susceptible to all antibiotics tested. Pulsed-field gel electrophoresis patterns of XbaI-digested genomic DNA of NTS from the humans and the chickens were different. However, S. Enteritidis from chickens, and S. Braenderup and S. Agona from cows and pigs were clustered together in one group. There was no significant relatedness between NTS isolates from humans and those from animals, food or the environment in close contact to humans.

Introduction: Shigatoxigenic Escherichia coli strains are food-borne bacterial pathogens that may cause haemorrhagic colitis (HC) in humans which can lead to life-threatening systemic complication, including haemolytic uremic syndrome (HUS). This study aimed to characterize and analyze virulence properties of pathogenic E. coli isolates among patients with diarrhoea from a Maasai community in Kenya. Methodology: Stool samples from 380 patients of all ages from the Kajiado and Narok districts of Kenya were investigated for the presence of enteric bacterial pathogens by conventional and molecular methods. Results: Bacterial diarrhoea was diagnosed in 141/380 (37.1%) cases, of which enterotoxigenic E. coli (ETEC) compromised 29.8%, shigatoxigenic E. coli (STEC) 24.1%, enteroaggregative E. coli (EAEC) 14.2%, enteroinvasive E. coli (EIEC) 12.8% and enteropathogenic E. coli (EPEC) 3.5%. Gene analysis for STEC virulence factors showed that 52.9% isolates carried stx1, 29.4% possessed stx2, 14.7% carried both stx1 and stx2, and 2.9% had stx2e. 23.5% isolates carried enterohaemolysin and 20.5% isolates possessed the Intimin gene. From 9 strains that exhibited adherence, 7 contained both Intimin and Haemolysin genes. Infections with Intimin-positive STEC strains (46%) were more frequent in patients with bloody diarrhoea, especially in children under 5 years of age, whereas Intimin-negative STEC infections dominated in adults. Conclusion: Although STEC infection as a cause of bloody diarrhoea has not attracted much attention as a medical problem in Kenya, our findings indicate that this is a problem that must be investigated. The 24.1% isolation rate of STEC among the Maasai is one of the highest reported rates worldwide.

Three typing methods commonly used for bacteria -phage typing, antimicrobial susceptibility and pulsed-field gel electrophoresis (PFGE) -were used to characterise 64 Salmonella enterica serotype Typhimurium isolates from individual adult patients from Nairobi, Kenya. The isolates encompassed 11 definitive phage types (DTs), which fell into eight PFGE clusters; 31.3% of isolates were either untypable or reacted nonspecifically with the phages used for typing and 26.6% were of DT 56. Plasmids of c. 100 kb were responsible for self-transferable multiresistance among the isolates. Analysis by PFGE and phage type demonstrated that multiresistant Typhimurium strains causing diarrhoea and invasive disease were multiclonal.