Genomic epidemiology of Escherichia coli:Antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

BackgroundLivestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism.MethodsWe conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock.ResultsWe detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households.ConclusionsFindings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control

Population genomics of <i>Escherichia coli</i> in livestock-keeping households across a rapidly developing urban landscape

Quantitative evidence for the risk of zoonoses and the spread of antimicrobial resistance remains lacking. Here, as part of the UrbanZoo project, we sampled Escherichia coli from humans, livestock and peri-domestic wildlife in 99 households across Nairobi, Kenya, to investigate its distribution among host species in this rapidly developing urban landscape. We performed whole-genome sequencing of 1,338 E. coli isolates and found that the diversity and sharing patterns of E. coli were heavily structured by household and strongly shaped by host type. We also found evidence for inter-household and inter-host sharing and, importantly, between humans and animals, although this occurs much less frequently. Resistome similarity was differently distributed across host and household, consistent with being driven by shared exposure to antimicrobials. Our results indicate that a large, epidemiologically structured sampling framework combined with WGS is needed to uncover strain-sharing events among different host populations in complex environments and the major contributing pathways that could ultimately drive the emergence of zoonoses and the spread of antimicrobial resistance

Genomic insights into the 2016-2017 cholera epidemic in Yemen.

Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype

Molecular characterisation of <it>Vibrio cholerae </it>O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007

<p>Abstract</p> <p>Background</p> <p>Over the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is paucity of information concerning the diversity and occurrence of mobile genetic elements in <it>Vibrio cholerae </it>strains implicated in these outbreaks. A total of 65 <it>Vibrio cholerae </it>O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs), conjugative plasmids and for their genotypic relatedness.</p> <p>Results</p> <p>All the strains were haemolytic on 5% sheep blood and positive for the <it>Vibrio cholerae </it>El Tor-specific haemolysin toxin gene (<it>hylA</it>) by PCR. They all contained <it>strB, sulII, floR </it>and the <it>dfrA1 </it>genes encoding resistance to streptomycin, sulfamethoxazole, chloramphenicol and trimethoprim respectively. These genes, together with an ICE belonging to the SXT/R391 family were transferable to the rifampicin-resistant <it>E. coli </it>C600 <it>en bloc</it>. All the strains were negative for integron class 1, 2 and 3 and for transposase gene of transposon <it>Tn</it>7 but were positive for integron class 4 and the <it>trpM </it>gene of transposon <it>Tn</it>21. No plasmids were isolated from any of the 65 strains. All the strains were also positive for all <it>V. cholera </it>El Tor pathogenic genes except the NAG- specific heat-stable toxin (<it>st</it>) gene. None of the strains were positive for virulence genes associated with the <it>V. cholerae </it>classical biotype. All the strains were positive for El Tor-specific CTXphi bacteriophage <it>rstrR </it>repressor gene (<it>CTX</it>^ET<it>Φ</it>) but negative for the Classical, Calcutta, and the Environmental repressor types. Pulse Field Gel Electrophoresis (PFGE) showed that regardless of the year of isolation, all the strains bearing the SXT element were clonally related.</p> <p>Conclusions</p> <p>This study demonstrates that the <it>V. cholerae </it>O1 strains carrying an SXT/R391-like element implicated in recent cholera outbreaks in Kenya has not changed significantly between 1994 and 2007 and are clonally related.</p

Molecular Characterisation of Vibrio Cholerae O1 Strains Carrying an SXT/R391-Like Element from Cholera Outbreaks in Kenya: 1994-2007

Journal ArticleOver the last decade, cholera outbreaks in parts of Kenya have become common. Although a number of recent studies describe the epidemiology of cholera in Kenya, there is paucity of information concerning the diversity and occurrence of mobile genetic elements in Vibrio cholerae strains implicated in these outbreaks. A total of 65 Vibrio cholerae O1 El Tor serotype Inaba isolated between 1994 and 2007 from various outbreaks in Kenya were investigated for mobile genetic elements including integrons, transposons, the integrating conjugative elements (ICEs), conjugative plasmids and for their genotypic relatedness. All the strains were haemolytic on 5% sheep blood and positive for the Vibrio cholerae El Torspecific haemolysin toxin gene (hylA) by PCR. They all contained strB, sulII, floR and the dfrA1 genes encoding resistance to streptomycin, sulfamethoxazole, chloramphenicol and trimethoprim respectively. These genes, together with an ICE belonging to the SXT/R391 family were transferable to the rifampicin-resistant E. coli C600 en bloc. All the strains were negative for integron class 1, 2 and 3 and for transposase gene of transposon Tn7 but were positive for integron class 4 and the trpM gene of transposon Tn21. No plasmids were isolated from any of the 65 strains. All the strains were also positive for all V. cholera El Tor pathogenic genes except the NAG- specific heat-stable toxin (st) gene. None of the strains were positive for virulence genes associated with the V. cholerae classical biotype. All the strains were positive for El Torspecific CTXphi bacteriophage rstrR repressor gene (CTXETΦ) but negative for the Classical, Calcutta, and the Environmental repressor types. Pulse Field Gel Electrophoresis (PFGE) showed that regardless of the year of isolation, all the strains bearing the SXT element were clonally related. This study demonstrates that the V. cholerae O1 strains carrying an SXT/R391-like element implicated in recent cholera outbreaks in Kenya has not changed significantly between 1994 and 2007 and are clonally related

Extrusion texturization of cricket flour and soy protein isolate: Influence of insect content, extrusion temperature, and moisture-level variation on textural properties

Due to the increasing global population and unsustainable meat production, the future supply of animal-derived protein is predicted to be insufficient. Currently, edible insects are considered as a potential and “novel” source of protein in the development of palatable meat analogues. This research used high moisture extrusion cooking (HMEC), at a screw speed of 150 rpm, to produce meat analogues using full- or low-fat cricket flours (CF) and soy protein isolate (SPI). Effects of water flow rate (WFR), cooking temperature (9 and 10 ml/min; 120, 140, and 160°C, respectively), and CF inclusions levels of 0, 15, 30, and 45% were analyzed. Cooking temperature and CF inclusion had a significant effect (p &lt; .05) on both tensile stress in parallel and perpendicular directions, while WFR had no significant effect (p = .3357 and 0.7700), respectively. The tensile stress increased with temperature but decreased with CF inclusion at both WFRs. Comparatively, the tensile stress was stronger at WFR of 9 ml/min than at 10 ml/min; however, the tensile stress in parallel was mostly greater than tensile stress in perpendicular directions. Fibrous meat analogues with high anisotropic indices (AIs) of up to 2.80 were obtained, particularly at WFR of 10 ml/min and at inclusions of 30% low-fat CF. By controlling HMEC conditions, full-/low-fat cricket flours at 15% and 30% inclusions can offer an opportunity to partially substitute SPI in manufacturing of fibrous meat analogues

Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin

Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013. </jats:p

Typhoid in Kenya Is Associated with a Dominant Multidrug-Resistant Salmonella enterica Serovar Typhi Haplotype That Is Also Widespread in Southeast Asia▿ †

In sub-Saharan Africa, the burden of typhoid fever, caused by Salmonella enterica serovar Typhi, remains largely unknown, in part because of a lack of blood or bone marrow culture facilities. We characterized a total of 323 S. Typhi isolates from outbreaks in Kenya over the period 1988 to 2008 for antimicrobial susceptibilities and phylogenetic relationships using single-nucleotide polymorphism (SNP) analysis. There was a dramatic increase in the number and percentage of multidrug-resistant (MDR) S. Typhi isolates over the study period. Overall, only 54 (16.7%) S. Typhi isolates were fully sensitive, while the majority, 195 (60.4%), were multiply resistant to most commonly available drugs—ampicillin, chloramphenicol, tetracycline, and cotrimoxazole; 74 (22.9%) isolates were resistant to a single antimicrobial, usually ampicillin, cotrimoxazole, or tetracycline. Resistance to these antibiotics was encoded on self-transferrable IncHI1 plasmids of the ST6 sequence type. Of the 94 representative S. Typhi isolates selected for genome-wide haplotype analysis, sensitive isolates fell into several phylogenetically different groups, whereas MDR isolates all belonged to a single haplotype, H58, associated with MDR and decreased ciprofloxacin susceptibility, which is also dominant in many parts of Southeast Asia. Derivatives of the same S. Typhi lineage, H58, are responsible for multidrug resistance in Kenya and parts of Southeast Asia, suggesting intercontinental spread of a single MDR clone. Given the emergence of this aggressive MDR haplotype, careful selection and monitoring of antibiotic usage will be required in Kenya, and potentially other regions of sub-Saharan Africa

Molecular Epidemiology of Geographically Dispersed Vibrio cholerae, Kenya, January 2009–May 2010

Isolates represent multiple genetic lineages, a finding consistent with multiple emergences from endemic reservoirs