The microbiomes of blowflies and houseflies as bacterial transmission reservoirs

Genotypic and phenotypic adaptation of pathogens: lesson from the genus Bordetella

PURPOSE OF REVIEW

To relate genomic changes to phenotypic adaptation and evolution from environmental bacteria to obligate human pathogens, focusing on the examples within Bordetella species.

RECENT FINDINGS

Recent studies showed that animal-pathogenic and human-pathogenic Bordetella species evolved from environmental ancestors in soil. The animal-pathogenic Bordetella bronchiseptica can hijack the life cycle of the soil-living amoeba Dictyostelium discoideum, surviving inside single-celled trophozoites, translocating to the fruiting bodies and disseminating along with amoeba spores. The association with amoeba may have been a 'training ground' for bacteria during the evolution to pathogens. Adaptation to an animal-associated life style was characterized by decreasing metabolic versatility and genome size and by acquisition of 'virulence factors' mediating the interaction with the new animal hosts. Subsequent emergence of human-specific pathogens, such as Bordetella pertussis from zoonoses of broader host range progenitors, was accompanied by a dramatic reduction in genome size, marked by the loss of hundreds of genes.

SUMMARY

The evolution of Bordetella from environmental microbes to animal-adapted and obligate human pathogens was accompanied by significant genome reduction with large-scale gene loss during divergence.

Highly diverse root endophyte bacterial community is driven by growth substrate and is plant genotype-independent in common bean (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet with an essential role in sustainable agriculture mostly based on the symbiotic relationship established between this legume and rhizobia, a group of bacteria capable of fixing atmospheric nitrogen in the roots nodules. Moreover, root-associated bacteria play an important role in crop growth, yield, and quality of crop products. This is particularly true for legume crops forming symbiotic relationships with rhizobia, for fixation of atmospheric N₂. The main objective of this work is to assess the substrate and genotype effect in the common bean (Phaseolus vulgaris L.) root bacterial community structure. To achieve this goal, we applied next-generation sequencing coupled with bacterial diversity analysis. The analysis of the bacterial community structures between common bean roots showed marked differences between substrate types regardless of the genotype. Also, we were able to find several phyla conforming to the bacterial community structure of the common bean roots, mainly composed by Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. Therefore, we determined that the substrate type was the main factor that influenced the bacterial community structure of the common bean roots, regardless of the genotype, following a substrate-dependent pattern. These guide us to develop efficient and sustainable strategies for crop field management based on the soil characteristics and the bacterial community that it harbors.

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors

Louse flies (Diptera: Hippoboscidae) are obligate ectoparasites that often cause behavioral, pathogenic, and evolutionary effects on their hosts. Interactions between ectoparasites and avian hosts, especially migrating taxa, may influence avian pathogen spread in tropical and temperate ecosystems and affect long-term survival, fitness and reproductive success. The purpose of this study was to characterize the vector-associated microbiome of ectoparasitic louse flies feeding on migrating raptors over the fall migration period. Surveys for louse flies occurred during fall migration (2015-2016) at a banding station in Pennsylvania, United States; flies were collected from seven species of migrating raptors, and we sequenced their microbial (bacteria and archaea) composition using high-throughput targeted amplicon sequencing of the 16S rRNA gene (V4 region). All louse flies collected belonged to the same species, Icosta americana. Our analysis revealed no difference in bacterial communities of louse flies retrieved from different avian host species. The louse fly microbiome was dominated by a primary endosymbiont, suggesting that louse flies maintain a core microbial structure despite receiving blood meals from different host species. Thus, our findings highlight the importance of characterizing both beneficial and potentially pathogenic endosymbionts when interpreting how vector-associated microbiomes may impact insect vectors and their avian hosts.

Potential bacterial biomarkers for insect colonization in forensic cases: preliminary quantitative data on Wohlfahrtiimonas chitiniclastica and Ignatzschineria indica dynamics

For the last decades, forensic microbiology became an emerging complementary tool in criminalistics. Although the insect-microbe interactions regarding pathogen transmission were extensively studied, only scarce information is available on bacterial transfer from necrophagous insects to host tissues. Our data provides the first report on the occurrence of Wohlfahrtiimonas chitiniclastica and Ignatzschineria indica in Lucilia illustris Meigen, 1826 (Diptera: Calliphoridae), and the quantitative dynamics of the two bacterial species along the insect life-stages and transfer to beef and pork host tissues using qPCR gyrase b specific primers. The content of both bacterial species increased along the insect life stages. W. chitiniclastica was detected in all developmental stages independent of the feeding substrate. I. indica was measurable with 10² gene copies ng⁻¹ DNA threshold starting from the third instar larvae when feeding on beef, and from the egg stage with a 10²× higher representation when using the pork substrate. The transfer of bacterial species to both tissues occurred after 3 colonization days except for I. indica that was visible in beef liver only during day 5. Considering the utilization of pork tissues as human analogues, these quantitative microbial dynamics data provides first insect-specific bacterial candidates as potential colonization biomarkers in forensic investigations.

New Insights Into Culturable and Unculturable Bacteria Across the Life History of Medicinal Maggots Lucilia sericata (Meigen) (Diptera: Calliphoridae)

Because of the nutritional ecology of dung- and carrion-feeding, bacteria are the integral part of Lucilia sericata life cycle. Nevertheless, the disinfected larvae of the blowfly are applied to treat human chronic wounds in a biosurgery named maggot debridement therapy (MDT). To realize the effects of location/diet on the gut bacteria, to infer the role of bacteria in the blowfly ecology plus in the MDT process, and to disclose bacteria circulating horizontally in and vertically between generations, bacterial communities associated with L. sericata specimens from various sources were investigated using culture-based and culture-independent methods. In total, 265 bacteria, including 20 families, 28 genera, and 40 species, were identified in many sources of the L. sericata. Culture-dependent method identified a number of 144 bacterial isolates, including 21 species, in flies reared in an insectary; specimens were collected from the field, and third-instar larvae retrieved from chronic wounds of patients. Metagenetic approach exposed the occurrences of 121 operational taxonomic units comprising of 32 bacterial species from immature and adult stages of L. sericata. Gammaproteobacteria was distinguished as the dominant class of bacteria by both methods. Bacteria came into the life cycle of L. sericata over the foods and transovarially infected eggs. Enterococcus faecalis, Myroides phaeus, Proteus species, Providencia vermicola, and Serratia marcescens were exchanged among individuals via transstadial transmission. Factors, including diets, feeding status, identification tool, gut compartment, and life stage, governed the bacteria species. Herein, we reemphasized that L. sericata is thoroughly connected to the bacteria both in numerous gut compartments and in different life stages. Among all, transstadially transmitted bacteria are underlined, indicating the lack of antagonistic effect of the larval excretions/secretions on these resident bacteria. While the culture-dependent method generated useful data on the viable aerobic gut bacteria, metagenomic method enabled us to identify bacteria directly from the tissues without any need for cultivation and to facilitate the identification of anaerobic and unculturable bacteria. These findings are planned to pave the way for further research to determine the role of each bacterial species/strain in the insect ecology, as well as in antimicrobial, antibiofilm, anti-inflammatory, and wound healing activities.

The fly factor phenomenon is mediated by interkingdom signaling between bacterial symbionts and their blow fly hosts

We tested the recent hypothesis that the "fly factor" phenomenon (food currently or previously fed on by flies attracts more flies than the same type of food kept inaccessible to flies) is mediated by bacterial symbionts deposited with feces or regurgitated by feeding flies. We allowed laboratory-reared black blow flies, Phormia regina (Meigen), to feed and defecate on bacterial Luria-Bertani medium solidified with agar, and isolated seven morphologically distinct bacterial colonies. We identified these using matrix-assisted laser desorption/ionization mass spectrometry and sequencing of the 16S rRNA gene. In two-choice laboratory experiments, traps baited with cultures of Proteus mirabilis Hauser, Morganella morganii subsp. sibonii Jensen, or Serratia marcescens Bizio, captured significantly more flies than corresponding control jars baited with tryptic soy agar only. A mixture of seven bacterial strains as a trap bait was more attractive to flies than a single bacterial isolate (M. m. sibonii). In a field experiment, traps baited with agar cultures of P. mirabilis and M. m. sibonii in combination captured significantly more flies than traps baited with either bacterial isolate alone or the agar control. As evident by gas chromatography-mass spectrometry, the odor profiles of bacterial isolates differ, which may explain the additive effect of bacteria to the attractiveness of bacterial trap baits. As "generalist bacteria," P. mirabilis and M. m. sibonii growing on animal protein (beef liver) or plant protein (tofu) are similarly effective in attracting flies. Bacteria-derived airborne semiochemicals appear to mediate foraging by flies and to inform their feeding and oviposition decisions.

In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae)

Avian influenza virus (AIV) H9N2 emerged in the 1990s as an economically important disease in poultry and occasionally infects humans and other mammals. The aim of this study was to evaluate the acquisition and retention of H9N2 AIV on and within the house fly, Musca domestica (Linnaeus 1758), under laboratory conditions. In first experiment, 100 adult house flies were divided into control and treatment groups equally. Treatment group was fed with a meal containing H9N2 virus, while control group was supplied with an identical meal without virus. Fifteen minutes after exposure in each group, flies were washed twice to remove surface particles, disinfected and then homogenized for testing. The two external body surface washes and the homogenate samples were tested for H9N2 to distinguish exterior from interior viral load. Second experiment was performed likewise but five flies from each group were taken at 0, 6, 24, 48, 72, 96, and 120 h post-exposure. All samples were subjected to real-time reverse-transcription polymerase chain reaction (RRT-PCR) for detecting H9-Specific viral RNA. Results of the first experiment showed that viral RNA was detectable in both of external surface and homogenates samples. Second experiment revealed that persistence of H9N2 AIVs on external body surface and within the body of M. domestica were 24 and 96 h, respectively. Moreover, viral RNAs concentration declined during the time after exposure to AIV H9N2 either outside or within house flies. Overall, house fly was able to acquire and preserve H9N2 AIV experimentally, which may contribute the spread of virus among poultry farms.

Biogeography of American Northwest Hot Spring A/B-Lineage Synechococcus Populations

Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B'-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by <50 km than among springs separated by >50 km, and springs separated by >800 km shared sequence variants only rarely. Phylogenetic analyses provided evidence for endemic lineages that could be related to geographic isolation and/or geochemical differences on regional scales. Ecotype Simulation 2 was used to predict putative ecotypes (ecologically distinct populations), and their membership, and canonical correspondence analysis was used to examine the geographical and geochemical bases for variation in their distribution. Across the range of Oregon and Yellowstone, geographical separation explained the largest percentage of the differences in distribution of ecotypes (9.5% correlated to longitude; 9.4% to latitude), with geochemical differences explaining the largest percentage of the remaining differences in distribution (7.4-9.3% correlated to magnesium, sulfate, and sulfide). Among samples within the Greater Yellowstone Ecosystem, geochemical differences significantly explained the distribution of ecotypes (6.5-9.3% correlated to magnesium, boron, sulfate, silicon dioxide, chloride, and pH). Nevertheless, differences in the abundance and membership of ecotypes in Yellowstone springs with similar chemistry suggested that allopatry may be involved even at local scales. Synechococcus populations have diverged both by physical isolation and physiochemical differences, and populations on surprisingly local scales have been evolving independently.

Direct and indirect effects of forest management on tree-hole inhabiting aquatic organisms and their functional traits

Ecological communities in forests have been shown to be strongly affected by forest management but a detailed understanding of how different components of management affect insect communities directly and indirectly via environmental variables, how management influences functional trait diversity and composition, and whether these results can be transferred to other functional groups besides insects (e.g. bacteria or nematodes) is still missing. To address these questions we used water-filled tree holes, which provide habitats for insect larvae and other aquatic organisms in forests, as a model system. We mapped all water-filled tree holes in 75 forest plots (1 ha) under different management intensity in three regions of Germany. We measured structural and climatic conditions at different spatial scales, sampled insect communities in 123 tree holes and bacterial and nematode communities in a subset of these. We found that forest management in terms of harvesting intensity and the proportion of non-natural tree species (species not part of the natural vegetation at the sites) negatively affected tree-hole abundance. An increased proportion of non-natural tree species had a positive direct effect on insect richness and functional diversity in the tree holes. However, a structural equation model showed that increasing management intensity had negative indirect effects on insect abundance and richness, operating via environmental variables at stand and tree-hole scale. Functional diversity and trait composition of insect communities similarly responded to changes in management-related variables. In contrast to insects, bacterial and nematode richness were not directly impacted by forest management but by other environmental variables. Our results suggest that forest management may strongly alter insect communities of tree holes, while nematodes and bacteria seem less affected. Most effects in our study were indirect and negative, indicating that management has often complex consequences for forest communities that should be taken into account in forest management schemes.

Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms

Background

Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear. We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used 16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms.

Results

Using GBS we identified 18,000 SNPs across 400 individuals sampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time.

Conclusion

We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next-generation sequencing (NGS) techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.

Exogenous and endogenous microbiomes of wild-caught Phormia regina (Diptera: Calliphoridae) flies from a suburban farm by 16S rRNA gene sequencing

The black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae) is one of the most abundant carrion flies in North America. Calliphorids are important in agriculture and animal production, veterinary sciences, forensics and medical entomology. While the role of flies in the epidemiology of human and animal diseases is an active area of research, little is known about the microorganisms associated with these insects. We examined the diversity of wild-caught black blow fly endogenous (internal body) and exogenous (external body) microbial communities using 16S rRNA gene sequencing. Overall, 27 phyla, 171 families and 533 genera were detected, and diversity was significantly higher (P < 0.05) on external body surfaces. At the genus level, Dysgonomonas, Ignatzschineria, Acinetobacter, Vagococcus, Myroides, and Wohlfahrtiimonas were predominant. Cloning and sequencing of nearly full-length fragments of the 16S rRNA gene showed that some of the species identified are known to be pathogenic to humans, animals, and plants. Myroides odoratimimus and Acinetobacter radioresistens are well-known, multi-drug resistant bacteria. These results provide a snapshot of the microbial communities harbored by adult black blow flies and call for more comprehensive studies to better characterize the role these flies may play in the transmission of pathogenic microorganisms.

A survey of bacteria associated with various life stages of primary colonizers: Lucilia sericata and Phormia regina

Blow flies are common primary colonizers of carrion, play an important role in the transfer of microbes between environments, and serve as a vector for many human pathogens. While some investigation has begun regarding the bacteria associated with different life stages of blow flies, a well replicated study is currently not available for the majority of blow flies. This study investigated bacteria associated with successive life stages of blow fly species Lucilia sericata and Phormia regina. A total of 38 samples were collected from four true replicates of L. sericata and P. regina. Variable region four (V4) of 16S ribosomal DNA (16S rDNA) was amplified and sequenced on MiSeq FGx sequencing platform using universal 16S rDNA primers and dual-index sequencing strategy. Bacterial communities associated with different life stages of L. sericata and P. regina didn't differ significantly from each other. In both blow fly species, Bacilli (e.g., Lactococcus) and Gammaproteobacteria (e.g., Providencia) constituted >95% of all bacterial classes across all life stages. At the genus level, Vagococcus and Leuconostoc were present at relatively high abundances in L. sericata whereas Yersinia and Proteus were present at comparatively high abundances in P. regina. Overall, information on bacterial structures associated with various life stages of blow flies can help scientists in better understanding or management of vector-borne pathogen dispersal and in increasing the accuracy of microbial evidence based postmortem interval (PMI) prediction models.

Relationship between African Biogeographical Ancestry and Helicobacter pylori infection in children of a large Latin American urban center

BACKGROUND AND AIM

The relationship between race/ethnicity and H pylori infection has been extensively reported, with a higher prevalence of infection observed in black individuals. Whether such differences are due to genetic factors underlying African ancestry remains to be clarified. In the present study, we evaluated the association between the proportion of individual African ancestry and H pylori infection in a sample of 1046 children living in a large Latin American urban center.

MATERIALS AND METHODS

Estimation of individual biogeographical ancestry was based on 370,539 SNPs and performed using the ADMIXTURE software. Multivariate logistic regression models and mediation analysis considering the influence of previously recognized socioenvironmental risk factors to H pylori infection were performed. All analyses were conducted using the statistical package STATA v.14.0.

RESULTS

Each 10% increase in the proportion of individual African ancestry was positively and independently associated with H pylori infection in our population (adjusted OR = 1.22, 95% CI = 1.10-1.36, P < .001). Mediation analysis demonstrated that only 9.23% of the effect of the individual African ancestry on H pylori infection was explained by factors such as household income, the absence of street paving and crowding.

CONCLUSIONS

The results suggest that genetic variants that covariate with African ancestry may explain an important part of the racial differences observed for the prevalence of H pylori infection.

Fly foregut and transmission of microbes

Two areas of research that have greatly increased in attention are: dipterans as vectors and the microbes they are capable of vectoring. Because it is the front-end of the fly that first encounters these microbes, this review focuses on the legs, mouthparts, and foregut, which includes the crop as major structures involved in dipteran vectoring ability. The legs and mouthparts are generally involved in mechanical transmission of microbes. However, the crop is involved in more than just mechanical transmission, for it is within the lumen of the crop that microbes are taken up with the meal of the fly, stored, and it is within the lumen that horizontal transmission of bacterial resistance has been demonstrated. In addition to storage of microbes, the crop is also involved in depositing the microbes via a process known as regurgitation. Various aspects of crop regulation are discussed and specific examples of crop involvement with microorganisms are discussed. The importance of biofilm and biofilm formation are presented, as well as, some physical parameters of the crop that might either facilitate or inhibit biofilm formation. Finally, there is a brief discussion of dipteran model systems for studying crop microbe interactions.

Microbial communities of the house fly Musca domestica vary with geographical location and habitat

House flies (Musca domestica) are widespread, synanthropic filth flies commonly found on decaying matter, garbage, and feces as well as human food. They have been shown to vector microbes, including clinically relevant pathogens. Previous studies have demonstrated that house flies carry a complex and variable prokaryotic microbiota, but the main drivers underlying this variability and the influence of habitat on the microbiota remain understudied. Moreover, the differences between the external and internal microbiota and the eukaryotic components have not been examined. To obtain a comprehensive view of the fly microbiota and its environmental drivers, we sampled over 400 flies from two geographically distinct countries (Belgium and Rwanda) and three different environments-farms, homes, and hospitals. Both the internal as well as external microbiota of the house flies were studied, using amplicon sequencing targeting both bacteria and fungi. Results show that the house fly's internal bacterial community is very diverse yet relatively consistent across geographic location and habitat, dominated by genera Staphylococcus and Weissella. The external bacterial community, however, varies with geographic location and habitat. The fly fungal microbiota carries a distinct signature correlating with the country of sampling, with order Capnodiales and genus Wallemia dominating Belgian flies and genus Cladosporium dominating Rwandan fly samples. Together, our results reveal an intricate country-specific pattern for fungal communities, a relatively stable internal bacterial microbiota and a variable external bacterial microbiota that depends on geographical location and habitat. These findings suggest that vectoring of a wide spectrum of environmental microbes occurs principally through the external fly body surface, while the internal microbiome is likely more limited by fly physiology.

Aedes spp. and Their Microbiota: A Review

Aedes spp. are a major public health concern due to their ability to be efficient vectors of dengue, Chikungunya, Zika, and other arboviruses. With limited vaccines available and no effective therapeutic treatments against arboviruses, the control of Aedes spp. populations is currently the only strategy to prevent disease transmission. Host-associated microbes (i.e., microbiota) recently emerged as a promising field to be explored for novel environmentally friendly vector control strategies. In particular, gut microbiota is revealing its impact on multiple aspects of Aedes spp. biology, including vector competence, thus being a promising target for manipulation. Here we describe the technological advances, which are currently expanding our understanding of microbiota composition, abundance, variability, and function in the two main arboviral vectors, the mosquitoes Aedes aegypti and Aedes albopictus. Aedes spp. microbiota is described in light of its tight connections with the environment, with which mosquitoes interact during their various developmental stages. Unraveling the dynamic interactions among the ecology of the habitat, the mosquito and the microbiota have the potential to uncover novel physiological interdependencies and provide a novel perspective for mosquito control.

Apibacter muscae sp. nov., a novel bacterial species isolated from house flies

We describe the isolation and characterization of three bacterial isolates from the common house fly, Musca domestica, caught in Londerzeel, Belgium and Huye District, Rwanda. Although isolated from distinct geographical locations, the strains show >99 % identical 16S rRNA gene sequences and are <95 % identical to type strains of Apibacter species. Whole-genome sequences were obtained for all three strains. The genomes are 2.4-2.5 Mb with a G+C content of ~30.3 mol%. Bacteriological and biochemical analysis of the strains demonstrate distinctly different characteristics compared to known Apibacter species. Particularly, the three strains investigated in this study can be distinguished from the known Apibacter species (Apibacter mensalisand Apibacter adventoris) through urease and β-glucosidase activities. Whole-cell fatty acid methyl ester analysis shows that the fatty acid composition of the novel strains is also unique. On the basis of phylogenetic, genotypic and phenotypic data, we propose to classify these isolates as representatives of a novel species of the genus Apibacter, Apibacter muscae sp. nov., in reference to its prevalence in house flies, with strain G8^T (=LMG 30898^T=DSM 107922^T) as the type strain.

Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli Isolated from Flies in the Urban Center of Berlin, Germany

Background: The monitoring of antimicrobial resistance (AMR) in microorganisms that circulate in the environment is an important topic of scientific research and contributes to the development of action plans to combat the spread of multidrug-resistant (MDR) bacteria. As a synanthropic vector for multiple pathogens and a reservoir for AMR, flies can be used for surveillance. Methods: We collected 163 flies in the inner city of Berlin and examined them for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli genotypically and phenotypically. Results: The prevalence of ESBL-producing E. coli in flies was 12.9%. Almost half (47.6%) of the ESBL-positive samples showed a co-resistance to ciprofloxacin. Resistance to carbapenems or colistin was not detected. The predominant ESBL-type was CTX-M-1, which is associated with wildlife, livestock, and companion animals as a potential major source of transmission of MDR E. coli to flies. Conclusions: This field study confirms the permanent presence of ESBL-producing E. coli in an urban fly population. For continuous monitoring of environmental contamination with multidrug-resistant (MDR) bacteria, flies can be used as indicators without much effort.

Helicobacter pullorum in broiler chickens and the farm environment: A one health approach

Aim: This study aimed to investigate the occurrence of Helicobacter pullorum in broiler chickens and their farm environment. Materials and Methods: The ceca from 100 broiler chickens from ten farms were sampled from processing sites or markets. The cecal contents were aseptically collected from each cecum and cultured. The farms were visited, and environmental samples were collected which included water, house flies, floor swabs and soils in chicken houses. Results: H. pullorum was present in 51% of the broilers; 17.5% of the flies were found to carry H. pullorum and Campylobacter spp., 30% of house floors were positive, while all water samples were negative. Conclusion: Flies could have picked up the organisms from the chickens' feces and/or the environment of the chicken houses or they could be one of the sources in the spread of the organisms. This study also showed that broiler chickens are potential reservoirs for H. pullorum and may serve as a source of infection for humans through the food chain.

Spatial and Temporal Variation of the Blowflies Community (Diptera: Calliphoridae) From an Urban Area in Northern South America

Blowflies (Diptera: Calliphoridae) are necrophagous flies with ecological, medical, veterinary, and forensic importance. These flies carry pathogens that they spread to animals and humans, and produce myiasis. Furthermore, they are useful tools in forensic science as indicators of postmortem intervals, and in biomedicine they are successfully used in larval therapy. This study aimed to assess the spatiotemporal variation of the blowflies community from the urban area of Sincelejo City, located in the Colombian Caribbean region. Samplings were conducted from May 2012 to April 2013, using Van Someren Rydon-traps baited with bovine meat, fish, and chicken that decomposed for 48 h. Six species were registered, Cochliomyia macellaria (Fabricius, 1775) was the most abundant, followed by Lucilia eximia (Wiedemann, 1819) and Chrysomya albiceps (Wiedemann, 1819), while Chloroprocta idioidea (Robineau-Desvoidy, 1830), Chrysomya megacephala (Fabricius, 1794), and Lucilia cuprina (Wiedemann, 1830) presented the least individuals. The blowflies community did not change significantly throughout the sampling months or between the periods of low or high rainfall, nor was it influenced by weather variables. Although the species composition was the same in all sampled localities, species abundances presented significant differences. The possible causes of this pattern are discussed herein. Sex ratios were female biased for all the recorded species, except C. idioidea. Our findings provide the first assessment of the blowflies community from the urban area of Sincelejo City.

Toxicity and oviposition deterrence of essential oils of Clinopodium nubigenum and Lavandula angustifolia against the myiasis-inducing blowfly Lucilia sericata

Cutaneous myiasis is a severe worldwide medical and veterinary issue. In this trial the essential oil (EO) of the Andean medicinal plant species Clinopodium nubigenum (Kunth) Kuntze was evaluated for its bioactivity against the myiasis-inducing blowfly Lucilia sericata (Meigen) (Diptera Calliphoridae) and compared with that of the well-known medicinal plant species Lavandula angustifolia Mill. The EOs were analysed and tested in laboratory for their oviposition deterrence and toxicity against L. sericata adults. The physiology of EO toxicity was evaluated by enzymatic inhibition tests. The antibacterial and antifungal properties of the EOs were tested as well. At 0.8 μL cm^-2, both EOs completely deterred L. sericata oviposition up to 3 hours. After 24 h, the oviposition deterrence was still 82.7% for L. angustifolia and the 89.5% for C. nubigenum. The two EOs were also toxic to eggs and adults of L. sericata. By contact/fumigation, the EOs, the LC₅₀ values against the eggs were 0.07 and 0.48 μL cm^-2 while, by topical application on the adults, LD₅₀ values were 0.278 and 0.393 μL per individual for C. nubigenum and L. angustifolia EOs, respectively. Inhibition of acetylcholine esterase of L. sericata by EOs (IC₅₀ = 67.450 and 79.495 mg L^-1 for C. nubigenum and L. angustifolia, respectively) suggested that the neural sites are targets of the EO toxicity. Finally, the observed antibacterial and antifungal properties of C. nubigenum and L. angustifolia EOs suggest that they could also help prevent secondary infections.

Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis

We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach that we used is that data analysis was time-consuming and specialized bioinformatics expertise was required, both of which are barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can interpret shotgun metagenomic data are emerging. In this study, we evaluated the CosmosID bioinformatics platform using shotgun metagenomic sequencing data derived from 408 sonicate fluid samples from our prior study with the goal of evaluating the platform vis-à-vis bacterial detection and antibiotic resistance gene detection for predicting staphylococcal antibacterial susceptibility. Samples were divided into a derivation set and a validation set, each consisting of 204 samples; results from the derivation set were used to establish cutoffs, which were then tested in the validation set for identifying pathogens and predicting staphylococcal antibacterial resistance. Metagenomic analysis detected bacteria in 94.8% (109/115) of sonicate fluid culture-positive PJIs and 37.8% (37/98) of sonicate fluid culture-negative PJIs. Metagenomic analysis showed sensitivities ranging from 65.7 to 85.0% for predicting staphylococcal antibacterial resistance. In conclusion, the CosmosID platform has the potential to provide fast, reliable bacterial detection and identification from metagenomic shotgun sequencing data derived from sonicate fluid for the diagnosis of PJI. Strategies for metagenomic detection of antibiotic resistance genes for predicting staphylococcal antibacterial resistance need further development.

A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.

The Clean India Mission: Public and animal health benefits

The Clean India Mission is a national campaign that aims for complete elimination of open defecation from the country. In India, 564 million people do not have access to toilets and defecate in the open environment. The 'Millennium development goals' have given increased weightage to elimination of open defecation for improving health, nutrition and productivity of developing country populations. The Indian economy bears an estimated annual total loss (in terms of health, education, access time and tourism) of US$ 54 billion due to lack of toilets, poor hygiene and over US$ 38.5 billion in treatment costs for diseases occurring due to poor hygiene. Out of 1415 human pathogens, at least more than 10% of pathogens are transmitted through the faecal-oral route. The practice of open defecation helps pathogens persist in the environment and cause diseases. This review focuses on the current status and harms of open defecation, as well as the public and animal health benefits of implementing 'The Clean India Mission' in India.

Epidemiology of Helicobacter pylori infection

This review provides the most recent data concerning the epidemiology of Helicobacter pylori infection. Overall, the trend of declining prevalence of H. pylori infection is continuing, with major evidence available from studies in Europe. However, in some parts of the world, for example, in some countries in the Middle East, the prevalence has remained relatively stable. A number of systematic reviews and meta-analyses have been published during the past year indicating the lowest prevalence rates of the infection in Oceania (24.4%), the highest in Africa (79.1%), and the global annual recurrence rate of H. pylori (4.3%). The recurrence rates were found to be directly related to the human development index and prevalence of infection. Several studies have addressed the correlation between H. pylori infection and sociodemographic conditions, source of drinking water and dietary factors. A hypothesis on the role of insects and yeasts in transmitting H. pylori has been suggested and addressed. Helicobacter sp. have been found in flow flies in Brazil. So far there is no evidence available that H. pylori may survive and persist on the outer body of the fly.

Carrier flies of multidrug-resistant Escherichia coli as potential dissemination agent in dairy farm environment

The life cycle of synanthropic flies and their behavior, allows them to serve as mechanical vectors of several pathogens. Given that flies can carry multidrug-resistant (MDR) bacteria, this study aimed to investigate the spread of genes of antimicrobial resistance in Escherichia coli isolated from flies collected in two dairy farms in Brazil. Besides antimicrobial resistance determinants, the presence of virulence genes related to bovine colibacillosis was also assessed. Of 94 flies collected, Musca domestica was the most frequently found in the two farms. We isolated 198 E. coli strains (farm A=135 and farm B=63), and >30% were MDR E. coli. We found an association between bla_TEM and phenotypical resistance to ampicillin, or chloramphenicol, or tetracycline; and bla_CTX-M and resistance to cefoperazone. A high frequency (86%) of phylogenetic group B1 among MDR strains and the lack of association between multidrug resistance and virulence factors suggest that antimicrobial resistance possibly is associated with the commensal bacteria. Clonal relatedness of MDR E. coli performed by Pulsed-Field Gel Electrophoresis showed wide genomic diversity. Different flies can carry clones, but with distinct antimicrobial resistance pattern. Sanger sequencing showed that the same class 1 integron arrangement is displayed by apparently unrelated strains, carried by different flies. Our conjugation results indicate class 1 integron transfer associated with tetracycline resistance. We report for the first time, in Brazil, that MDR E. coli is carried by flies in the milking environment. Therefore, flies can act as carriers for MDR strains and contribute to dissemination routes of antimicrobial resistance.

Soft Rot Enterobacteriaceae Are Carried by a Large Range of Insect Species in Potato Fields

Pathogenic soft rot Enterobacteriaceae (SRE) belonging to the genera Pectobacterium and Dickeya cause diseases in potato and numerous other crops. Seed potatoes are the most important source of infection, but how pathogen-free tubers initially become infected remains an enigma. Since the 1920s, insects have been hypothesized to contribute to SRE transmission. To validate this hypothesis and to map the insect species potentially involved in SRE dispersal, we have analyzed the occurrence of SRE in insects recovered from potato fields over a period of 2 years. Twenty-eight yellow sticky traps were set up in 10 potato fields throughout Norway to attract and trap insects. Total DNA recovered from over 2,000 randomly chosen trapped insects was tested for SRE, using a specific quantitative PCR (qPCR) TaqMan assay, and insects that tested positive were identified by DNA barcoding. Although the occurrence of SRE-carrying insects varied, they were found in all the tested fields. While Delia species were dominant among the insects that carried the largest amount of SRE, more than 80 other SRE-carrying insect species were identified, and they had different levels of abundance. Additionally, the occurrence of SRE in three laboratory-reared insect species was analyzed, and this suggested that SRE are natural members of some insect microbiomes, with herbivorous Delia floralis carrying more SRE than the cabbage moth (Plutella xylostella) and carnivorous green lacewing larvae (Chrysoperla carnea). In summary, the high proportion, variety, and ubiquity of insects that carried SRE show the need to address this source of the pathogens to reduce the initial infection of seed material.IMPORTANCE Soft rot Enterobacteriaceae are among the most important pathogens of a wide range of vegetables and fruits. The bacteria cause severe rots in the field and in storage, leading to considerable harvest losses. In potato, efforts to understand how soft rot bacteria infect and spread between healthy plants have been made for over a century. Early on, fly larvae were implicated in the transmission of these bacteria. This work aimed at investigating the occurrence of soft rot bacteria in insects present in potato fields and at identifying the species of these insects to better understand the potential of this suspected source of transmission. In all tested potato fields, a large proportion of insects were found to carry soft rot bacteria. This suggests a need to give more weight to the role of insects in soft rot ecology and epidemiology to design more effective pest management strategies that integrate this factor.

Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated from Tropical Air Collected in Singapore

Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.

Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism

Enterococci are important human commensals and significant opportunistic pathogens. Biofilm-related enterococcal infections, such as endocarditis, urinary tract infections, wound and surgical site infections, and medical device-associated infections, often become chronic upon the formation of biofilm. The biofilm matrix establishes properties that distinguish this state from free-living bacterial cells and increase tolerance to antimicrobial interventions. The metabolic versatility of the enterococci is reflected in the diversity and complexity of environments and communities in which they thrive. Understanding metabolic factors governing colonization and persistence in different host niches can reveal factors influencing the transition to biofilm pathogenicity. Here, we report a form of iron-dependent metabolism for Enterococcus faecalis where, in the absence of heme, extracellular electron transfer (EET) and increased ATP production augment biofilm growth. We observe alterations in biofilm matrix depth and composition during iron-augmented biofilm growth. We show that the ldh gene encoding l-lactate dehydrogenase is required for iron-augmented energy production and biofilm formation and promotes EET.

Bacterial metabolic versatility can often influence the outcome of host-pathogen interactions, yet causes of metabolic shifts are difficult to resolve. The bacterial biofilm matrix provides the structural and functional support that distinguishes this state from free-living bacterial cells. Here, we show that the biofilm matrix can immobilize iron, providing access to this growth-promoting resource which is otherwise inaccessible in the planktonic state. Our data show that in the absence of heme, Enterococcus faecalisl-lactate dehydrogenase promotes EET and uses matrix-associated iron to carry out EET. Therefore, the presence of iron within the biofilm matrix leads to enhanced biofilm growth.