Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections.

Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE: Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.

First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador.

Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.

NDM-1 carbapenemase in Acinetobacter baumannii sequence type 32 in Ecuador.

OBJECTIVES: To describe a clinical case of Acinetobacter baumannii sequence type (ST) 32 harbouring a New Delhi metallo-ß-lactamase (NDM) in Ecuador. METHODS: We used multilocus sequence typing (MLST) to confirm the bacterial species and the sequence type of an A. baumannii isolate. We used synergy with the imipenem-EDTA disc method and the carbapenem inactivation method (CIM) to determine carbapenemase production; the presence of a carbapenemase gene was confirmed by PCR amplification and amplicon sequencing. RESULTS: Molecular characterization revealed the presence of A. baumannii ST32 harbouring the bla NDM-1 gene in Ecuador. The bla NDM-1 gene was isolated through PCR and amplified from a purified plasmid. CONCLUSIONS: To the best of our knowledge, this is the first report of A. baumannii ST32 harbouring the bla NDM-1 gene.

Impacts of small-scale chicken farming activity on antimicrobial-resistant Escherichia coli carriage in backyard chickens and children in rural Ecuador.

The emergence, spread, and persistence of antimicrobial resistance (AMR) remains a pressing global concern. Increased promotion of commercial small-scale agriculture within low-resource settings has facilitated an increased use in antimicrobials as growth promoters globally, creating antimicrobial-resistant animal reservoirs. We conducted a longitudinal field study in rural Ecuador to monitor the AMR of Escherichia coli populations from backyard chickens and children at three sample periods with approximately 2-month intervals (February, April, and June 2017). We assessed AMR to 12 antibiotics using generalized linear mixed effects models (GLMM). We also sampled and assessed AMR to the same 12 antibiotics in one-day-old broiler chickens purchased from local venders. One-day-old broiler chickens showed lower AMR at sample period 1 compared to sample period 2 (for 9 of the 12 antibiotics tested); increases in AMR between sample periods 2 and 3 were minimal. Two months prior to the first sample period (December 2016) there was no broiler farming activity due to a regional collapse followed by a peak in annual farming in February 2017. Between sample periods 1 and 2, we observed significant increases in AMR to 6 of the 12 antibiotics in children and to 4 of the 12 antibiotics in backyard chickens. These findings suggest that the recent increase in farming, and the observed increase of AMR in the one-day old broilers, may have caused the increase in AMR in backyard chickens and children. Small-scale farming dynamics could play an important role in the spread of AMR in low- and middle-income countries.

Campylobacter fetus Bacteremia in a Healthy Patient Returning from a Trip to the Ecuadorian Amazonia.

Campylobacter fetus is an opportunistic pathogen which causes bacteremia and other invasive infections in immunocompromised patients who have been exposed to livestock or ingested animal products (uncooked meat or unpasteurized milk). The present report describes a C. fetus infection in a healthy adult (immunocompetent) who returned from a visit to the Ecuadorian Amazonia and who did not report exposure to the typical sources of infection.

First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador.

Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, EcEs062_16 and EcEs089_16, isolated from the sera of febrile patients in Esmeraldas City, in the northern coastal province of Esmeraldas, Ecuador, in April 2016. These are the first complete ZIKV genomes to be reported from Ecuador.

Cloning of the pfaP gene of Leptospira borgpetersenii.

A lambda gt11 library constructed with Leptospira borgpetersenii DNA was screened with monoclonal antibodies (mAb) recognizing a periplasmic flagella-associated protein. A plaque expressing a fusion protein (lambda F15) which reacted with the mAb was isolated and the nucleotide sequence analyzed. The deduced amino-acid (aa) sequence indicates that the pfaP gene belongs to a group of bacterial genes whose products share aa sequence and possibly functional homologies with sppA, an Escherichia coli signal peptidase-encoding gene.

A cheA cheW operon in Borrelia burgdorferi, the agent of Lyme disease.

Borrelia burgdorferi sensu stricto homologues of cheA and cheW were cloned and characterized. A combination of strategies such as polymerase chain reaction (PCR) using degenerate primers, random-primed gene walking PCR and construction of a lamda library were used to identify the putative cheA gene. Sequence analysis of the DNA fragments obtained from the CT strain identified a 2,592-bp open reading frame (ORF) encoding an 864-amino-acid protein with significant similarity (53-64.6% identical residues) to the CheA of several genera of eubacteria. In particular, hallmarks of a histidine kinase family were found such as the location of the histidine autophosphorylation domain very close to the NH2 terminus and the nucleotide-binding site. A second ORF located immediately downstream from the putative borrelial cheA gene encoded a 195-amino-acid protein which displayed a high level of similarity to bacterial CheW. Using reverse transcription PCR, we demonstrated that cheA and cheW form an operon with an upstream, unidentified ORF. The cheA and cheW homologues were located at 722-737 kbp, 738-768 kbp and 743-824 kbp on the linear chromosomes of B. burgdorferi sensu stricto, B. garinii and B. afzelii, respectively. Identification of cheA and cheW is the first step toward elucidation of a possible role of chemotaxis in virulence of the Lyme disease borreliae.

Detection of Fasciola hepatica infection in a community located in the Ecuadorian Andes.

The presence of fascioliasis was assessed in four Andean communities using an enzyme-linked immunosorbent assay (ELISA) test to measure antibodies against Fasciola hepatica excretion-secretion antigens. Six percent (9 out of 150) of the individuals in one community were ELISA-positive for these antibodies. Fecal samples from two of the ELISA-positive individuals contained F. hepatica ova. All of the ELISA-positive cases, except for one, were children within the ages of 9 to 12 years.

Detection of dengue virus neutralizing antibodies in bats from Costa Rica and Ecuador.

Neutralizing antibodies for dengue virus serotypes 1 and 2 and serotypes 2 and 3 were detected in 1998 in 12 of 53 (22.6%) and 3 of 10 (30.0%) bats sampled in Costa Rica and Ecuador, respectively. Dengue is a consistent health problem in the two Costa Rican communities in which bats were sampled. The high percentage of bats with neutralizing antibodies to dengue virus in these two Costa Rican communities suggests that bats may become infected with dengue virus. This appears to be the case in Costa Rica and Ecuador.

Evaluation of an enzyme immunoassay for diagnosis of bovine leptospirosis caused by Leptospira interrogans serovar hardjo type hardjo-bovis.

Sensitivity and specificity of 4 different antigen preparations from Leptospira interrogans serovar hardjo were compared in an enzyme immunoassay for detection of antibodies against serovar hardjo type hardjo-bovis in serum. Two antigens prepared using detergents showed serogroup cross-reactivity. A mechanically extracted membrane and a lipopolysaccharide antigen showed a high degree of leptospiral serogroup specificity. The lipopolysaccharide antigen was the most suitable antigen for detection of anti-hardjo antibodies. Enzyme immunoassay was more sensitive than the microscopic agglutination test for detecting antibodies in serum from experimentally and naturally infected cattle. It was not possible to differentiate vaccinated from infected animals or to detect a secondary immune response in vaccinated animals that were subsequently infected.

Comparison of three techniques to detect Leptospira interrogans serovar hardjo type hardjo-bovis in bovine urine.

Nucleic acid hybridization, bacteriologic culture, and a fluorescent antibody test were compared for detection of Leptospira interrogans serovar hardjo type hardjo-bovis in bovine urine. Seventy-five urine samples were collected from pregnant cows challenge exposed with type hardjo-bovis. Twenty samples were collected from steers not exposed to hardjo-bovis. Sediments from each sample were examined, using fluorescent antibodies and a repetitive sequence element nucleic acid probe, to detect the presence of leptospires. Urine samples were processed for bacteriologic culture, using standard techniques. Under laboratory conditions typically used for these techniques, leptospires were detected in 60 of 75 urine samples from challenge exposed cows by nucleic acid hybridization, in 24 samples by fluorescent antibody test, and in 13 samples by bacteriologic culture. Leptospires were not detected in the urine of steers not exposed to hardjo-bovis.

Effect of vaccination with a pentavalent leptospiral vaccine containing Leptospira interrogans serovar hardjo type hardjo-bovis on type hardjo-bovis infection of cattle.

Effectiveness of 2 pentavalent leptospiral vaccines containing Leptospira interrogans serovar hardjo was evaluated for protection of steers from infection with serovar hardjo type hardjo-bovis. The hardjo component of 1 vaccine was prepared from serovar hardjo type hardjoprajitno. The hardjo component of the other vaccine was prepared from serovar hardjo type hardjo-bovis. Two steers were vaccinated once and 4 steers were vaccinated twice with the pentavalent vaccine containing type hardjoprajitno. Four steers were vaccinated once and 4 steers were vaccinated twice with the pentavalent vaccine containing type hardjo-bovis. Four steers were maintained as non-vaccinated controls. Steers given vaccine containing type hardjo-bovis developed higher mean serum microscopic agglutination titers against serovar hardjo than steers given vaccine containing hardjoprajitno. Six months after the first vaccination, all steers were challenge-exposed on 3 occasions by conjunctival instillation of 10(7) serovar hardjo type hardjo-bovis organisms, and on 1 occasion by conjunctival instillation of urine from a steer shedding hardjo-bovis. All control and all vaccinated steers became infected and shed serovar hardjo type hardjo-bovis in the urine. Lesions were detected in kidneys of 3 of 4 nonvaccinated control steers, 5 of 6 steers given hardjoprajitno vaccine, and 6 of 8 steers given hardjo-bovis vaccine. Leptospires were detected in kidneys of 4 of 4 control steers and 13 of 14 vaccinated steers.

Effect of vaccination with a monovalent Leptospira interrogans serovar hardjo type hardjo-bovis vaccine on type hardjo-bovis infection of cattle.

Effectiveness of 2 concentrations of a monovalent vaccine containing Leptospira interrogans serovar hardjo type hardjo-bovis was evaluated for protection of heifers from infection with type hardjo-bovis. Nine heifers were given 2 doses of low-dose vaccine (8.32 x 10(8) cells/dose); 9 heifers were given 2 doses of high-dose vaccine (8.32 x 10(9) cells/dose); and 1 steer and 1 heifer were maintained as nonvaccinated controls. Groups of vaccinated cattle were challenge-exposed with serovar hardjo type hardjo-bovis at 7 (n = 6), 11 (n = 6), or 15 (n = 6) weeks after completion of vaccination. All cattle were challenge-exposed by conjunctival instillation of 1 x 10(5) hardjo-bovis cells on 3 consecutive days. Both control and all vaccinated cattle became infected and shed serovar hardjo type hardjo-bovis in their urine. Leptospires were detected in 15 of 16 (94%) urine samples from control cattle and in 124 of 143 (87%) samples from vaccinated cattle. Leptospires were detected in kidneys of 17 of 18 vaccinated cattle and 2 of 2 control cattle and in the uterus or oviducts of 13 of 18 vaccinates and the 1 control heifer.

Morphometric and molecular characterization of the series Guyanensis (Diptera, Psychodidae, Psychodopygus) from the Ecuadorian Amazon Basin with description of a new species.

Several populations of the series Guyanensis (Diptera, Psychodidae, Psychodopygus) were collected from the Yasuní National Park in the Ecuadorian Amazon region. The specimens comprised the species Psychodopygus geniculatus, Psychodopygus luisleoni and Psychodopygus corossoniensis. Within Ps. geniculatus, we observed two populations, one with a narrow paramere and relatively short genital filaments and the other characterized by a wider coxite and longer genital filaments. A multiple approach combining morphology, morphometry and DNA sequencing of the ribosomal internal transcribed spacer 2 (ITS2) and the mitochondrial cytochrome b gene was carried out. Morphological, morphometric and molecular data strongly suggested the presence of two populations within Ps. geniculatus. The lack of intermediate forms within these populations supported the proposal of two sympatric species. This report describes Psychodopygus francoisleponti n. sp.

A study of a population of Nyssomyia trapidoi (Diptera: Psychodidae) caught on the Pacific coast of Ecuador.

BACKGROUND: Cutaneous leishmaniasis is endemic to the Pacific coast of Ecuador, and Nyssomyia trapidoi is considered to be its main vector. Dujardin et al. [1] recorded some differences in body pigmentation and isoenzymatic profiles in sympatric populations of Ny. trapidoi from the Pacific coast of Ecuador and suggested the existence of two cryptic species. METHODS: Entomological collections were performed in November 2008 and March 2011 in the locality of Paraíso Escondido using CDC miniature light traps and human bait. Morphological, isoenzymatical and molecular (sequencing of cytochome b and cytochrome c oxidase 1 of the mitochondrial DNA) analyses, such as detection of Leishmania DNA and phlebovirus RNA in some females, were performed. RESULTS: Neighbor-joining trees from mitochondrial sequences grouped all of Ecuadorian Ny. trapidoi (including the two color variants) in one cluster, except for two specimens which clustered separately in both genes. Isoenzymatic characterization confirmed that the color variants belong to the same population. Additionally, 11.5% of females were found by PCR to contain Endotrypanum monterogeii kinetoplastid DNA. All pools of Ny. trapidoi were negative for phlebovirus RNA. CONCLUSION: Analysis of mitochondrial gene sequences and isoenzymes was unable to support the existence of two sibling species within Ny. trapidoi, which is a probable vector of Endotrypanum monterogeii.