The enzymatic properties of Arabidopsis thaliana DNA polymerase λ suggest a role in base excision repair

Base excision repair (BER) generates gapped DNA intermediates containing a 5'-terminal 2-deoxyribose-5-phosphate (5'-dRP) group. In mammalian cells, gap filling and dRP removal are catalyzed by Pol β, which belongs to the X family of DNA polymerases. In higher plants, the only member of the X family of DNA polymerases is Pol λ. Although it is generally believed that plant Pol λ participates in BER, there is limited experimental evidence for this hypothesis. Here we have characterized the biochemical properties of Arabidopsis thaliana Pol λ (AtPol λ) in a BER context, using a variety of DNA repair intermediates. We have found that AtPol λ performs gap filling inserting the correct nucleotide, and that the rate of nucleotide incorporation is higher in substrates containing a C in the template strand. Gap filling catalyzed by AtPol λ is most efficient with a phosphate at the 5'-end of the gap and is not inhibited by the presence of a 5'-dRP mimic. We also show that AtPol λ possesses an intrinsic dRP lyase activity that is reduced by mutations at two lysine residues in its 8-kDa domain, one of which is present in Pol λ exclusively and not in any Pol β homolog. Importantly, we also found that the dRP lyase activity of AtPol λ allows efficient completion of uracil repair in a reconstituted short-patch BER reaction. These results suggest that AtPol λ plays an important role in plant BER.

Dominance of ST131, B2, blaCTX-M-15, and papA-papC-kpsMII-uitA among ESBL Escherichia coli isolated from bloodstream infections in Quito, Ecuador: a 10-year surveillance study (2009-2019)

AIMS

This study aimed to examine antibiotic resistance and the epidemiology of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli associated with bloodstream infections over a period of 10 years.

METHODS AND RESULTS

Isolates were collected from January 2009 to December 2019 and those testing for E. coli were included. Antibiotic susceptibility was tested using the VITEK® system. Selected isolates were further characterized by amplification of marker genes (virulence traits, phylogroups, and sequence types). A total of 166 ESBL-producing E. coli were recovered. The blaCTX-M-15 allele was the most abundant. Most of the isolates were resistant to ceftriaxone, cefepime, ceftazidime, ampicillin/sulbactam, piperacillin/tazobactam, and ciprofloxacin. No resistance to carbapenems was registered. More than 80% of bacteria were classified as extraintestinal pathogenic E. coli (ExPEC), and the combination of virulence traits:papA-papC-kpsMII-uitA was the most common. Phylogroup B2 was the most prevalent, and bacteria predominantly belonged to ST131.

CONCLUSIONS

There was an increase in the ExPEC ESBL-E coli in bloodstream infections and the relationship between the isolates found in these infections during these 10 years.

Antibiotic Resistance Awareness among Undergraduate Students in Quito, Ecuador

The inappropriate use of antibiotics leads to antibiotic resistance, which reduces their efficacy. The education of undergraduates is likely to influence their practices. Assessing awareness is critical in the general effort to confront the spread of antibiotic resistance. This cross-sectional investigation was carried out using the questionnaire “Antibiotic resistance: Multi-country public awareness” developed by the World Health Organization. Students from different backgrounds at the Central University participated in the study (n = 733). The survey comprised five sections: demographics, knowledge, usage, sources of information, and attitudes. The rate of correct answers was 64.88%; differences were detected between programs of study (p < 0.001); effect size analysis showed that these differences cannot be considered large. Individuals from applied sciences scored higher than their counterparts from social studies. Mostly, interviewees were knowledgeable about usage, but mistakenly associated antibiotics with conditions such as cold/flu or viral illnesses; also, they associated antibiotic resistance with the patient and not with bacteria. Despite these misconceptions, positive attitudes were registered overall, and students generally adhered to common practices. They cited doctors/nurses and teachers as sources of information. As a consequence, it is recommended to develop courses that address deficient knowledge regarding antibiotic resistance, especially for individuals affiliated to social disciplines.

Investigating the dynamics of Salmonella contamination in integrated poultry companies using a whole genome sequencing approach

The study of non-typhoid Salmonella in broiler integrations has been limited by the resolution of typing techniques. Although serotyping of Salmonella isolates is used as a traditional approach, it is not of enough resolution to clearly understand the dynamics of this pathogen within poultry companies. The aim of this research was to investigate the epidemiology and population dynamics of Salmonella serotypes in 2 poultry integrations using a whole genome sequencing approach. Two hundred and forty-three Salmonella isolates recovered from the broiler production chain of 2 integrated poultry companies were whole genome sequenced and analyzed with dedicated databases and bioinformatic software. The analyses of sequences revealed that S. Infantis was the most frequent serotype (82.3%). Most isolates showed a potential for resistance against medically important antibiotics and disinfectants. Furthermore, 97.5% of isolates harbored the pESI-like mega plasmid, that plays an important role in the global dissemination of AMR. SNP tree analysis showed that there were clones that are niche-specific while other ones were distributed throughout the broiler production chains. In this study, we demonstrated the potential of whole genome sequencing analysis for a comprehensive understanding of Salmonella distribution in integrated poultry companies. Data obtained with these techniques allow determination of the presence of genetic factors that play an important role in the environmental fitness and pathogenicity of Salmonella.

Administration of Dietary Microalgae Ameliorates Intestinal Parameters, Improves Body Weight, and Reduces Thawing Loss of Fillets in Broiler Chickens: A Pilot Study

This pilot investigation aimed at studying the feasibility of using a low dose (0.2%) of dietary microalgae as a means of improving intestinal morphometry, body weight, and selected meat quality parameters in broilers. A total of 72 one-day-old ROSS 308 male chicks were randomly separated into four groups; three experimental pens in which the birds were fed with biomass from Tysochrysis lutea, Tetraselmis chuii, and Porphyridium cruentum over 30 days and a control group. T. chuii and P. cruentum had a positive effect with regard to body weight. In treated animals, duodenal and ileal sections showed characteristic tall and thin villi, with serrated surfaces and goblet cell differentiation. In both sections, values of the villus-height-to-crypt-depth ratio were increased by microalgae ingestion. The thawing weight loss of fillets was reduced in T. chuii-fed animals. The positive effects exerted by T. chuii and P. cruentum on intestinal architecture were associated with the improved body weight. Arguably, these outcomes exhibit the potential of using these species to enhance growth performance in broiler chickens by promoting gut homeostasis and thus nutrient absorption.

Evidence of SARS-CoV-2 reinfection within the same clade in Ecuador: A case study

Objectives

To date, reported SARS-CoV-2 reinfection cases are mainly from strains belonging to different clades. As the pandemic advances, a few lineages have become dominant in certain areas leading to reinfections by similar strains. Here, we report a reinfection case within the same clade of the initial infection in a symptomatic 28-year-old-male in Quito-Ecuador.

Methods

Infection was detected by reverse transcription-polymerase chain reaction, and immune response evaluated by antibody testing. Whole-genome sequencing was performed and phylogenetic analysis conducted to determine relatedness.

Results

Both the infection and the reinfection strains were assigned as Nextstrain 20B, Pangolin lineage B.1.1 and GISAID clade O. Our analysis indicated 4–6 fold more nucleotide changes than are expected for reactivation or persistence compared with the natural rate of SARS-CoV-2 mutation (∼2–3 nucleotide changes per month), thus supporting reinfection. Furthermore, approximately 3 months after the second infection, COVID-19 antibodies were not detectable in the patient, suggesting potential vulnerability to a third infection.

Conclusions

Our results showed evidence of SARS-CoV-2 reinfection within the same clade in Ecuador, indicating that previous exposure to SARS-CoV-2 does not guarantee immunity in all cases.

Broiler Farms and Carcasses Are an Important Reservoir of Multi-Drug Resistant Escherichia coli in Ecuador

Antimicrobial resistance (AMR) is a major health threat for public and animal health in the twenty-first century. In Ecuador, antibiotics have been used by the poultry industry for decades resulting in the presence of multi-drug resistant (MDR) bacteria in the poultry meat production chain, with the consequent risk for public health. This study evaluated the prevalence of ESBL/AmpC and mcr genes in third-generation cephalosporin-resistant Escherichia coli (3GC-R E. coli) isolated from broiler farms (animal component), broiler carcasses (food component), and human enteritis (human component) in Quito-Ecuador. Samples were collected weekly from November 2017 to November 2018. For the animal, food, and human components, 133, 335, and 302 samples were analyzed, respectively. Profiles of antimicrobial resistance were analyzed by an automated microdilution system. Resistance genes were studied by PCR and Sanger sequencing. From all samples, 122 (91.7%), 258 (77%), and 146 (48.3%) samples were positive for 3GC-R E. coli in the animal, food, and human components, respectively. Most of the isolates (472/526, 89.7%) presented MDR phenotypes. The ESBL bla_CTX-M-55, bla_CTX-M-3, bla_CTX-M-15, bla_CTX-M-65, bla_CTX-M-27, and bla_CTX-M-14 were the most prevalent ESBL genes while bla_CMY-2 was the only AmpC detected gene. The mcr-1 gene was found in 20 (16.4%), 26 (10.1%), and 3 (2.1%) of isolates from animal, food, and human components, respectively. The implication of poultry products in the prevalence of ESBL/AmpC and mcr genes in 3GC-R must be considered in the surveillance of antimicrobial resistance.

Effects of Lactobacillus Fermentum Supplementation on Body Weight and Pro-Inflammatory Cytokine Expression in Campylobacter Jejuni-Challenged Chickens

Due to the interest in using probiotic bacteria in poultry production, this research was focused on evaluating the effects of Lactobacillus fermentum Biocenol CCM 7514 administration on body weight gain and cytokine gene expression in chickens challenged with Campylobacter jejuni. One-hundred and eight 1-day old COBB 500 broiler chickens were equally assigned to four experimental groups at random. In the control group (C) chicks were left untreated, whereas in groups LB and LBCj a suspension of L. fermentum was administered. A suspension of C. jejuni was subsequently applied to groups Cj and LBCj. Body weight was registered, and the individuals were later slaughtered; cecum samples were collected at 12, 36 and 48 h post-infection (hpi). The entire experiment lasted seven days. Reverse transcription quantitative PCR (RT-qPCR) was used to determine expression levels of IL-1β, IL-15, IL-17, and IL-18 at each time point. Pathogen-infected individuals were observed to weigh significantly less than those fed with the probiotic. Significant differences were also found in transcript abundance; expression of IL-15 was downregulated by the probiotic and upregulated by C. jejuni. The effects of bacterial treatments were time-dependent, as the expression profiles differed at later stages. The present outcomes demonstrate that L. fermentum both reduces the impact of C. jejuni infection on chicken body weight and regulates positively pro-inflammatory cytokine expression, which ultimately increase bird well-being and improves production.

High quantities of multidrug-resistant Escherichia coli are present in the Machángara urban river in Quito, Ecuador

Urban river pollution by multidrug-resistant (MDR) bacteria constitutes an important public health concern. Epidemiologically important strains of MDR Escherichia coli transmissible at the human-animal-environment interfaces are especially worrying. Quantifying and characterizing MDR E. coli at a molecular level is thus imperative for understanding its epidemiology in natural environments and its role in the spread of resistance in precise geographical areas. Cefotaxime-resistant E. coli was characterized along the watercourse of the major urban river in Quito. Our results showed high quantities of cefotaxime-resistant E. coli (2.7 × 10³-5.4 × 10⁵ CFU/100 mL). The antimicrobial resistance index (ARI) revealed the exposure of the river to antibiotic contamination, and the multiple antibiotic resistance index indicated a high risk of contamination. The bla_CTX-M-15 gene was the most prevalent in our samples. Isolates also had class 1 integrons carrying aminoglycoside-modifying enzymes and folate pathway inhibitors. The isolates belonged to phylogroups A, B1 and D. Clonal complex 10 was found to be the most prevalent (ST10, ST44 and ST 167), followed by ST162, ST394 and ST46. Our study provides a warning about the high potential of the major urban river in Quito for spreading the epidemiologically important MDR E. coli.

Genetic diversity and drug resistance of Mycobacterium tuberculosis in Ecuador

BACKGROUND

The genetic diversity of Mycobacterium tuberculosis in Quito, Ecuador is not well known.

OBJECTIVE

To investigate mutations related to drug resistance and bacterial genotypes in M. tuberculosis strains in Ecuador.

DESIGN

This was a retrospective study of M. tuberculosis isolates from 104 patients. Isolates were phenotypically resistant to rifampicin (RMP) and/or isoniazid (INH). The genotype was determined using 24-locus mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR).

RESULTS

Isolates showed mutations in the rpoB and katG genes, and the inhA promoter. In rpoB, we found 13 genetic alterations at codons 511, 513, 514, 515, 516, 526 and 531. Forty-six (44.2%) RMP-resistant isolates belonged to codon 531. In katG, there were nine genetic alterations at codons 296, 312, 314, 315, 322, 324 and 351. Fifty-three (51%) INH-resistant isolates belonged to codon 315. Five mutations not previously described were identified in katG: Thr324Ser, Thr314Ala, Ala312Pro, Trp351Stop and deleted G at 296 codon. The Latin American Mediterranean (LAM) (33.7%) and Ghana (30.8%) lineages presented most of the main mutations observed.

CONCLUSION

This is the first report from Ecuador; it describes five new mutations in katG and indicates that LAM is the most prevalent lineage.

Ready-to-eat street food: a potential source for dissemination of multidrug-resistant Escherichia coli epidemic clones in Quito, Ecuador

Ready-to-eat food contamination with ESBL-producing Escherichia coli is a growing health concern. Some of these strains also are epidemic clones and can cause community-associated infections that are difficult to treat. In this study, the occurrence of ESBL-producing E. coli contaminated ready-to-eat street food in Quito, Ecuador was evaluated. In total, 150 samples were collected randomly in the most crowded sites of the city. In all, 34 samples (34/150; 22·6%) were positive for total thermotolerant (44·5°C) coliforms resistant to cefotaxime. MALDI-TOF analysis identified that the E. coli was found in 20 food samples (20/34; 59%). ESBL gene bla_CTX-M-55 was identified in nine isolates, bla_CTX-M-15 in six isolates, bla_CTX-M-14 in two isolates, and one isolate each harboured bla_CTX-M-24 , bla_CTX-M-65 , bla_CTX-M-55 and bla_CTX-M-8 . Phylogenetic groups like A and B1 were the most common, followed by groups D and B2. MLST analysis identified 12 different sequence types (STs), the most common was ST162. Recognized epidemic clonal groups ST410, ST131 and ST744 were encountered. Ready-to-eat street food is a potential way of spreading ESBL-producing E. coli epidemic clones in Quito, Ecuador. SIGNIFICANCE AND IMPACT OF THE STUDY: This study identified ESBL-producing Escherichia coli epidemic clones: ST131, ST410 and ST744 in ready-to-eat street food samples. Street food is a possible way to spread harm multidrug-resistant (MDR) E. coli strains in the community. Studies to identify the contamination sources of this kind of food are needed to tackle MDR E. coli dissemination.

Ecuadorian mainland industrial poultry production is free of H5/H7 Avian influenza virus: National surveillance program in 2016

Avian influenza (AI) is a disease caused by influenza viruses type A that belong to the Orthomyxoviridae family. AI induces high economic losses in poultry production worldwide. Due to a possible outbreak, a national surveillance program was needed. From April to July 2016, 152 industrial poultry farms were randomly sampled. All samples were analyzed by competitive ELISA for Influenza type A viruses. Suspicious and positive sera were further analyzed by Hemagglutination Inhibition (HI) in order to serotype H5 or H7 low pathogenic avian influenza virus (LPAIV). The farms sampled showed 94.08%, 3.95% and 1.97% of negative, positive and suspicious results, respectively. However, serotyping revealed all positive and suspicious samples were negative to H5/H7 LPAIV. Our results show the absence of AI in the mainland Ecuadorian industrial poultry production.

Multidrug-resistant Escherichia coli isolated from canine faeces in a public park in Quito, Ecuador

OBJECTIVES

This study focused on estimating the prevalence of extended-spectrum β-lactamases (ESBLs), plasmid-mediated AmpC β-lactamases, carbapenemases and MCR-1-producing Escherichia coli in canine faeces from a public park in Quito, Ecuador.

METHODS

Phenotypic and genotypic characterisation of E. coli isolated from 50 canine faecal samples recovered from a city park in Quito was performed. In addition, a multiple choice survey was conducted among 50 dog owners.

RESULTS

Of the 50 faecal samples, 20 (40.0%) presented E. coli resistant to ceftriaxone. Moreover, 23 E. coli isolates were recovered for further analysis. All of the isolates showed as multidrug-resistant (MDR) phenotype (resistant to three or more antibiotic families). Resistance to carbapenems, tigecycline and amikacin was not observed. No major clonal relatedness was observed among the resistant isolates. The ESBL genes bla_CTX-M-15, bla_CTX-M-55 and bla_CTX-M-65 were the most common. Two isolates harboured the bla_CMY-2 gene and one isolate harboured both mcr-1 and bla_CTX-M-65. Statistical analysis showed that older people were more conscious of collecting and disposing of dog faeces than subjects aged <35 years (P < 0.05).

CONCLUSION

The finding of MDR E. coli in dog faeces in a city park in Ecuador illustrates the importance of analysing canine faeces in public settings (e.g. parks, playgrounds) as part of surveillance programmes for MDR E. coli. In addition, this research might be a sentinel sampling method to gain a better understanding of community sources of antibiotic-resistant Enterobacteriaceae at human-animal-environment interfaces.

Characterization of cefotaxime resistant Escherichia coli isolated from broiler farms in Ecuador

Antimicrobial resistance (AR) is a worldwide concern. Up to a 160% increase in antibiotic usage in food animals is expected in Latin American countries. The poultry industry is an increasingly important segment of food production and contributor to AR. The objective of this study was to evaluate the prevalence, AR patterns and the characterization of relevant resistance genes in Extended Spectrum β-lactamases (ESBL) and AmpC-producing E. coli from large poultry farms in Ecuador. Sampling was performed from June 2013 to July 2014 in 6 slaughterhouses that slaughter broilers from 115 farms totaling 384 flocks. Each sample of collected caeca was streaked onto TBX agar supplemented with cefotaxime (3 mg/l). In total, 176 isolates were analyzed for AR patterns by the disk diffusion method and for blaCTX-M, blaTEM, blaCMY, blaSHV, blaKPC, and mcr-1 by PCR and sequencing. ESBL and AmpC E. coli were found in 362 flocks (94.3%) from 112 farms (97.4%). We found that 98.3% of the cefotaxime-resistant isolates were multi-resistant to antibiotics. Low resistance was observed for ertapenem and nitrofurantoin. The most prevalent ESBL genes were the ones belonging to the blaCTX-M group (90.9%), specifically the blaCTX-M-65, blaCTX-M-55 and blaCTX-M-3 alleles. Most of the AmpC strains presented the blaCMY-2 gene. Three isolates showed the mcr-1 gene. Poultry production systems represent a hotspot for AR in Ecuador, possibly mediated by the extensive use of antibiotics. Monitoring this sector in national and regional plans of AR surveillance should therefore be considered.

Assessing knowledge of genetics in undergraduate students in Quito, Ecuador

Knowledge of genetics is crucial for understanding genetic and genomic tests and for interpreting personal genomic information. Despite this relevance, no data are available about the level of knowledge of genetics in an Ecuadorian population. This investigation sought to survey such knowledge in undergraduate students affiliated with private and public institutions in Quito, the capital city of Ecuador. A total of 350 individuals responded to a validated questionnaire measuring knowledge of genetics. Scores ranged from 45% to 87% (mean: 66.8%), and students achieved slightly better results when asked about genetics and diseases (mean score: 68.3%) than when asked about genetic facts (mean score: 64.9%). Additionally, no significant differences in performance were found among students from private and public institutions. Surprisingly, the lower score obtained (45%) was from a question about how chromosomes are passed to the next generation. The highly educated status of the surveyed population could explain the overall results; nonetheless, the possibility that the correct responses were given by chance cannot be ignored. Therefore, the actual knowledge of genetics among the participants might be different than that revealed by the percentages of correct answers. Consequently, to achieve the goal of ensuring informed decision-making concerning genetic and genomic tests, it seems evident that the national education programs of Ecuador require improvement in the teaching of genetic concepts.

Escherichia coli hyperepidemic clone ST410-A harboring blaCTX-M-15 isolated from fresh vegetables in a municipal market in Quito-Ecuador

Dissemination of Extended spectrum β-lactamases (ESBL) Enterobacteriaceae is a major medical threat. Vegetables and fruits, which are usually consumed raw, are a very suitable pathway for the spread of these bacteria from farm-to-fork. However, limited information exists regarding resistant bacteria and epidemic clones that are disseminated in vegetables and tap water in South America. We processed a total of 90 samples in triplicate of nine typically consumed raw vegetables from a central municipal market, and tap water samples were processed from twenty-one locations in Quito, Ecuador. The samples were analyzed for total coliforms and ESBL Enterobacteriaceae contamination using the dilution filtration method. ESBL Escherichia coli isolates were phenotypically and genotypically characterized. The water was free of Enterobacteriaceae, but all the vegetables and fruits (except for blackberries) presented total coliform counts. Watercress had the highest load of total coliforms (3.3 × 10E4). ESBL E. coli was detected in alfalfa, leaf lettuce and parsley/cilantro samples. Alfalfa had the highest load of ESBL E. coli/total coliforms (1/3.3 × 10E2). We identified E. coli ST44-A and ST410-A harboring bla_CTX-M-15 downstream of ISEcp1. Alfalfa and parsley/cilantro were contaminated with hyperepidemic E. coli ST410-A, which was resistant to quinolones and harbored bla_CTX-M-15. For the first time, we report ESBL E. coli ST410-A from vegetables and express an alert regarding the health risk this could represent.

Local circulating clones of Staphylococcus aureus in Ecuador

The spread of pandemic Staphylococcus aureus clones, mainly methicillin-resistant S. aureus (MRSA), must be kept under surveillance to assemble an accurate, local epidemiological analysis. In Ecuador, the prevalence of the USA300 Latin American variant clone (USA300-LV) is well known; however, there is little information about other circulating clones. The aim of this work was to identify the sequence types (ST) using a Multiple-Locus Variable number tandem repeat Analysis 14-locus genotyping approach. We analyzed 132 S. aureus strains that were recovered from 2005 to 2013 and isolated in several clinical settings in Quito, Ecuador. MRSA isolates composed 46.97% (62/132) of the study population. Within MRSA, 37 isolates were related to the USA300-LV clone (ST8-MRSA-IV, Panton-Valentine Leukocidin [PVL] +) and 10 were related to the Brazilian clone (ST239-MRSA-III, PVL−). Additionally, two isolates (ST5-MRSA-II, PVL−) were related to the New York/Japan clone. One isolate was related to the Pediatric clone (ST5-MRSA-IV, PVL−), one isolate (ST45-MRSA-II, PVL−) was related to the USA600 clone, and one (ST22-MRSA-IV, PVL−) was related to the epidemic UK-EMRSA-15 clone. Moreover, the most prevalent MSSA sequence types were ST8 (11 isolates), ST45 (8 isolates), ST30 (8 isolates), ST5 (7 isolates) and ST22 (6 isolates). Additionally, we found one isolate that was related to the livestock associated S. aureus clone ST398. We conclude that in addition to the high prevalence of clone LV-ST8-MRSA-IV, other epidemic clones are circulating in Quito, such as the Brazilian, Pediatric and New York/Japan clones. The USA600 and UK-EMRSA-15 clones, which were not previously described in Ecuador, were also found. Moreover, we found evidence of the presence of the livestock associated clone ST398 in a hospital environment.

Characterization of the first report of Mycobacterium timonense infecting an HIV patient in an Ecuadorian hospital

Mycobacterium timonense is a non-tuberculous mycobacteria (NTM) described in southern France in 2009, and to our knowledge, not reported again as a human pathogen in indexed literature. The aim of this work was to characterize the first clinical isolate of M. timonense in Ecuador. Time of growth, biochemical tests, thin layer growth test, PCR-RFLP analysis of the hsp65 gene and MALDI-TOF spectra analysis were not able to identify the species. The species identification was achieved through sequencing of rrs, hsp65 and rpoB genes. The results highlight the necessity to set up a sequencing method to identify emerging NTM in Ecuadorian clinical facilities.