Endogenous origin of Pseudomonas aeruginosa infecting hospitalized patients in Ecuador

Summary: Recent evidence suggests that Pseudomonas aeruginosa, a bacterium that has the ability to cause deadly infections in hospitalized patients, could originate in the patient's own flora. We employed the Oxford Nanopore platform to obtain whole genome sequences (WGS) from clinical and rectal screen P. aeruginosa strains belonging to 15 patients from two hospitals. Our study found evidence that clinical and rectal isolates were clonal, with some evidence suggesting that the infecting strain was present in the patient's intestine at the time of admission, ruling out hospital acquisition. The use of WGS analysis is crucial to detect alternative sources of P. aeruginosa to develop new preventive measures against these serious infections

SARS-CoV-2 detection and sequencing in heart tissue associated with myocarditis and persistent arrhythmia: A case report

Background: SARS-CoV-2 uses the human cell receptor angiotensin-converting enzyme (ACE2). ACE2 is widely present in the cardiovascular system including the myocardium and the conduction system. COVID-19 patients that present severe symptoms have been reported to have complications involving myocardial injuries caused by the virus. Here we report the detection of SARS-CoV-2 by whole genome sequencing in the endocardium of a patient with severe bradycardia. Case presentation: We report a case of a 34-year-old male patient with COVID-19 tested by PCR, he started with gastrointestinal symptoms, however, he quickly deteriorated his hemodynamic state by means of myocarditis and bradycardia. After performing an endocardium biopsy, it was possible to identify the presence of SARS-CoV-2 in the heart tissue and to sequence its whole genome using the ARTIC-Network protocol and a modified tissue RNA extraction method. The patient’s outcome was improved after a permanent pacemaker was implanted. Conclusions: It was possible to identify a SARS-CoV-2 clade 20A in the endocardium of the reported patient

Molecular phylogenetic analysis of a 466 bp fragment obtained by concatenating a 266 bp fragment of the <i>16S rRNA</i> and a 200 bp fragment of the <i>SecY</i> genes.

Bootstrap values (500 replicates) > 0.90 are indicated with “*”. The tree was rooted with sequences from Leptonema illini DSM 21528 (not depicted on the tree). The samples sequenced from this project are indicated by green text.</p

Geographic location of study sites in the Yasuní Biosphere Reserve.

The five Kichwa communities that were sampled are shown as grey dots: Pompeya (lat:-0.44148, long:-76.60161), Indillama (lat:-0.44281, long:-76.5184), Nueva Providencia (lat:-0.48804, long:-76.48771), Sani Isla (lat:-0.48152, long:-76.27553), and San Roque (lat:-0.45611, long:-76.20086). Dark gray color shows the boundaries for the Yasuní National Park, and the lighter gray color indicates the park buffer zone. Maps were created using ArcGIS software by ESRI (https://www.esri.com/en-us/home) ArcGIS and ArcMap are the intellectual property of ESRI and are used herein under license. Copyright Esri. All rights reserved. Base layer was obtained from: (https://wcs-global.maps.arcgis.com/ - Reserva de Biósfera Yasuní) and (https://www.portal30x30.com - Áreas Protegidas Ecuador SNAP).</p

<i>Leptospira</i> seropositivity, and detection and identification of pathogenic <i>Leptospira</i> DNA in dog urine samples.

Leptospira seropositivity, and detection and identification of pathogenic Leptospira DNA in dog urine samples.</p

<i>Leptospira</i> serogroups detected in domestic dogs living in Kichwa communities.

Leptospira serogroups detected in domestic dogs living in Kichwa communities.</p

Serological analysis of 48 dogs by MAT.

BackgroundLeptospirosis is the world’s most common zoonotic disease. Mitigation and control rely on pathogen identification and understanding the roles of potential reservoirs in cycling and transmission. Underreporting and misdiagnosis obscure the magnitude of the problem and confound efforts to understand key epidemiological components. Difficulties in culturing hamper the use of serological diagnostics and delay the development of DNA detection methods. As a result, especially in complex ecosystems, we know very little about the importance of different mammalian host species in cycling and transmission to humans.Methodology/principal findingsWe sampled dogs from five indigenous Kichwa communities living in the Yasuní National Park in the Ecuadorian Amazon basin. Blood and urine samples from domestic dogs were collected to assess the exposure of these animals to Leptospira and to identify the circulating species. Microscopic Agglutination Tests with a panel of 22 different serovars showed anti-leptospira antibodies in 36 sampled dogs (75%), and 7 serogroups were detected. Two DNA-based detection assays revealed pathogenic Leptospira DNA in 18 of 19 dog urine samples (94.7%). Amplicon sequencing and phylogenetic analysis of 16S rRNA and SecY genes from 15 urine samples revealed genetic diversity within two of three different Leptospira species: noguchii (n = 7), santarosai (n = 7), and interrogans (n = 1).Conclusions/significanceThe high prevalence of antibodies and Leptospira DNA provides strong evidence for high rates of past and current infections. Such high prevalence has not been previously reported for dogs. These dogs live in the peridomestic environment in close contact with humans, yet they are free-ranging animals that interact with wildlife. This complex web of interactions may explain the diverse types of pathogenic Leptospira observed in this study. Our results suggest that domestic dogs are likely to play an important role in the cycling and transmission of Leptospira. Future studies in areas with complex ecoepidemiology will enable better parsing of the significance of genotypic, environmental, and host characteristics.</div

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.ISSN:2057-157