Klebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador. The main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K. pneumoniae KPC-3 gene producers in Ecuador. Our WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.

Background: Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is increasingly recognized as a multidrug-resistant (MDR) nosocomial pathogen. However, subspecies-level genomic data from Ecuador remain limited. Methods: Four clinical E. hormaechei isolates from a hospital in northern Ecuador were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Genomic characterization included multilocus sequence typing (MLST), resistome profiling, plasmid replicon detection, integron screening, genomic island analysis, and phylogenetic comparison with publicly available Ecuadorian genomes. Results: WGS identified three isolates as subsp. xiangfangensis (ST136 and ST337) and one as subsp. hoffmannii (ST145). Two ST136 isolates exhibited extensive MDR phenotypes associated with bla_CTX-M-15, bla_OXA-1, bla_ACT-16, and additional aminoglycoside and fluoroquinolone resistance genes. ST145 showed moderate resistance, whereas ST337 remained largely susceptible despite harboring bla_ACT-16. Multiple genomic islands and plasmid replicons (IncF/IncR or IncHI2) were detected. Phylogenetic analysis demonstrated clustering with previously reported Ecuadorian lineages. Conclusions: This study provides subspecies-level genomic characterization of clinical E. hormaechei in Ecuador and describes heterogeneous resistance profiles and associated mobile genetic elements, contributing baseline data for regional surveillance.

Background: Escherichia coli is a leading cause of urinary tract infections (UTIs) in children, and increasing antimicrobial resistance complicates empirical treatment. However, genomic information on pediatric urinary E. coli associated with urinary tract infection in Ecuador remains limited. Objective: This exploratory study analyzed four E. coli isolates obtained from urine samples of pediatric patients at a tertiary hospital in Guayaquil, Ecuador. Methods: Whole-genome sequencing (WGS) was performed to determine sequence types (STs), serotypes, antimicrobial resistance genes (ARGs) virulence factors (VFs), and phylogenetic relationships. Results: Two isolates were assigned to the globally disseminated high-risk clone ST1193 and carried extended-spectrum β-lactamase (ESBL) genes, including bla_CTX-M-27, whereas one isolate was assigned to ST162 and carried bla_CTX-M-65. The remaining isolate could not be assigned to a complete ST because of missing MLST loci, but it harbored bla_CTX-M-15, bla_OXA-1, and bla_TEM-1. Fluoroquinolone resistance-associated substitutions were detected in gyrA, parC, and parE in three isolates. The isolates shared a conserved set of VFs involved in adhesion, iron acquisition, and secretion systems. ARGs were frequently associated with insertion sequences and IncF plasmid replicons, indicating a potential contribution of mobile genetic elements (MGEs) to the dissemination of antimicrobial resistance. Conclusions: Despite the limited number of isolates, these findings provide preliminary genomic evidence of the presence of ST1193 and diverse ESBL-producing urinary E. coli lineages among pediatric patients in Guayaquil, supporting the need for expanded genomic surveillance and antimicrobial stewardship efforts at the hospital level.

Staphylococcus aureus is characterized by substantial genomic diversity, with lineages differing in antimicrobial resistance, virulence-associated determinants, and accessory genetic content. However, genomic data from Ecuador remain comparatively limited. Here, we characterized five clinical S. aureus isolates recovered in Ibarra, Ecuador, using phenotypic antimicrobial susceptibility testing and whole-genome sequencing, and compared them with publicly available Ecuadorian genomes. The isolates represented four sequence types (ST8, ST30, ST72, and ST2625), including four MRSA isolates and one MSSA isolate. Whole-genome analysis identified differences in antimicrobial resistance determinants, virulence-associated genes, and replicons, while phenotypic susceptibility profiles generally corresponded with the detected resistance traits. The Ecuadorian collection showed a diverse population structure, with ST8 predominating. Placement within globally circulating lineages showed that the ST8 isolates clustered with USA300-LV (CA12), the ST30 isolate with G2-Sg2-Pr, and the ST72 isolate with clade B. A focused phylogenomic analysis of ST2625 showed limited genomic divergence among Ecuadorian and international isolates, with broadly similar resistance and virulence-associated profiles. These findings add genomic data from northern Ecuador and illustrate variation in the genetic composition of circulating S. aureus lineages. Continued genomic surveillance across additional geographic settings may help clarify the distribution and diversity of S. aureus in the country.

Carbapenem resistance in Enterobacteriaceae poses a major threat to public health because of the limited therapeutic options. The dissemination of the bla _KPC gene, which encodes KPC carbapenemases, typically occurs through Tn 4401 transposons and plasmids that facilitate its transmission. In this study, we analysed 802 genomes of ESKAPE pathogens and other Enterobacteriaceae from Ecuador, including both clinical and non-clinical isolates, to determine the prevalence and genetic context of bla _KPC-2 and bla _KPC-3 and their associated mobile genetic elements. Whole-genome analysis revealed several isolates carrying bla _KPC , with bla _KPC-3 restricted to Klebsiella pneumoniae . While most isolates harboured the Tn 4401a transposon, we identified a novel variant, Tn 4401l , in two K. pneumoniae isolates collected between 2020 and 2021. Additionally, two putative plasmids carrying Tn 4401a were reconstructed: pECU0072020, a mosaic multidrug-resistant plasmid with a unique genetic organization, and pECU0062021, a more compact structure carrying only bla _KPC-2 . The findings demonstrate the wide distribution of bla _KPC within diverse bacterial hosts across multiple regions of Ecuador, the emergence of a novel Tn 4401l variant and the presence of putative plasmids that could potentially accelerate multidrug resistance dissemination. This study highlights the need for continuous genomic surveillance and coordinated strategies and practices regarding the use of antibiotics to mitigate the risk of outbreaks and interspecies transmission of carbapenem resistance.

Uropathogenic Escherichia coli (UPEC) is one of the main causative agents of urinary tract infections (UTIs) worldwide, placing constant pressure on the healthcare systems of countries, particularl...