Molecular characterization of carbapenemase-producing Enterobacterales in a tertiary hospital in Lima, Peru.

Carbapenemase-producing Enterobacterales (CPE) are a growing threat to global health and the economy. Understanding the interactions between resistance and virulence mechanisms of CPE is crucial for managing difficult-to-treat infections and informing outbreak prevention and control programs. Here, we report the characterization of 21 consecutive, unique clinical isolates of CPE collected in 2018 at a tertiary hospital in Lima, Peru. Isolates were characterized by phenotypic antimicrobial susceptibility testing and whole-genome sequencing to identify resistance determinants and virulence factors. Seven Klebsiella pneumoniae isolates were classified as extensively drug-resistant. The remaining Klebsiella, Enterobacter hormaechei, and Escherichia coli isolates were multidrug-resistant. Eighteen strains carried the metallo-ß-lactamase NDM-1, two the serine-carbapenemase KPC-2, and one isolate had both carbapenemases. The blaNDM-1 gene was located in the truncated ΔISAba125 element, and the blaKPC-2 gene was in the Tn4401a transposon. ST147 was the most frequent sequence type among K. pneumoniae isolates. Our findings highlight the urgent need to address the emergence of CPE and strengthen control measures and antibiotic stewardship programs in low- and middle-income settings.IMPORTANCEGenomic surveillance of antimicrobial resistance contributes to monitoring the spread of resistance and informs treatment and prevention strategies. We characterized 21 carbapenemase-producing Enterobacterales collected at a Peruvian tertiary hospital in 2018, which exhibited very high levels of resistance and carried numerous resistance genes. We detected the coexistence of carbapenemase-encoding genes (blaNDM-1 and blaKPC-2) in a Klebsiella pneumoniae isolate that also had the PmrB(R256G) mutation associated with colistin resistance. The blaKPC-2 genes were located in Tn4401a transposons, while the blaNDM-1 genes were in the genetic structure Tn125 (ΔISAba125). The presence of high-risk clones among Klebsiella pneumoniae (ST11 and ST147) and Escherichia coli (ST410) isolates is also reported. The study reveals the emergence of highly resistant bacteria in a Peruvian hospital, which could compromise the effectiveness of current treatments and control.

Rapid Detection of SARS-CoV-2 RNA Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA) with Lateral Flow for N-Protein Gene and Variant-Specific Deletion-Insertion Mutation in S-Protein Gene.

Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion-insertion mutations (del211/ins214). Both tests had a detection limit of 10 copies/µL in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (>9015.7 copies/µL, cycle quantification (Cq): < 25) and moderate (385.5-9015.7 copies/µL, Cq: 25-29.9) viral load, 83.3% for low (16.5-385.5 copies/µL, Cq: 30-34.9), and 14.3% for very low (<16.5 copies/µL, Cq: 35-40). The sensitivities of the Omicron BA.1 (S) RT-RPA-LF were 94.9%, 78%, 23.8%, and 0%, respectively, and the specificity against non-BA.1 SARS-CoV-2-positive samples was 96%. The assays seemed more sensitive than rapid antigen detection in moderate viral load samples. Although implementation in resource-limited settings requires additional improvements, deletion-insertion mutations were successfully detected by the RT-RPA-LF technique.

First Report of OXA-181-Producing Enterobacterales Isolates in Latin America.

We characterized five carbapenemase-producing Enterobacterales (CPE) isolates from two health care institutions in Lima, Peru. The isolates were identified as Klebsiella pneumoniae (n = 3), Citrobacter portucalensis (n = 1), and Escherichia coli (n = 1). All were identified as blaOXA-48-like gene carriers using conventional PCR. Whole-genome sequencing found the presence of the blaOXA-181 gene as the only carbapenemase gene in all isolates. Genes associated with resistance to aminoglycosides, quinolones, amphenicols, fosfomycins, macrolides, tetracyclines, sulfonamides, and trimethoprim were also found. The plasmid incompatibility group IncX3 was identified in all genomes in a truncated Tn6361 transposon flanked by ΔIS26 insertion sequences. The qnrS1 gene was also found downstream of blaOXA-181, conferring fluoroquinolone resistance to all isolates. CPE isolates harboring blaOXA-like genes are an increasing public health problem in health care settings worldwide. The IncX3 plasmid is involved in the worldwide dissemination of blaOXA-181, and its presence in these CPE isolates suggests the wide dissemination of blaOXA-181 in Peru. IMPORTANCE Reports of carbapenemase-producing Enterobacterales (CPE) isolates are increasing worldwide. Accurate detection of the ß-lactamase OXA-181 (a variant of OXA-48) is important to initiate therapy and preventive measures in the clinic. OXA-181 has been described in CPE isolates in many countries, often associated with nosocomial outbreaks. However, the circulation of this carbapenemase has yet to be reported in Peru. Here, we report the detection of five multidrug-resistant CPE clinical isolates harboring blaOXA-181 in the IncX3-type plasmid, a potential driver of dissemination in Peru.

Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru.

E. coli that produce extended-spectrum ß-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK®2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities.

Frequency of colistin resistance in Pseudomonas aeruginosa: first report from Peru. / Frecuencia de resistencia a la colistina en Pseudomonas aeruginosa: primer reporte en el Perú.

This study aimed to determine the frequency of colistin resistance in Pseudomonas aeruginosa isolates obtained from three healthcare facilities in Lima and cryopreserved at the Laboratorio de Resistencia Antimicrobianos e Inmunopatología of the Universidad Peruana Cayetano Heredia (UPCH). The colistin broth disk elution method was used for the phenotypic identification of colistin resistance. We detected the expression of the mcr-1 gene by using the phenotypic diffusion method with combined colistin and ethylenediaminetetraacetic acid (EDTA) disks; and polymerase chain reaction (PCR) was used for molecular identification of the gene. Of the 97 isolates, 7 (7.2%) were resistant to colistin; however, none carried the mcr-1 gene. This is the first report from Peru on clinical isolates of colistin-resistant Pseudomonas aeruginosa, which suggests the need for implementation of appropriate methodologies for the epidemiological surveillance of colistin-resistant pathogens.

El objetivo del estudio fue determinar la frecuencia de resistencia a la colistina en Pseudomonas aeruginosa provenientes de tres establecimientos de salud de Lima, criopreservados en el banco de cepas del Laboratorio de Resistencia a Antimicrobianos e Inmunopatología de la Universidad Peruana Cayetano Heredia (UPCH). El método de elución de discos de colistina en caldo fue empleado para la identificación fenotípica de la resistencia a la colistina; la detección de la expresión del gen mcr-1 se realizó mediante el método fenotípico de difusión de discos combinados de colistina y ácido etilendiaminotetraacético (EDTA) y la reacción en cadena de la polimerasa (PCR) para la identificación molecular del gen. De los 97 aislados estudiados, 7 (7,2%) fueron resistentes a la colistina y ninguno fue portador del gen mcr-1. Este estudio constituye el primer reporte en el Perú de aislados clínicos de Pseudomonas aeruginosa resistentes a la colistina, lo que implica la necesidad de implementar metodologías apropiadas para la vigilancia epidemiológica de patógenos resistentes a la colistina.

Draft Genome Sequence of a blaKPC-2-Carrying Citrobacter braakii Isolate from Pediatric Hospital Wastewater in Peru.

Here, we report a draft genome sequence of a blaKPC-2-carrying Citrobacter braakii isolate from pediatric hospital effluent. Genome CF248 represents a multidrug-resistant C. braakii isolate derived from a clinical environment in Peru.

Frecuencia de resistencia a la colistina en Pseudomonas aeruginosa: primer reporte en el Perú

El objetivo del estudio fue determinar la frecuencia de resistencia a la colistina en Pseudomonas aeruginosa provenientes de tres establecimientos de salud de Lima, criopreservados en el banco de cepas del Laboratorio de Resistencia a Antimicrobianos e Inmunopatología de la Universidad Peruana Cayetano Heredia (UPCH). El método de elución de discos de colistina en caldo fue empleado para la identificación fenotípica de la resistencia a la colistina; la detección de la expresión del gen mcr-1 se realizó mediante el método fenotípico de difusión de discos combinados de colistina y ácido etilendiaminotetraacético (EDTA) y la reacción en cadena de la polimerasa (PCR) para la identificación molecular del gen. De los 97 aislados estudiados, 7 (7,2%) fueron resistentes a la colistina y ninguno fue portador del gen mcr-1. Este estudio constituye el primer reporte en el Perú de aislados clínicos de Pseudomonas aeruginosa resistentes a la colistina, lo que implica la necesidad de implementar metodologías apropiadas para la vigilancia epidemiológica de patógenos resistentes a la colistina.

This study aimed to determine the frequency of colistin resistance in Pseudomonas aeruginosa isolates obtained from three healthcare facilities in Lima and cryopreserved at the Laboratorio de Resistencia Antimicrobianos e Inmunopatología of the Universidad Peruana Cayetano Heredia (UPCH). The colistin broth disk elution method was used for the phenotypic identification of colistin resistance. We detected the expression of the mcr-1 gene by using the phenotypic diffusion method with combined colistin and ethylenediaminetetraacetic acid (EDTA) disks; and polymerase chain reaction (PCR) was used for molecular identification of the gene. Of the 97 isolates, 7 (7.2%) were resistant to colistin; however, none carried the mcr-1 gene. This is the first report from Peru on clinical isolates of colistin-resistant Pseudomonas aeruginosa, which suggests the need for implementation of appropriate methodologies for the epidemiological surveillance of colistin-resistant pathogens.

Draft Genome Sequence of a New Delhi Metallo-ß-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru.

Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-ß-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.