Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms.

OBJECTIVES: To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQⓇ CS application and other bioinformatic platforms. METHODS: Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQⓇ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii. RESULTS: For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQⓇ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, 3 of 24 (12.4%) carried blaOXA-232, and 1 carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. CONCLUSION: Compared to the other available platforms, EPISEQⓇ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.

Carbapenemase-Encoding Genes and Colistin Resistance in Gram-Negative Bacteria During the COVID-19 Pandemic in Mexico: Results from the Invifar Network.

In this study, we report the carbapenemase-encoding genes and colistin resistance in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa in the second year of the COVID-19 pandemic. Clinical isolates included carbapenem-resistant K. pneumoniae, carbapenem-resistant E. coli, carbapenem-resistant A. baumannii, and carbapenem-resistant P. aeruginosa. Carbapenemase-encoding genes were detected by PCR. Carbapenem-resistant K. pneumoniae and carbapenem-resistant E. coli isolates were analyzed using the Rapid Polymyxin NP assay. mcr genes were screened by PCR. Pulsed-field gel electrophoresis and whole-genome sequencing were performed on representative isolates. A total of 80 carbapenem-resistant E. coli, 103 carbapenem-resistant K. pneumoniae, 284 carbapenem-resistant A. baumannii, and 129 carbapenem-resistant P. aeruginosa isolates were recovered. All carbapenem-resistant E. coli and carbapenem-resistant K. pneumoniae isolates were included for further analysis. A selection of carbapenem-resistant A. baumannii and carbapenem-resistant P. aeruginosa strains was further analyzed (86 carbapenem-resistant A. baumannii and 82 carbapenem-resistant P. aeruginosa). Among carbapenem-resistant K. pneumoniae and carbapenem-resistant E. coli isolates, the most frequent gene was blaNDM (86/103 [83.5%] and 72/80 [90%], respectively). For carbapenem-resistant A. baumannii, the most frequently detected gene was blaOXA-40 (52/86, 60.5%), and for carbapenem-resistant P. aeruginosa, was blaVIM (19/82, 23.2%). For carbapenem-resistant A. baumannii, five indistinguishable pulsotypes were detected. Circulation of K. pneumoniae New Delhi metallo-ß-lactamase (NDM) and E. coli NDM was detected in Mexico. High virulence sequence types (STs), such as K. pneumoniae ST307, E. coli ST167, P. aeruginosa ST111, and A. baumannii ST2, were detected. Among K. pneumoniae isolates, 18/101 (17.8%) were positive for the Polymyxin NP test (two, 11.0% positive for the mcr-1 gene, and one, 5.6% with disruption of the mgrB gene). All E. coli isolates were negative for the Polymyxin NP test. In conclusion, K. pneumoniae NDM and E. coli NDM were detected in Mexico, with the circulation of highly virulent STs. These results are relevant in clinical practice to guide antibiotic therapies considering the molecular mechanisms of resistance to carbapenems.

Increment Antimicrobial Resistance During the COVID-19 Pandemic: Results from the Invifar Network.

Aim: This study aims to assess the changes in antimicrobial resistance among some critical and high-priority microorganisms collected previously and during the coronavirus disease 2019 (COVID-19) pandemic in Mexico. Methods: We collected antimicrobial susceptibility data for critical and high-priority microorganisms from blood, urine, respiratory samples, and from all specimens, in which the pathogen may be considered a causative agent. Data were stratified and compared for two periods: 2019 versus 2020 and second semester 2019 (prepandemic) versus the second semester 2020 (pandemic). Results: In the analysis of second semester 2019 versus the second semester 2020, in blood samples, increased resistance to oxacillin (15.2% vs. 36.9%), erythromycin (25.7% vs. 42.8%), and clindamycin (24.8% vs. 43.3%) (p ≤ 0.01) was detected for Staphylococcus aureus, to imipenem (13% vs. 23.4%) and meropenem (11.2% vs. 21.4) (p ≤ 0.01), for Klebsiella pneumoniae. In all specimens, increased ampicillin and tetracycline resistance was detected for Enterococcus faecium (p ≤ 0.01). In cefepime, meropenem, levofloxacin, and gentamicin (p ≤ 0.01), resistance was detected for Escherichia coli; and in piperacillin-tazobactam, cefepime, imipenem, meropenem, ciprofloxacin, levofloxacin, and gentamicin (p ≤ 0.01), resistance was detected for Pseudomonas aeruginosa. Conclusion: Antimicrobial resistance increased in Mexico during the COVID-19 pandemic. The increase in oxacillin resistance for S. aureus and carbapenem resistance for K. pneumoniae recovered from blood specimens deserves special attention. In addition, an increase in erythromycin resistance in S. aureus was detected, which may be associated with high azithromycin use. In general, for Acinetobacter baumannii and P. aeruginosa, increasing resistance rates were detected.

Drug resistance phenotypes and genotypes in Mexico in representative gram-negative species: Results from the infivar network.

AIM: This report presents phenotypic and genetic data on the prevalence and characteristics of extended-spectrum ß-lactamases (ESBLs) and representative carbapenemases-producing Gram-negative species in Mexico. MATERIAL AND METHODS: A total of 52 centers participated, 43 hospital-based laboratories and 9 external laboratories. The distribution of antimicrobial resistance data for Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae complex, Acinetobacter baumannii complex, and Pseudomonas aeruginosa in selected clinical specimens from January 1 to March 31, 2020 was analyzed using the WHONET 5.6 platform. The following clinical isolates recovered from selected specimens were included: carbapenem-resistant Enterobacteriaceae, ESBL or carbapenem-resistant E. coli, and K. pneumoniae, carbapenem-resistant A. baumannii complex, and P. aeruginosa. Strains were genotyped to detect ESBL and/or carbapenemase-encoding genes. RESULTS: Among blood isolates, A. baumannii complex showed more than 68% resistance for all antibiotics tested, and among Enterobacteria, E. cloacae complex showed higher resistance to carbapenems. A. baumannii complex showed a higher resistance pattern for respiratory specimens, with only amikacin having a resistance lower than 70%. Among K. pneumoniae isolates, blaTEM, blaSHV, and blaCTX were detected in 68.79%, 72.3%, and 91.9% of isolates, respectively. Among E. coli isolates, blaTEM, blaSHV, and blaCTX were detected in 20.8%, 4.53%, and 85.7% isolates, respectively. For both species, the most frequent genotype was blaCTX-M-15. Among Enterobacteriaceae, the most frequently detected carbapenemase-encoding gene was blaNDM-1 (81.5%), followed by blaOXA-232 (14.8%) and blaoxa-181(7.4%), in A. baumannii was blaOXA-24 (76%) and in P. aeruginosa, was blaIMP (25.3%), followed by blaGES and blaVIM (13.1% each). CONCLUSION: Our study reports that NDM-1 is the most frequent carbapenemase-encoding gene in Mexico in Enterobacteriaceae with the circulation of the oxacillinase genes 181 and 232. KPC, in contrast to other countries in Latin America and the USA, is a rare occurrence. Additionally, a high circulation of ESBL blaCTX-M-15 exists in both E. coli and K. pneumoniae.

The Evolution of Antimicrobial Resistance in Mexico During the Last Decade: Results from the INVIFAR Group.

Background: Surveillance of antimicrobial resistance (AMR) requires an international approach with national and local strategies. Our aim was to summarize a retrospective 10-year report of antibiotic resistance of gram-positive and gram-negative bacteria in Mexico. Methods: A total of 46 centers from 22 states of Mexico participated. Databases of AMR from January 2009 to December 2018 were included for most species. The 10-year period was divided into five 2-year periods. Results: For Staphylococcus aureus, a decrease in resistance in all specimens was observed for erythromycin and oxacillin (p < 0.0001 for each). For Enterobacter spp., resistance to meropenem increased for urine specimens (p = 0.0042). For Klebsiella spp., increased drug resistance in specimens collected from blood was observed for trimethoprim/sulfamethoxazole, gentamicin, tobramycin (p < 0.0001 for each), meropenem (p = 0.0014), and aztreonam (p = 0.0030). For Acinetobacter baumannii complex, high drug resistance was detected for almost all antibiotics, including carbapenems, except for tobramycin, which showed decreased resistance for urine, respiratory, and blood isolates (p < 0.0001 for each), and for amikacin, which showed a decrease in resistance in urine specimens (p = 0.0002). An increase in resistance to cefepime was found for urine, respiratory, and blood specimens (p < 0.0001 for each). For Pseudomonas aeruginosa, aztreonam resistance increased for isolates recovered from blood (p = 0.0001). Conclusion: This laboratory-based surveillance of antibiotic resistance shows that resistance is increasing for some antibiotics in different bacterial species in Mexico and highlights the need for continuous monitoring of antibiotic resistance.

Early discharge of pediatric patients with cancer, fever, and neutropenia with low-risk of systemic infection / Egreso temprano en pacientes pediátricos con cáncer, fiebre y neutropenia con bajo riesgo de infección sistémica

Abstract: Background: Ambulatory therapy in low-risk patients with cancer, fever, and neutropenia seems to be a secure and effective alternative. This study aimed to compare the effectiveness and safety of the antimicrobial treatment in early discharge vs. in-hospital treatment in children with cancer and febrile neutropenia (FN) with low risk of invasive bacterial infection (IBI). Methods: Quasi-experimental design with a historical cohort control group. Children with cancer during an episode of FN and low risk of IBI were included. The control group were inpatient children that received intravenous piperacillin/tazobactam. The experimental group was early discharge patients, who received 48 h of IV treatment and were switched to oral treatment. Outcomes: fever resolution, readmissions, and mortality. Results: Eighty low-risk FN episodes were included; the median age was 6 years old (2.6-11 years), and 43 (54%) were female. Main diagnoses were solid tumors (52 patients) and leukemia or lymphoma (28 patients). Forty-three patients received in-hospital treatment, and 37 were selected for early discharge (31 patients received ciprofloxacin and six received amoxicillin/clavulanate). Two patients were readmitted, one due to a relapse of fever with tumor progression and the other due to epistaxis. Adverse effects occurred in 21.6% of the early discharge group and 12% of the inpatient treatment group (p = 0.04). Conclusions: Early discharge in pediatric patients with cancer, fever, and neutropenia is an acceptable and safe alternative for low-risk patients.

Resumen: Introducción: El tratamiento ambulatorio en pacientes con cáncer, fiebre y neutropenia de bajo riesgo parece ser una alternativa segura y efectiva. El objetivo de este trabajo fue comparar la efectividad y la seguridad del tratamiento antimicrobiano en la modalidad de egreso temprano vs. el tratamiento intrahospitalario en niños con cáncer y neutropenia febril (NF), con bajo riesgo de infección bacteriana invasiva (IBI). Métodos: Diseño cuasi-experimental con un grupo control histórico. Se incluyeron niños con cáncer durante un episodio de NF con bajo riesgo de IBI. El grupo control fue constituido por pacientes que recibieron tratamiento hospitalario con piperacilina-tazobactam intravenosa. Los pacientes en el grupo de egreso temprano recibieron 48 horas de tratamiento intravenoso y egresaron con antimicrobianos por vía oral. Desenlaces: resolución de la fiebre, reingreso al hospital y muerte. Resultados: Se incluyeron 80 pacientes con NF de bajo riesgo; la mediana de edad fue de 6 años; 43 pacientes (54%) eran de sexo femenino. Los diagnósticos principales fueron tumores sólidos (52) y leucemia o linfoma (28). Cuarenta y tres pacientes recibieron tratamiento hospitalario y 37 fueron seleccionados para egreso temprano. En el grupo de egreso temprano, 31 pacientes recibieron ciprofloxacino y 6 recibieron amoxicilina-clavulanato. Dos pacientes reingresaron, uno por fiebre secundaria a progresión tumoral y otro por epistaxis. Los efectos adversos se presentaron en el 21.6% de los pacientes en el grupo de egreso temprano y en el 12% del grupo de tratamiento hospitalario (p = 0.04). Conclusiones: El egreso temprano para niños con cáncer y NF de bajo riesgo es una alternativa aceptable y segura.

Early discharge of pediatric patients with cancer, fever, and neutropenia with low-risk of systemic infection.

Background: Ambulatory therapy in low-risk patients with cancer, fever, and neutropenia seems to be a secure and effective alternative. This study aimed to compare the effectiveness and safety of the antimicrobial treatment in early discharge vs. in-hospital treatment in children with cancer and febrile neutropenia (FN) with low risk of invasive bacterial infection (IBI). Methods: Quasi-experimental design with a historical cohort control group. Children with cancer during an episode of FN and low risk of IBI were included. The control group were inpatient children that received intravenous piperacillin/tazobactam. The experimental group was early discharge patients, who received 48 h of IV treatment and were switched to oral treatment. Outcomes: fever resolution, readmissions, and mortality. Results: Eighty low-risk FN episodes were included; the median age was 6 years old (2.6-11 years), and 43 (54%) were female. Main diagnoses were solid tumors (52 patients) and leukemia or lymphoma (28 patients). Forty-three patients received in-hospital treatment, and 37 were selected for early discharge (31 patients received ciprofloxacin and six received amoxicillin/clavulanate). Two patients were readmitted, one due to a relapse of fever with tumor progression and the other due to epistaxis. Adverse effects occurred in 21.6% of the early discharge group and 12% of the inpatient treatment group (p = 0.04). Conclusions: Early discharge in pediatric patients with cancer, fever, and neutropenia is an acceptable and safe alternative for low-risk patients.

Introducción: El tratamiento ambulatorio en pacientes con cáncer, fiebre y neutropenia de bajo riesgo parece ser una alternativa segura y efectiva. El objetivo de este trabajo fue comparar la efectividad y la seguridad del tratamiento antimicrobiano en la modalidad de egreso temprano vs. el tratamiento intrahospitalario en niños con cáncer y neutropenia febril (NF), con bajo riesgo de infección bacteriana invasiva (IBI). Métodos: Diseño cuasi-experimental con un grupo control histórico. Se incluyeron niños con cáncer durante un episodio de NF con bajo riesgo de IBI. El grupo control fue constituido por pacientes que recibieron tratamiento hospitalario con piperacilina-tazobactam intravenosa. Los pacientes en el grupo de egreso temprano recibieron 48 horas de tratamiento intravenoso y egresaron con antimicrobianos por vía oral. Desenlaces: resolución de la fiebre, reingreso al hospital y muerte. Resultados: Se incluyeron 80 pacientes con NF de bajo riesgo; la mediana de edad fue de 6 años; 43 pacientes (54%) eran de sexo femenino. Los diagnósticos principales fueron tumores sólidos (52) y leucemia o linfoma (28). Cuarenta y tres pacientes recibieron tratamiento hospitalario y 37 fueron seleccionados para egreso temprano. En el grupo de egreso temprano, 31 pacientes recibieron ciprofloxacino y 6 recibieron amoxicilina-clavulanato. Dos pacientes reingresaron, uno por fiebre secundaria a progresión tumoral y otro por epistaxis. Los efectos adversos se presentaron en el 21.6% de los pacientes en el grupo de egreso temprano y en el 12% del grupo de tratamiento hospitalario (p = 0.04). Conclusiones: El egreso temprano para niños con cáncer y NF de bajo riesgo es una alternativa aceptable y segura.

[Kawasaki disease: clinical behaviour and cardiovascular complications in children in a tertiary-care level hospital]. / Enfermedad de Kawasaki: comportamiento clínico y complicaciones cardiovasculares en niños atendidos en un hospital de tercer nivel.

OBJECTIVES: To describe the clinical characteristics, outcome, and treatment response in a series of patients with Kawasaki disease (KD). METHODS: Case-series, review of clinical records of children with KD diagnosis cared for from november 1999 to september 2006. RESULTS: 22 patients were included, male:female ratio, 1.4:1, 82% younger than 5 years, 14% with atypical presentation. Of the 22 patients, 10 (45%) received intravenous gammaglobulin (IVGG) in the first 10 days of symptoms onset at the recommended dose; four of them had coronary artery damage but none developed residual aneurysmatic lesions. Eight received IVGG in a different dose or after 10 days, six of them had coronary lesions and in two the damage was permanent. Four patients did not receive IVGG, and two had residual aneurysmatic lesions. None of those who received adequate treatment developed coronary residual damage, in comparison with 33% who received inadequate or no treatment, but difference was not statistically significant (P =.06). CONCLUSIONS: KD is a rare clinical entity in our country; even though most of the cases occurred with classic clinical criteria, late referral and delay of treatment worsen the prognosis.

Enfermedad de Kawasaki: comportamiento clínico y complicaciones cardiovasculares en niños atendidos en un hospital de tercer nivel / Kawasaki disease: clinical behaviour and cardiovascular complications in children in a tertiary-care level hospital

OBJECTIVES: To describe the clinical characteristics, outcome, and treatment response in a series of patients with Kawasaki disease (KD). METHODS: Case-series, review of clinical records of children with KD diagnosis cared for from november 1999 to september 2006. RESULTS: 22 patients were included, male:female ratio, 1.4:1, 82% younger than 5 years, 14% with atypical presentation. Of the 22 patients, 10 (45%) received intravenous gammaglobulin (IVGG) in the first 10 days of symptoms onset at the recommended dose; four of them had coronary artery damage but none developed residual aneurysmatic lesions. Eight received IVGG in a different dose or after 10 days, six of them had coronary lesions and in two the damage was permanent. Four patients did not receive IVGG, and two had residual aneurysmatic lesions. None of those who received adequate treatment developed coronary residual damage, in comparison with 33% who received inadequate or no treatment, but difference was not statistically significant (P =.06). CONCLUSIONS: KD is a rare clinical entity in our country; even though most of the cases occurred with classic clinical criteria, late referral and delay of treatment worsen the prognosis.