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Thirty-nine clinical isolates of Pseudomonas aeruginosa collected from 11 cystic fibrosis (CF) patients at two CF attention centers over 10 years were subjected to whole genome sequencing (WGS). Phenotypic tests (i.e., elastase, motility, biofilm, growth rate, and antibiotic susceptibility) were performed to correlate results. A single strain of P. aeruginosa was found to persist over time in longitudinal isolates. No transmission between patients or centers was observed. A tendency to lack genes related to pyoverdine, flagellum, pili, and O-antigen was observed, whereas those related to biofilm, phenazine, and pyochelin were conserved among isolates. In a patient with a 10-year follow-up, a single strain of P. aeruginosa persisted and showed a gradual decrease in elastase activity and growth rate, demonstrating an adaptive phenotype. IMPORTANCE This study investigates the genomic and phenotypic characteristics of Pseudomonas aeruginosa isolates from Mexican cystic fibrosis (CF) patients, an underrepresented group in CF research. To our knowledge, it is the first to use whole genome sequencing (WGS) to study longitudinally collected P. aeruginosa isolates from this population, evaluating both genomic features and clonal relationships. Remarkably, the study includes samples from one patient over 10 years, offering an extended observation time compared to existing literature. Unlike similar studies, which often lack phenotypic testing, this research incorporates various virulence-related phenotypic assays, enhancing our understanding of gene-to-phenotype correlations. Two potential mechanisms for the loss of elastolytic activity were identified. Furthermore, we conduct an in-depth mobilome analysis, an area that remains largely unexplored in CF contexts. Whole genome sequencing data are publicly available through the NCBI SRA database, facilitating further re-analysis for studies on P. aeruginosa in CF, as well as epidemiological and population structure research.

The classification of carbapenemases can help guide therapy. The present study evaluated the performance of the CPO detection test, included in the BD Phoenix ™ NMIC-501 panel for the detection and classification of carbapenemases on the representative molecularly characterized strains collection from Mexico. Carbapenem non-susceptible isolates collected in Mexico were included. The clinical isolates ( n = 484) comprised Klebsiella pneumoniae ( n = 154), Escherichia coli ( n = 150), and P. aeruginosa ( n = 180). BD Phoenix CPO NMIC-504 and NMIC-501 panels were used for the identification of species, antimicrobial susceptibility tests, and detection of CPOs. For the detection of carbapenemase-encoding genes, E. coli and K. pneumoniae were evaluated using PCR assays for bla NDM-1 , bla KPC , bla VIM , bla IMP , and bla OXA-48-like . For P. aeruginosa , bla VIM, bla IMP, and bla GES were detected using PCR. Regarding E. coli , the CPO panels had a sensitivity of 70% and specificity of 83.33% for the detection of a class B carbapenemase ( bla NDM in the molecular test). Regarding K. pneumoniae , the panels had a sensitivity of 75% and specificity of 100% for the detection of a class A carbapenemase ( bla KPC in the molecular test). The Phoenix NMIC-501 panels are reliable for detecting class B carbapenemases in E. coli . The carbapenemase classification in K. pneumoniae for class A carbapenemases has a high specificity and PPV; thus, a positive result is of high value.

We analyzed the antimicrobial resistance (AMR) data of 6519 clinical isolates of Escherichia coli ( n = 3985), Klebsiella pneumoniae ( n = 775), Acinetobacter baumannii ( n = 163), Pseudomonas aeruginosa ( n = 781), Enterococcus faecium ( n = 124), and Staphylococcus aureus ( n = 691) from 43 centers in Mexico. AMR assays were performed using commercial microdilution systems (37/43) and the disk diffusion susceptibility method (6/43). The presence of carbapenemase-encoding genes was assessed using PCR. Data from centers regarding site of care, patient age, and clinical specimen were collected. According to the site of care, the highest AMR was observed in E. coli , K. pneumoniae , and P. aeruginosa isolates from ICU patients. In contrast, in A. baumannii , higher AMR was observed in isolates from hospitalized non-ICU patients. According to age group, the highest AMR was observed in the ≥60 years age group for E. coli , E. faecium , and S. aureus , and in the 19-59 years age group for A. baumannii and P. aeruginosa . According to clinical specimen type, a higher AMR was observed in E. coli , K. pneumoniae , and P. aeruginosa isolates from blood specimens. The most frequently detected carbapenemase-encoding gene in E. coli was bla NDM (84%).

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 bla NDM-1 explained carbapenem non-susceptibility in 18 strains and bla KPC-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 bla NDM , 3 of 24 (12.4%) carried bla OXA-232 , and 1 carried bla OXA -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 bla OXA-72 , followed by bla OXA-66 . Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, bla VIM , bla IMP , and bla GES 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., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

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 bla NDM (86/103 [83.5%] and 72/80 [90%], respectively). For carbapenem-resistant A. baumannii , the most frequently detected gene was bla OXA-40 (52/86, 60.5%), and for carbapenem-resistant P. aeruginosa , was bla VIM (19/82, 23.2%). For carbapenem-resistant A. baumannii , five indistinguishable pulsotypes were detected. Circulation of K. pneumoniae New Delhi metallo-β-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.

Background: Antimicrobial resistance is a global concern. Analysis of sterile fluids is essential because microorganisms are defined as significant in most cases. Blood, cerebrospinal, and pleural fluids are frequently received in the microbiology lab because they are associated with considerable rates of morbi-mortality. Knowledge of epidemiology in these samples is needed to choose proper empirical treatments due to the importance of reducing selection pressure., Methods: We used retrospective laboratory data of blood, CSF, and pleural fluid collected from patients in Mexico between 2019 and 2020. Each laboratory identified the strains and tested susceptibility using its routine methods. For Streptococcus pneumoniae , a comparative analysis was performed with data from the broth microdilution method., Results: Forty-five centers participated in the study, with 30,746 clinical isolates from blood, 2,429 from pleural fluid, and 2,275 from CSF. For blood and CSF, Staphylococcus epidermidis was the most frequent. For blood, among gram negatives, the most frequent was Escherichia coli . Among Enterobacterales , 9.8% of K. pneumoniae were carbapenem-resistant . For S. pneumoniae , similar resistance percentages were observed for levofloxacin, cefotaxime, and vancomycin. For CSF, the most frequent gram-negative was E. coli. In Acinetobacter baumannii , carbapenem resistance was 71.4%. The most frequent species detected for pleural fluid was E. coli ; in A. baumannii , carbapenem resistance was 96.3%., Conclusion: Gram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae , the routine, conventional methods showed good agreement in detecting resistance percentages for erythromycin, levofloxacin, and vancomycin., Competing Interests: Daniel Romero-Romero is employed by Análisis Bioquímico Clínicos “Louis Pasteur” and Guadalupe Soledad Huirache-Villalobos is employed by Laboratorios del Centro. The authors declare there are no competing interests., (©2023 Garza-González et al.)

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.

Aim: This report presents phenotypic and genetic data on the prevalence and characteristics of extended-spectrum β-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., Competing Interests: The authors have declared that no competing interests exist.

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.

Aim: We aimed to assess the resistance rates of antimicrobial-resistant, in bacterial pathogens of epidemiological importance in 47 Mexican centers., Material and Methods: In this retrospective study, we included a stratified sample of 47 centers, covering 20 Mexican states. Selected isolates considered as potential causatives of disease collected over a 6-month period were included. Laboratories employed their usual methods to perform microbiological studies. The results were deposited into a database and analyzed with the WHONET 5.6 software., Results: In this 6-month study, a total of 22,943 strains were included. Regarding Gram-negatives, carbapenem resistance was detected in ≤ 3% in Escherichia coli, 12.5% in Klebsiella sp. and Enterobacter sp., and up to 40% in Pseudomonas aeruginosa; in the latter, the resistance rate for piperacillin-tazobactam (TZP) was as high as 19.1%. In Acinetobacter sp., resistance rates for cefepime, ciprofloxacin, meropenem, and TZP were higher than 50%. Regarding Gram-positives, methicillin resistance in Staphylococcus aureus (MRSA) was as high as 21.4%, and vancomycin (VAN) resistance reached up to 21% in Enterococcus faecium. Acinetobacter sp. presented the highest multidrug resistance (53%) followed by Klebsiella sp. (22.6%) and E. coli (19.4%)., Conclusion: The multidrug resistance of Acinetobacter sp., Klebsiella sp. and E. coli and the carbapenem resistance in specific groups of enterobacteria deserve special attention in Mexico. Vancomycin-resistant enterococci (VRE) and MRSA are common in our hospitals. Our results present valuable information for the implementation of measures to control drug resistance., Competing Interests: The authors have declared that no competing interests exist.

Introduction: Among beta-hemolytic streptococci, Streptococcus pyogenes causes a wide variety of human disease including pharyngitis, necrotizing fasciitis and streptococcal toxic syndrome. Group A Streptococcus (GAS) uses a variety of virulence traits to colonize and then cause damage to the host; others species of beta-hemolytic streptococci are considered as emerging pathogens for humans. Despite its recognized virulence, only few studies have investigated virulence factors of GAS strains isolated in Mexico., Methodology: We conducted an epidemiological study to investigate the prevalence of GAS strains in child illnesses in Chiapas Mexico. Virulence genes encoding proteases, DNases, superantigens, as well as susceptibility to antibiotics were investigated., Results: During 2010, 2013 and 2014, beta-hemolytic streptococci (N=12) were isolated from cases of bacterial infections including pharyngitis and bacteremia, with a prevalence of 0.42, 0.04 and 0.20%, respectively. S. pyogenes was the most frequent species (33%) followed by S. agalactiae and S. dysgalactiae subsp. equisimilis (25%, each). Most GAS strains encoded genes for proteases: scpA, speB, spyCEP and mac (75%), followed by sdaD and sdaB (DNases) (50%), speA and speG (superantigens; 50 and 25%, respectively). The scpA gene was amplified in all S. agalactiae strains and in ~35% of SDSE strains. Strains were all susceptible to beta-lactams, cephalosporins and quinolones., Conclusions: The present study provides evidence on the epidemiology of beta-hemolytic streptococci infecting children at the southeast Mexico, their virulence traits and sensitivity to first-line antibiotics.