Multidrug-resistant Raoultella ornithinolytica misidentified as Klebsiella oxytoca carrying blaOXA ß-lactamases: antimicrobial profile and genomic characterization.

Class D ß-lactamases OXA-232 and OXA-48 hydrolyze penicillin, cephalosporins and carbapenems, limiting the pharmacological therapeutics in bacteraemia. OXA producer microorganisms are considered a great emergent threat, especially in nosocomial environments. To determine the resistance profile and genomic characterization of two isolates initially identified as potential carbapenemase-producer Klebsiella oxytoca in a third level hospital. Automated platform BD Phoenix-100 System was used to identify and to biochemically characterize both isolates. Furthermore, the resistance profile was determined through CLSI methods and the whole genome sequences were obtained using Next-Generation Sequencing. Resistance genes were analyzed, and the virtual fingerprinting was determined to corroborate the similarity with related bacteria. Both strains correspond to Raoultella ornithinolytica carrying OXA 232 and OXA-48 genes, confirming the class D ß-lactamases assay results. Here, we present the genetic and phenotypic analysis of multidrug resistance R. ornithinolytica, representing the first report in Mexico.

Parameters to Predict the Outcome of Severe and Critical COVID-19 Patients when Admitted to the Hospital.

Manifestations of COVID-19 are diverse and range from asymptomatic to severe, critical illness and death. Cases requiring hospital care (in severe and critical illnesses) are associated with comorbidities and hyperactivation of the immune system. Therefore, in this exploratory observational study, we analyzed which parameters are associated with mortality. We evaluated: demographic characteristics (age, sex and comorbidities), laboratory data (albumin, leukocytes, lymphocytes, platelets, ferritin), days of hospital stay, interleukins (IL-2, IL-6, IL-7, IL-10, IL-17) and sP-selectin in 40 Mexican patients admitted to medical emergencies with a confirmed diagnosis of COVID-19, a complete clinical record, and who signed the informed consent. Twenty severe (they required intermediate care with non-invasive ventilation) and twenty critically ill patients (they required mechanical ventilation) were classified, and these were subsequently compared with healthy and recovered subjects. A significant difference was found between the hospitalized groups in the parameters of age, ferritin, days of hospital stay and death with p values = 0.0145, p = 0.0441, p = 0.0001 and p = 0.0001, respectively. In the determination of cytokines and P-selectin, a significant difference was found between the following groups: recovered patients and healthy volunteers compared with hospitalized patients in severe and critical condition. Importantly, IL-7 remained elevated one year later in recovered patients. Taken together, these values determined at the time of hospital admission could be useful to monitor patients closely and evaluate in-hospital progress, hospital discharge, and out-of-hospital progress.

ESKAPE bacteria characterization reveals the presence of Acinetobacter baumannii and Pseudomonas aeruginosa outbreaks in COVID-19/VAP patients.

INTRODUCTION: A decrease of detection of outbreaks by multidrug-resistant bacteria in critical areas has been reduced due to COVID-19 pandemic. Therefore, molecular epidemiological surveillance should be a primary tool to reveal associations not evident by classical epidemiology. The aim of this work was to demonstrate the presence of hidden outbreaks in the first wave of the COVID-19 pandemic and to associate their possible origin. METHODS: A population of 96 COVID-19 patients was included in the study (April to June 2020) from Hospital Juárez de México. Genetic identification and antimicrobial susceptibility testing of VAP causative agents isolated from COVID-19 patients was performed. Resistance phenotypes were confirmed by PCR. Clonal association of isolates was performed by analysis of intergenic regions obtained. Finally, the association of clonal cases of VAP patients was performed by timelines. RESULTS: ESKAPE and non-ESKAPE bacteria were identified as causative agents of VAP. ESKAPE bacteria were classified as MDR and XDR. Only A. baumannii and P. aeruginosa were identified as clonally distributed in 13 COVID-19/VAP patients. Time analysis showed that cross-transmission existed between patients and care areas. CONCLUSIONS: Acinetobacter baumannii and Pseudomonas aeruginosa were involved in outbreaks non-detected in COVID-19/VAP patients in the first wave of COVID-19 pandemic.

Brachybacterium conglomeratum Is Associated with Cervicovaginal Infections and Human Papilloma Virus in Cervical Disease of Mexican Female Patients.

Brachybacterium conglomeratum, traditionally considered an environmental bacterium, has recently garnered attention for its potential involvement in human health. While prior research hinted at its pathogenic role in humans, our study aims to determine its prevalence and associations in diverse clinical contexts. We examined vaginal swabs from three distinct patient groups: patients with low-grade squamous intraepithelial lesions (LSIL), patients with cervicovaginal infections, and patients with a history of precancerous lesions undergoing follow-up. B. conglomeratum was present in all three patient groups, with the highest prevalence observed in the LSIL group. Statistically significant associations were primarily identified in the LSIL group, where B. conglomeratum was present in 60% of cases. Notably, the LSIL group exhibited coinfections with multiple high-risk oncogenotypes of human papillomavirus (HPV), suggesting potential synergistic effects, and understanding these microbial relationships and their influence on viral persistence, particularly with HPV, holds promise for mitigating HPV-related carcinogenesis. Furthermore, Gardnerella vaginalis and Atopobium vaginae were frequently detected in this group, along with Ureaplasma parvum as the predominant sexually transmitted bacterium. In all cases, B. conglomeratum was found in association with these microorganisms rather than as a sole pathogen. This coexistence underscores the intricate microbial interactions within cervicovaginal infections and precancerous lesions. This study marks the first report of B. conglomeratum prevalence in women with these clinical conditions.

Klebsiella pneumoniae blaNDM-1 carrying a class 1 integron causing a hospital outbreak in a Mexican attention center.

INTRODUCTION: Infections acquired in hospitals are the cause of high morbidity and mortality and with the emergence of resistant bacteria, the problem is greater. The aim of this work was to determine the genetic characteristics and timeline of Klebsiella pneumoniae blaNDM-1 carrying a class 1 integron involved in an intrahospital outbreak. METHODOLOGY: Investigation was made from the first detection of K. pneumoniae blaNDM-1, strain "466", and the last clone "423". 16S rRNA gene analysis showed that 466 strain and clones were related to K. pneumoniae. Extended-spectrum ß-lactamases (ESBL) was detected according to the Clinical and Laboratory Standards Institute (CLSI) and real time-PCR. Typing of K. pneumoniae blaNDM-1 strains was carried by ERIC-PCR and sequencing the variable region of the integrons were performed. RESULTS: A cluster of six resistant isolates of K. pneumoniae blaNDM-1 was detected in intensive care unit (ICU), internal medicine (IM) and orthopedics (OT). Timeline revealed that the first bacterial identification was in ICU and the last clone in OT service. The array genetic of variable region was "IntI/aadA5-drfA17/qacEΔ1-Sul1". CONCLUSIONS: The evidences highlight the importance of the epidemiological surveillance of Extended-spectrum ß-lactamases (ESBL) strains, as well as the need for molecular epidemiological studies to identify the routes of transmission and the contamination sources within health personnel.

Clonal dispersion of Acinetobacter baumannii in an intensive care unit designed to patients COVID-19.

INTRODUCTION: SARS-CoV2 pandemic marks the need to pay attention to bacterial pathogens that can complicate the hospital stay of patients in the intensive care unit (ICU). ESKAPE bacteria which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae are considered the most important, because of their close relationship with the development of ventilator-associated pneumonia (VAP). The aim of this work was to identify and characterize ESKAPE bacteria and to detect their possible clonal spread in medical devices, patients, and medical personnel of the ICU for COVID-19 patients of the Hospital Juarez de Mexico. METHODOLOGY: Genetic identification of ESKAPE bacteria was performed by analyzing the 16S rRNA gene. Resistance assays were performed according to the CLSI guidelines. Assembly of AdeABCRS operon and inhibition assays of pumps efflux in Acinetobacter baumannii isolates were performed. Associated gene involved in biofilm formation (icaA) was performed in isolates belonging to the Staphylococcus genus. Finally, typing by ERIC-PCR and characterization of mobile genetic element SCCmec were done. RESULTS: Heterogeneous distribution of ESKAPE and non-ESKAPE bacteria was detected in various medical devices, patients, and medical personnel. Acinetobacter baumannii and Staphylococcus aureus were the predominant ESKAPE members. The analysis of intergenic regions revealed an important clonal distribution of A. baumannii (AdeABCRS+). Genotyping of SCCmec mobile genetic elements and the icaA gene showed that there is no clonal distribution of S. aureus. CONCLUSIONS: Clonal spread of A. baumannii (AdeABCRS+) highlights the importance of adopting good practices for equipment disinfection, surfaces and management of COVID-19 patients.

Hsp65 phylogenetic assay for molecular diagnosis of nontuberculous mycobacteria isolated in Mexico.

BACKGROUND AND AIMS: Nontuberculous mycobacteria (NTM) are mainly distributed as important emerging pathogens in patients with chronic or immunosuppressive diseases. Accurate identification of causative species is crucial for proper treatment and patient follow-up. However, several difficulties are associated with phenotypic and molecular diagnostic methods for precise identification at the species level due to shared metabolic and genetic characteristics. We undertook this study to evaluate the application of the phylogenetic method based on hsp65 gene into Telenti's PCR-restriction enzyme analysis (PRA) for molecular identification of NTM. METHODS: The study population was comprised of 1646 Mycobacterium clinical isolates (AFB positive) collected from 2008-2011, of which 537 (32.6%) were MNT identified by PRA analysis. DNA sequencing of hsp65 in 53 isolates (10%) was performed. Sequence identification through NCBI-Basic Local Alignment Search Tool (BLAST) achieved correct identification in 23 isolates. Phylogenetic trees including hsp65 available GenBank sequences for all described genres of NTM and hsp65 obtained sequences were constructed using Mega 5.05 software. We compared sequence identification based on phylogenetic clustering and BLAST similarity search. RESULTS: Phylogenetic clustering allowed more specific differentiation of closely related species and clearer identification in comparison with BLAST; 30 Mycobacterium species (this is the first report of isolation of some of these from clinical samples in Mexico) were identified in this way. CONCLUSIONS: The proposed 440 bp hsp65 phylogenetic method allows a better identification tool to differentiate Mycobacterium species and is useful to complement diagnosis and epidemiological surveillance of NTM.

[Outbreak caused by Escherichia coli in Chalco, Mexico]. / Brote causado por Escherichia coli en Chalco, México.

OBJECTIVE: To identify the etiologic agent responsible for a disease outbreak following an overflow of sewage water in Valle de Chalco, Mexico. MATERIAL AND METHODS: A retrospective cross-sectional study was carried out. Rectal samples were collected from the population of Chalco valley, who suffered from diarrhea and vomiting during a natural disaster that took place on May 31, 2000. The Instituto de Diagnóstico y Referencia Epidemiológicos (Epidemic Reference and Diagnosis Institute, InDRE, Ministry of Health), received 1521 rectal swab samples from diarrhea cases, to test for E. coli strains. Statistical analysis was performed to find a difference of proportions between cases and non-cases (chi-squared test). ETEC, EIEC, EPEC and EHEC pathogenic E. coli groups were hybridized by colony blot. RESULTS: Strains isolated were ETEC (62.2%), EIEC (0.84%), EPEC (0.84%), and EHEC non-O157:H7 (0.08%); there was no hybridization in 36.02% of E. coli strains. Other isolated microorganisms were Salmonella spp (0.45%) and Shigella spp (0.06%). CONCLUSIONS: Enterotoxigenic E. coli was the most likely etiologic agent. Sanitary control strategies should be targeted to preventing outbreaks caused by this pathogenic agent. The English version of this paper is available at: http://www.insp.mx/salud/index.html.

Brote causado por Escherichia coli en Chalco, México / Outbreak caused by Escherichia coli in Chalco, Mexico

OBJECTIVE: To identify the etiologic agent responsible for a disease outbreak following an overflow of sewage water in Valle de Chalco, Mexico. MATERIAL AND METHODS: A retrospective cross-sectional study was carried out. Rectal samples were collected from the population of Chalco valley, who suffered from diarrhea and vomiting during a natural disaster that took place on May 31, 2000. The Instituto de Diagnóstico y Referencia Epidemiológicos (Epidemic Reference and Diagnosis Institute, InDRE, Ministry of Health), received 1521 rectal swab samples from diarrhea cases, to test for E. coli strains. Statistical analysis was performed to find a difference of proportions between cases and non-cases (chi-squared test). ETEC, EIEC, EPEC and EHEC pathogenic E. coli groups were hybridized by colony blot. RESULTS: Strains isolated were ETEC (62.2), EIEC (0.84), EPEC (0.84), and EHEC non-O157:H7 (0.08); there was no hybridization in 36.02 of E. coli strains. Other isolated microorganisms were Salmonella spp (0.45) and Shigella spp (0.06). CONCLUSIONS: Enterotoxigenic E. coli was the most likely etiologic agent. Sanitary control strategies should be targeted to preventing outbreaks caused by this pathogenic agent.