WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil.

The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974-2019). One hundred sixty-seven genomes were analyzed extracting clinically relevant information (i.e., resistome, virulome, mobilome, sequence types [STs], and phylogenomic). The endemic status of extended-spectrum ß-lactamase (ESBL)-positive strains carrying a wide diversity of blaCTX-M variants, and the growing number of colistin-resistant isolates carrying mcr-type genes was associated with the successful expansion of international ST10, ST38, ST115, ST131, ST354, ST410, ST648, ST517, and ST711 clones; phylogenetically related and shared between human and nonhuman hosts, and polluted aquatic environments. Otherwise, carbapenem-resistant ST48, ST90, ST155, ST167, ST224, ST349, ST457, ST648, ST707, ST744, ST774, and ST2509 clones from human host harbored blaKPC-2 and blaNDM-1 genes. A broad resistome to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and pesticides was further predicted. Wide virulome associated with invasion/adherence, exotoxin and siderophore production was related to phylogroup B2. The convergence of wide resistome and virulome has contributed to the persistence and rapid spread of international high-risk clones of critical priority E. coli at the human-animal-environmental interface, which must be considered a One Health challenge for a post-pandemic scenario. IMPORTANCE A One Health approach for antimicrobial resistance must integrate whole-genome sequencing surveillance data of critical priority pathogens from human, animal and environmental sources to track hot spots and routes of transmission and developing effective prevention and control strategies. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data of WHO critical priority carbapenemase-resistant, ESBL-producing, and/or colistin-resistant Escherichia coli strains isolated from humans and nonhuman sources in Brazil, a country with continental proportions and high levels of antimicrobial resistance. The present study provided evidence of epidemiological and clinical interest, highlighting that the convergence of wide virulome and resistome has contributed to the persistence and rapid spread of international high-risk clones of E. coli at the human-animal-environmental interface, which must be considered a One Health threat that requires coordinated actions to reduce its incidence in humans and nonhuman hosts.

Novel ST1465/CC216 Nosocomial Lineage of Carbapenem-Resistant Acinetobacter baumannii Harboring an Unusual Plasmid Carrying blaNDM-1 Gene.

This study used whole-genome sequencing to analyze the first case of NDM-1-producing Acinetobacter baumannii belonging to the novel sequence type 1465/CC216 recovered in Brazil. The study identified an unusual plasmid carrying blaNDM-1 gene, in which some genes of the Tn125 transposon were lost. Besides, on the chromosome, the strain reported here presented blaOXA-106 gene, a variant of blaOXA-51 gene, and blaADC-25 with ISAba1 upstream. The isolation of new STs of A. baumannii carrying blaNDM-1 genes elicits our concerns about the possible spread of these genes among clinically relevant bacteria.

IncX3 plasmid harboring a non-Tn4401 genetic element (NTEKPC) in a hospital-associated clone of KPC-2-producing Klebsiella pneumoniae ST340/CG258.

IncX-type plasmids have achieved clinical significance for their contribution in the dissemination of genes confering resistance to carbapenems (most blaKPC- and blaNDM-type genes) and polymyxins (mcr-type genes), both antibiotics considered last resort for multidrug-resistant Gram-negative infections. In this study, we report the identification and complete sequence analysis of an IncX3 plasmid (designated pKP1194a) carrying a non-Tn4401 genetic element (NTEKPC) of tnpR-tnpA (partial)-blaKPC-2-ΔISKpn6/traN, originating from a hospital-associated lineage of K. pneumoniae belonging to the ST340/CG258, with epidemiological link to Brazil.

Pressure ulcer as a reservoir of multiresistant Gram-negative bacilli: risk factors for colonization and development of bacteremia

Abstract The purpose of this study was to identify the risk factors that predispose patients who are hospitalized with pressure ulcers (PUs) colonized by Gram-negative bacilli (GNB) to develop bacteremia. In addition, we also detected main phenotypes of resistance in infected and uninfected PUs. A prospective cohort study was conducted at the Clinical Hospital of the Federal University of Uberlândia including patients with Stage II or greater PUs, colonized or not with GNB, from August 2009 to July 2010. Infected ulcers were defined based on clinical signs and on positive evaluation of smears of wound material translated by a ratio of polymorphonuclear cells to epithelial cells ≥2:1, after Giemsa staining. A total of 60 patients with Stage II PUs were included. Of these 83.3% had PUs colonized and/or infected. The frequency of polymicrobial colonization was 74%. Enterobacteriaceae and GNB non-fermenting bacteria were the most frequent isolates of PUs with 44.0% of multiresistant isolates. Among patients who had infected PUs, six developed bacteremia by the same microorganism with a 100% mortality rate. In addition, PUs in hospitalized patients were major reservoir of multiresistant GNB, also a high-risk population for the development of bacteremia with high mortality rates.

Pressure ulcer as a reservoir of multiresistant Gram-negative bacilli: risk factors for colonization and development of bacteremia.

The purpose of this study was to identify the risk factors that predispose patients who are hospitalized with pressure ulcers (PUs) colonized by Gram-negative bacilli (GNB) to develop bacteremia. In addition, we also detected main phenotypes of resistance in infected and uninfected PUs. A prospective cohort study was conducted at the Clinical Hospital of the Federal University of Uberlândia including patients with Stage II or greater PUs, colonized or not with GNB, from August 2009 to July 2010. Infected ulcers were defined based on clinical signs and on positive evaluation of smears of wound material translated by a ratio of polymorphonuclear cells to epithelial cells ≥2:1, after Giemsa staining. A total of 60 patients with Stage II PUs were included. Of these 83.3% had PUs colonized and/or infected. The frequency of polymicrobial colonization was 74%. Enterobacteriaceae and GNB non-fermenting bacteria were the most frequent isolates of PUs with 44.0% of multiresistant isolates. Among patients who had infected PUs, six developed bacteremia by the same microorganism with a 100% mortality rate. In addition, PUs in hospitalized patients were major reservoir of multiresistant GNB, also a high-risk population for the development of bacteremia with high mortality rates.

A sustained endemic outbreak of vancomycin-resistant Enterococcus faecium: A 30-month surveillance study.

BACKGROUND: The assessment of risk factors for the nosocomial acquisition of colonization and infection by vancomycin-resistant Enterococcus faecium (VREfm) is often problematic due to scarce data on antibiotic use. A 30-month prospective cohort study was conducted to characterize VREfm strains isolated during an outbreak and endemic period, identifying the risk factors, antibiotic consumption, and prevalence of virulence determinants. METHODS: The study was conducted in a tertiary care hospital. A representative number (171 patients) of isolates that were classified as resistant to high-level vancomycin (minimum inhibitory concentration (MIC) ≥ 256 µg/ml) were investigated. RESULTS: Among 171 colonized patients, 22 (12.9%) developed VRE infection. All VREfm isolates harboured vanA genes. Genes codifying virulence factors such as enterococcal surface protein (esp), aggregation substance 1 (asa1), and gelatinase (gelE) were detected in the VREfm studied. All patients infected with VRE had previously been colonized and became infected on average 14 days after colonization. Only previous use of aminoglycosides was a risk factor independently associated with VRE infection; however, glycopeptide consumption in defined daily doses (DDD) per 1000 patient-days was associated with the presence of this microorganism. The monthly colonization pressure ranged from 0.004% to 1.32% during the 30-month study period. CONCLUSIONS: We found a high incidence of VRE in a tertiary care hospital, independently associated with the prior use of aminoglycosides and the administration of glycopeptides.

Nosocomial bloodstream infections: organisms, risk factors and resistant phenotypes in the Brazilian University Hospital.

Bacteremia is one of the most frequent and challenging hospital-acquired infection and it is associated with high attributable morbidity and mortality and additional use of healthcare resources. The objective of this work was to determine the frequencies of its occurrence, organisms and resistance phenotypes associated to nosocomial acquired bloodstream infections. A total number of 51 nosocomial bacteremia by Gram-negative and 99 by Gram-positive were evaluated and compared during a 15-month period. The risk factors associated with these bacteremias were analyzed and antibiotic use and surgery were associated with bacteremia by Gram-negative and > 2 invasive devices with Gram-positive. The resistance phenotypes ESBL (extended-spectrum beta-lactamases) (23.5%) and AmpC/others (17.6%) correspond to 41.2 % with predominance of E. agglomerans among AmpC (44.4%) and K. pneumoniae among ESBLs (38.5%). Among S. aureus bacteremia, approximately 40% were associated to MRSA (methicillin-resistant Staphylococcus aureus).

Nosocomial bloodstream infections: organisms, risk factors and resistant phenotypes in the Brazilian University Hospital

Bacteremia is one of the most frequent and challenging hospital-acquired infection and it is associated with high attributable morbidity and mortality and additional use of healthcare resources. The objective of this work was to determine the frequencies of its occurrence, organisms and resistance phenotypes associated to nosocomial acquired bloodstream infections. A total number of 51 nosocomial bacteremia by Gram-negative and 99 by Gram-positive were evaluated and compared during a 15-month period. The risk factors associated with these bacteremias were analyzed and antibiotic use and surgery were associated with bacteremia by Gram-negative and > 2 invasive devices with Gram-positive. The resistance phenotypes ESBL (extended-spectrum beta-lactamases) (23.5 percent) and AmpC/others (17.6 percent) correspond to 41.2 percent with predominance of E. agglomerans among AmpC (44.4 percent) and K. pneumoniae among ESBLs (38.5 percent). Among S. aureus bacteremia, approximately 40 percent were associated to MRSA (methicillin-resistant Staphylococcus aureus).

Comparing hospital infections in the elderly versus younger adults: an experience in a Brazilian University Hospital.

The elderly population will grow rapidly over the next 25 years, however there is little information about hospital infections in this group of patients in Brazil. We examined the prevalence of nosocomial and community infections in elderly ((3) 65 years) patients and their relationship with intrinsic and extrinsic risk factors in a Brazilian University Hospital. A total of 155 hospitalized elderly patients were evaluated, and clinical and demographic information about each patient was obtained from hospital records. The rates of nosocomial and community infections were 16.1% and 25.6%, respectively. When the elderly group with and without nosocomial infections was analyzed, practically all the risk factors considered (use of antibiotics, invasive devices, surgery and time of hospitalization) were significantly more associated with the patients with hospital infection. All patients with nosocomial infections were taking antibiotics and most of them (56.0%) were being treated with two or more antibiotics; the length of hospitalization was double (p=0.007) compared to patients who had not acquired hospital infection. The most frequent sites of nosocomial and community infections were surgical (56.0%) and the skin (37.1%), and most of the patients (47.5%) were in the surgical clinic wards. In conclusion, the elderly patients were more likely to develop a nosocomial infection (16.1% prevalence). Surgical infection accounted for the majority (56.0%) of the nosocomial infections, in contrast with North American studies that indicate urinary tract infections to be the commonest.

Comparing hospital infections in the elderly versus younger adults: an experience in a Brazilian University Hospital

The elderly population will grow rapidly over the next 25 years, however there is little information about hospital infections in this group of patients in Brazil. We examined the prevalence of nosocomial and community infections in elderly (>65 years) patients and their relationship with intrinsic and extrinsic risk factors in a Brazilian University Hospital. A total of 155 hospitalized elderly patients were evaluated, and clinical and demographic information about each patient was obtained from hospital records. The rates of nosocomial and community infections were 16.1 percent and 25.6 percent, respectively. When the elderly group with and without nosocomial infections was analyzed, practically all the risk factors considered (use of antibiotics, invasive devices, surgery and time of hospitalization) were significantly more associated with the patients with hospital infection. All patients with nosocomial infections were taking antibiotics and most of them (56.0 percent) were being treated with two or more antibiotics; the length of hospitalization was double (p=0.007) compared to patients who had not acquired hospital infection. The most frequent sites of nosocomial and community infections were surgical (56.0 percent) and the skin (37.1 percent), and most of the patients (47.5 percent) were in the surgical clinic wards. In conclusion, the elderly patients were more likely to develop a nosocomial infection (16.1 percent prevalence) . Surgical infection accounted for the majority (56.0 percent) of the nosocomial infections, in contrast with North American studies that indicate urinary tract infections to be the commonest