[Latin American consensus to define, categorize, and report multidrug-resistant, extensively drug-resistant, or pandrug-resistant pathogensConsenso latino-americano para definição, categorização e notificação de patógenos multirresistentes, com resistência ampliada ou panresistentes]

Detection of KPC-producing Enterobacterales species in wastewater samples from the Gran Concepción Metropolitan area, Chile

BACKGROUND

Carbapenemase-mediated resistance to carbapenems is a significant public health concern due to its potential for widespread dissemination. The KPC family of carbapenemases, encoded by the blaKPC gene and often associated with Tn4401-like transposons, is particularly important for its ability to be transferred through diverse plasmid types. In Chile, KPC-producing Gram-negative bacteria have been detected in clinical settings; however, their occurrence in wastewater (WW) remains unknown. This study addresses this gap by characterizing carbapenem-resistant Enterobacterales isolates from a wastewater treatment plant (WWTP) in the Gran Concepción Metropolitan Area, Chile.

RESULTS

This study identifies three carbapenem-resistant Enterobacterales isolates, namely Klebsiella pasteurii M2/A/C/34, Klebsiella pneumoniae subsp. pneumoniae M3/A/M/3, and Citrobacter freundii sensu stricto. M4/A/C/32, all exhibiting multidrug-resistant profiles and carrying the blaKPC-2 gene encoding KPC-like carbapenemases. These isolates also possessed genes for extended-spectrum β-lactamases (ESBLs) and aminoglycoside-modifying enzymes (AMEs). Sequence typing revealed that M2/A/C/34, M3/A/M/3, and M4/A/C/32 belonged to novel sequence types, specifically ST470, ST273, and ST214, respectively. All isolates carried plasmids belonging to groups commonly associated with ARGs, including IncF, IncP, and IncA. Both Klebsiella isolates (M2/A/C/34 and M3/A/M/3) carried the class 1 integron (intl1) gene. Phylogenomic analysis reveals that M2/A/C/34 is related to strains from China and Pakistan, while M3/A/M/3 shares similarities with a strain from Germany, indicating their potential dissemination.

CONCLUSIONS

This study represents the first detection of carbapenem-resistant Enterobacterales carrying blaKPC-2 in Chilean WW, including the novel identification of K. pasteurii. These findings emphasize the critical role of genomic surveillance in WW under the One Health framework, enabling the monitoring of carbapenemase-producing bacteria and associated ARGs. Sustained surveillance efforts are essential to comprehend the dynamics of antibiotic resistance in environmental reservoirs and to develop strategies for its containment and mitigation.

High proportions of multidrug-resistant Klebsiella pneumoniae isolates in community-acquired infections, Brazil

Klebsiella pneumoniae is one of the leading causes of bloodstream (BSI) and urinary tract infections (UTI), but limited data is available regarding community-acquired (CA) infections. This study characterized the clinical aspects of CA-BSI and CA-UTI caused by K. pneumoniae and the molecular features of isolates, including their resistance profiles. Sixty-five isolates (CA-BSI, n = 24; CA-UTI, n = 41) underwent antimicrobial susceptibility testing, β-lactamase and virulence gene assessment, capsular genotyping, and molecular typing. Older age, male gender, and comorbidities, particularly kidney disease, were significantly associated with CA-BSI. The MDR and carbapenem resistance rates for K. pneumoniae from CA infections were 24.6% and 4.6%, respectively. CA-BSI isolates were more antibiotic-resistant and had a higher proportion of ESBL-producing (37.5% versus 9.8%) and MDR isolates (45.8% versus 12.2%) than CA-UTI. The blaCTX-M-like or blaKPC-like genes was found in all ESBL-producing isolates, while blaKPC-like and blaNDM-like were detected exclusively in CA-BSI strains. The isolates' virulence profiles were similar between the groups, although one CA-BSI and two CA-UTI isolates presented hypervirulence biomarkers. A high clonal diversity was observed, with a majority of MDR (81.3%) (ST11, ST15, ST101, ST258, ST307, and ST6852) and hypervirulent (2/3) (ST23 and ST65) isolates being high-risk pandemic clones in humans. Our data highlight the high prevalence of MDR K. pneumoniae in CA infections in Brazil, with CA-BSI showing significant differences in resistance profiles compared to CA-UTI.

Assessing the burden of disease of gram-negative bloodstream infections in a Brazilian hospital: A retrospective cohort study from 2015 to 2019

Objectives

This study aimed to estimate the disease burden of BSIs caused by gram-negative bacteria (GNB-BSIs) in a Brazilian hospital from 2015 to 2019, measured in disability-adjusted life-years (DALYs).

Methods

A retrospective cohort study of adult patients with GNB-BSI was conducted from April 01, 2015 to March 31, 2019. This study was carried out in a 356-bed private hospital with a 68-bed medical intensive care unit located in Salvador, Brazil. Demographic and clinical data were collected through a review of medical records. DALYs were estimated using Monte Carlo Simulations, using life tables for Brazilians estimated for 2020 and the Global Burden of Diseases 2010 (GBD 2010).

Results

A total of 519 GNB-BSI episodes in 498 individuals were identified. The mean age was 59.92 ± 17.97 years, with 61.1% being male. The most common bacterial infections were Klebsiella pneumoniae and Escherichia coli (66.5%), whereas carbapenem-resistant gram-negative bacteria (CR-GNB) accounted for 32.7% of cases. The highest overall DALYs were observed in 2018 (752, 95% confidence interval [CI]: 520-1021 with Brazilian Life Tables and 782, 95% CI: 540-1062 with GBD 2010). Infections due to CR-GNB had the highest DALYs, particularly, in 2017, reaching 7050 (95% CI: 3200-12,150 with Brazilian Life Tables and 7350, 95% CI: 3350-12,700 with GBD 2010) DALYs per 1000 patient days and an estimated mortality rate of 40% per 1000 patient days.

Conclusions

The persistently high DALYs associated with CR-GNB raise alarming concerns, potentially leading to over 300 deaths per 1000 patient days in the coming years. These findings underscore the urgency of addressing GNB-BSI as a significant public health issue in Brazil. These results are expected to provide helpful information for public health policymakers to prioritize interventions for infections due to antibiotic-resistant bacteria.

Correlation between Antibiotics-Resistance, Virulence Genes and Genotypes among Klebsiella pneumoniae Clinical Strains Isolated in Guangzhou, China

Klebsiella pneumoniae is an important opportunistic pathogen causing community-acquired and hospital-acquired infections. This aim of this study was to analysis the antibiotic-resistance phenotypes, carbapenemase genes, virulence genes, and genotypes the 62 K. pneumoniae clinical isolates, and to explore the correlations between these isolates. The antimicrobial susceptibility profiles were determined using the BD Phoenix-100 system. Carbapenemase and virulence genes were detected using multiplex PCR. Out of the 62 K. pneumoniae clinical isolates, 79.0% were exhibited resistance to antibiotics, with 69.4% displaying multi-drug resistance. The rate of antibiotic-resistance was highest for penicillin (71.0%), followed by cephalosporins (66.1%), and lowest for carbapenems (29.0%). The detection rates of carbapenemase genes were as follows: KPC (56.5%), VIM (35.5%), and NDM (1.61%). Additionally, seven virulence genes were detected with the highest prevalence rates, of which entB and mrkD were at the top of the carrier rates with 95.2% each. The study classified 62 isolates into 13 clusters and 46 genotypes using ERIC-PCR. Cluster A6 exhibited the highest genetic diversity, comprising 20 strains and 13 genotypes. The statistical analysis revealed a strong correlation between MDR and resistance to penicillin and cephalosporin. Furthermore, genes related to siderophores were closely associated with mrkD. Genotypes identified by ERIC-PCR showed a negative correlation with allS. The study revealed a negative correlation between antibiotic resistance and genes kfu, ybtS, iutA, rmpA, and allS. Conversely, a positive correlation was observed between antibiotic resistance and genes entB and mrkD. The correlations identified in this study provide insights into the occurrence of hospital-acquired infections. The findings of this study may guide the prevention and control of K. pneumoniae outbreaks by utilizing appropriate medication.

Antibacterial activity of Nocardia spp. and Streptomyces sp. on multidrug-resistant pathogens causing neonatal sepsis

Neonatal sepsis leads to severe morbidity and occasionally death among neonates within the first week following birth, particularly in low- and middle-income countries. Empirical therapy includes antibiotics recommended by WHO. However, these have been ineffective against antimicrobial multidrug-resistant bacterial strains such as Klebsiella spp, Escherichia coli, and Staphylococcus aureus species. To counter this problem, new molecules and alternative sources of compounds with antibacterial activity are sought as options. Actinobacteria, particularly pathogenic strains, have revealed a biotechnological potential still underexplored. This study aimed to determine the presence of biosynthetic gene clusters and the antimicrobial activity of actinobacterial strains isolated from clinical cases against multidrug-resistant bacteria implicated in neonatal sepsis. In total, 15 strains isolated from clinical cases of actinomycetoma were used. PCR screening for the PKS-I, PKS-II, NRPS-I, and NRPS-II biosynthetic systems determined their secondary metabolite-producing potential. The strains were subsequently assayed for antimicrobial activity by the perpendicular cross streak method against Escherichia fergusonii Sec 23, Klebsiella pneumoniae subsp. pneumoniae H1064, Klebsiella variicola H776, Klebsiella oxytoca H793, and Klebsiella pneumoniae subsp. ozaenae H7595, previously classified as multidrug-resistant. Finally, the strains were identified by 16S rRNA gene sequence analysis. It was found that 100% of the actinobacteria had biosynthetic systems. The most frequent biosynthetic system was NRPS-I (100%), and the most frequent combination was NRPS-I and PKS-II (27%). All 15 strains showed antimicrobial activity. The strain with the highest antimicrobial activity was Streptomyces albus 94.1572, as it inhibited the growth of the five multidrug-resistant bacteria evaluated.

Antibiotic resistance in tick-borne bacteria: A One Health approach perspective

The emergence and re-emergence of tick-borne bacteria (TBB) as a public health problem raises the uncertainty of antibiotic resistance in these pathogens, which could be dispersed to other pathogens. The impact of global warming has led to the emergence of pathogenic TBB in areas where they were not previously present and is another risk that must be taken into account under the One Health guides. This review aimed to analyze the existing information regarding antibiotic-resistant TBB and antibiotic-resistance genes (ARG) present in the tick microbiome, considering the potential to be transmitted to pathogenic microorganisms. Several Ehrlichia species have been reported to exhibit natural resistance to fluoroquinolones and typhus group Rickettsiae are naturally susceptible to erythromycin. TBB have a lower risk of acquiring ARG due to their natural habitat, but there is still a probability of acquiring them; furthermore, studies of these pathogens are limited. Pathogenic and commensal bacteria coexist within the tick microbiome along with ARGs for antibiotic deactivation, cellular protection, and efflux pumps; these ARGs confer resistance to antibiotics such as aminoglycosides, beta-lactamase, diaminopyrimidines, fluoroquinolones, glycopeptides, sulfonamides, and tetracyclines. Although with low probability, TBB can be a reservoir of ARGs.

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.

Gram-negative ESKAPE bacteria bloodstream infections in patients during the COVID-19 pandemic

Bloodstream infections due to bacteria are a highly consequential nosocomial occurrences and the organisms responsible for them are usually multidrug-resistant. The aims of this study were to describe the incidence of bacteremia caused by Gram-negative ESKAPE bacilli during the COVID-19 pandemic and characterize the clinical and microbiological findings including antimicrobial resistance. A total of 115 Gram-negative ESKAPE isolates were collected from patients with nosocomial bacteremia (18% of the total bacteremias) in a tertiary care center in Mexico City from February 2020 to January 2021. These isolates were more frequently derived from the Respiratory Diseases Ward (27), followed by the Neurosurgery (12), Intensive Care Unit (11), Internal Medicine (11), and Infectious Diseases Unit (7). The most frequently isolated bacteria were Acinetobacter baumannii (34%), followed by Klebsiella pneumoniae (28%), Pseudomonas aeruginosa (23%) and Enterobacter spp (16%). A. baumannii showed the highest levels of multidrug-resistance (100%), followed by K. pneumoniae (87%), Enterobacter spp (34%) and P. aeruginosa (20%). The blaCTX-M-15 and blaTEM-1 genes were identified in all beta-lactam-resistant K. pneumoniae (27), while blaTEM-1 was found in 84.6% (33/39) of A. baumannii isolates. The carbapenemase gene blaOXA-398 was predominant among carbapenem-resistant A. baumannii (74%, 29/39) and blaOXA-24was detected in four isolates. One P. aeruginosa isolate was blaVIM-2 gene carrier, while two K. pneumoniae and one Enterobacter spp were blaNDM gene carriers. Among colistin-resistant isolates mcr-1 gene was not detected. Clonal diversity was observed in K. pneumoniae, P. aeruginosa and Enterobacter spp. Two outbreaks caused by A. baumannii ST208 and ST369 were detected, both belonging to the clonal complex CC92 and IC2. A. baumannii was associated with a death rate of 72% (28/32), most of them (86%, 24/28) extensively drug-resistant or pandrug-resistant isolates, mainly in patients with COVID-19 (86%, 24/28) in the Respiratory Diseases Ward. A. baumannii isolates had a higher mortality rate (72%), which was higher in patients with COVID-19. There was no statistically significant association between the multidrug-resistant profile in Gram-negative ESKAPE bacilli and COVID-19 disease. The results point to the important role of multidrug-resistant Gram-negative ESKAPE bacteria causing bacteremia in nosocomial settings before and during the COVID-19 epidemic. Additionally, we were unable to identify a local impact of the COVID-19 pandemic on antimicrobial resistance rates, at least in the short term.

Prevalencia de aislamientos de Escherichia coli y Klebsiella pneumoniae productoras de betalactamasas de espectro extendido en pacientes cubanos ambulatorios con infección del tracto urinario

Introducción. Las infecciones del tracto urinario (UTI) adquiridas en la comunidad causadas por enterobacterias productoras de β-lactamasas de espectro extendido (BLEE) son un fenómeno creciente a nivel mundial. Objetivo. Determinar la prevalencia de aislamientos de Escherichia coli y Klebsiella pneumoniae productoras de BLEE obtenidos de muestras de orina de pacientes ambulatorios con ITU adquirida en la comunidad, así como los perfiles de resistencia a antibióticos asociados al fenotipo BLEE. Materiales y métodos. Estudio descriptivo retrospectivo. Se analizaron 304 aislamientos de E. coli y 34 de K. pneumoniae obtenidos de urocultivos de pacientes con ITU adquirida en la comunidad atendidos entre enero 1 de 2019 y diciembre 31 de 2020 en el Hospital Clínico-Quirúrgico Docente Aleida Fernández Chardiet, provincia Mayabeque, Cuba. Se realizó un análisis bivariado (prueba x2) para determinar diferencias en las tasas de resistencia antibiótica entre las bacterias productoras de BLEE y las no productoras. Resultados. El 16.77% (51/304) y el 17.64 % (6/34) de los aislamientos de E. coli y K. pneumoniae se clasificaron como bacterias productoras de BLEE. En el caso de los aislados de E. coli productoras de BLEE, BLEE+ciprofloxacina fue el patrón de resistencia más frecuente (22/51; 43.13%), seguido por BLEE+ciprofloxacino y amikacina (14/51; 27.45%). Además, 41.17% (21/51); fueron multirresistentes. En el caso de K. pneumoniae productoras de BLEE, predominó el patrón de resistencia BLEE + ciprofloxacino, amikacina y nitrofurantoina (2/6; 33.33%), y 50 % (3/6) fueron multirresistentes. Conclusiones. Los resultados confirman la presencia de E. coli y K. pneumoniae productoras de BLEE, con una alta prevalencia de multirresistencia en pacientes con ITU adquirida en la comunidad en el municipio de Güines, Cuba.

Colistin Resistance in Aeromonas spp

The increase in the use of antimicrobials such as colistin for the treatment of infectious diseases has led to the appearance of Aeromonas strains resistant to this drug. However, resistance to colistin not only occurs in the clinical area but has also been determined in Aeromonas isolates from the environment or animals, which has been determined by the detection of mcr genes that confer a resistance mechanism to colistin. The variants mcr-1, mcr-3, and mcr-5 have been detected in the genus Aeromonas in animal, environmental, and human fluids samples. In this article, an overview of the resistance to colistin in Aeromonas is shown, as well as the generalities of this molecule and the recommended methods to determine colistin resistance to be used in some of the genus Aeromonas.

Antimicrobial profile of Acinetobacter baumannii at a tertiary hospital in Honduras: a cross-sectional analysis

Acinetobacter baumannii is considered to be a worldwide threat to public health due to its high antimicrobial resistance rates and the severe infections it can cause. Little is known about this pathogen’s resistance in Central America. This report aims to describe the antimicrobial resistance profile of A. baumannii at a tertiary hospital in Honduras. The cross-sectional analysis was conducted at the tertiary care laboratory hospital in San Pedro Sula in 2015 – 2017. A total of 113 consecutive microbiological reports were analyzed, comprising 100 individuals from whom A. baumannii was isolated. Epidemiological and microbiological data, including the isolation setting and patient information, were recorded. Prevalence of multi-drug and extensive-drug resistance was assessed according to international standards. The median age of individuals was 22 years (2 – 35 years); female was the predominant gender (53%). The hospital’s pediatric wards had the highest number of isolates (n = 48). The most frequent specimen from which A. baumannii was isolated was skin and soft tissue (n = 39). Resistance to carbapenems was reported to be 40.7% among the isolates (n = 46); multi-drug resistant, 35.4% (n = 40); and extensively-drug resistant, 7.1% (n = 8). This report reveals the threat of this pathogen to public health in Honduras and appeals for antibiotic stewardship programs throughout Central America.

[Evolution of the performance of Latin America Reference Laboratories in the detection of mechanisms of antimicrobial resistanceEvolução do desempenho dos Laboratórios de Referência na América Latina na detecção de mecanismos de resistência antimicrobiana]

Objective

The objective is to present the results of the Latin American Program for Quality Assurance in Bacteriology and Antimicrobial Resistance (LA-EQAS) between 2000 and 2018 and the evolution of the detection of resistance mechanisms with clinical impact.

Methods

The participating National Reference Laboratories (NRLs) received 25 surveys with 10 strains in each one, representing a total of 86 bacterial species and 40 resistance mechanisms. To evaluate the performance of the NRLs, five indicators were analyzed: bacterial identification, interpretation of susceptibility testing, acceptable ranges for zones of inhibition, inferred resistance mechanism, and delay time for the response.

Results

The average concordance was 82.6% (range: 74-95%) for bacterial identification, 93.3% (85-98%) for the interpretation of susceptibility testing, 84.6% (70-94%) for the zones of inhibition, and 82.5% (73-96%) for the inferred resistance mechanisms. The average delay time for the response was 34 days. Improvements in the detection of mechanisms of clinical importance, such as resistance to methicillin, macrolides and glycopeptides in Gram-positive cocci, and extended-spectrum, AmpC plasmid and carbapenemase beta-lactamases in Gram-negative bacilli, were observed.

Conclusions

The LA-EQAS is an excellent tool for continuous quality improvement in the diagnosis of infections due to multiresistant microorganisms in NRLs in Latin America.