Acinetobacter baumannii Infections in Times of COVID-19 Pandemic.

The COVID-19 pandemic has generated an overuse of antimicrobials in critically ill patients. Acinetobacter baumannii frequently causes nosocomial infections, particularly in intensive care units (ICUs), where the incidence has increased over time. Since the WHO declared the COVID-19 pandemic on 12 March 2020, the disease has spread rapidly, and many of the patients infected with SARS-CoV-2 needed to be admitted to the ICU. Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. However, we cannot neglect the increased incidence of antimicrobial resistance, which may be attributed to the excess use of antimicrobial agents during the COVID-19 pandemic. Patients with COVID-19 could be vulnerable to other infections owing to multiple comorbidities with severe COVID-19, prolonged hospitalization, and SARS-CoV-2-associated immune dysfunction. These patients have acquired secondary bacterial infections or superinfections, mainly bacteremia and urinary tract infections. This review will summarize the prevalence of A. baumannii coinfection and secondary infection in patients with COVID-19.

Surveillance of antimicrobial resistant bacteria in flies (Diptera) in Rio de Janeiro city.

Antimicrobial-resistant bacteria were isolated from muscoid dipterans collected at five different areas of Rio de Janeiro city, in proximity to hospitals. Extracts obtained by maceration of flies were diluted and used as inocula for different culture media, with or without antibiotic (ceftriaxone 1 mg/L) supplementation. Purified isolates were submitted to antimicrobial susceptibility testing (AST). Bacterial identification was performed by MALDI TOF Microflex LT (Bruker Daltonics). A total of 197 bacterial strains were obtained from 117 dipterous muscoids. Forty-two flies (35.9%) carried bacteria resistant to at least one antimicrobial, while 7 insects (5.9%) carried multidrug-resistant bacteria (MDR), which were all members of the family Enterobacteriaceae. Among 10 MDR bacteria (5%), 5 strains (2,5%) were positive by PCR for one or more of the following antibiotic resistance genes: aac(6')-Ib, blaTEM-1, blaCTX-M-15, blaKPC-2 and blaNDM-1. Analysis of variance (ANOVA) and cluster analysis compared the number of resistant isolates per collection point and showed that a single location was statistically different from the others with regard to resistance. Although there are still no criteria to determine the environmental contamination by resistant bacteria the fact that they have been isolated from flies is an indication of a disseminated contamination. As such, these insects may be useful in monitoring programs of antibiotic resistance in non-hospital environments, where they could function as sentinels.

High rate of detection of OXA-23-producing Acinetobacter from two general hospitals in Brazil.

INTRODUCTION: In recent decades, the prevalence of carbapenem-resistant Acinetobacter isolates has increased, and the production of oxacillinase (OXA)-type carbapenemases is the main mechanism underlying resistance. We evaluated OXA production from 114 Acinetobacter isolates collected between March and December 2013 from different clinical specimens of patients in two hospitals (Hospital 1 [n = 61] and Hospital 2 [n = 53]) located in Niterói, Rio de Janeiro, Brazil. We also evaluated the genetic diversity of OXA-producing isolates. METHODS: All the isolates were identified through the automated system Vitek II and matrix-assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF MS as belonging to the A. baumannii-A. calcoaceticuscomplex. Antimicrobial susceptibility profiles were verified through agar diffusion tests. The presence of OXA-encoding genes was confirmed by PCR. The genetic diversity of isolates positive for carbapenemase production was analyzed through pulsed-field gel electrophoresis. RESULTS: There was a high rate of resistance to carbapenems in the isolates (imipenem: 96%; meropenem: 92%) from both hospitals. Moreover, a high percentage (95.6%) of OXA-23-positive isolates was observed for both hospitals, indicating that this was the main mechanism of carbapenem-resistance among the studied population. In addition, most isolates (96.5%) were positive for bla OXA-51. A high genetic diversity and a few major genotypes were found among the OXA-23-positive isolates analyzed. Only intra-hospital dissemination was observed. CONCLUSIONS: The elevated dissemination of bla OXA-23-like observed among Acinetobacter isolates from both the studied hospitals highlights the need for continuous epidemiological surveillance in these institutions.

Genetic information on OXA-23-producing Acinetobacter baumannii strain CCBH15815, belonging to ST730/ST783, isolated from Brazil.

In Brazil, A. baumannii has been described as nosocomial pathogens causing hospital-acquired infections. Current WGS technologies have been useful in identifying of genetic features between Acinetobacter isolates. Here, we report the draft genome sequence of OXA-23 producing A. baumannii CCBH15815 clinical isolate, belonging to ST730/ST783, recovered from a 21-year-old hospitalised patient. We observed important resistance determinant genes, especially beta-lactamases-encoding genes, in an estimated genome size of 4,058,633 bp with 3839 predicted coding regions.

High rate of detection of OXA-23-producing Acinetobacter from two general hospitals in Brazil

Abstract INTRODUCTION In recent decades, the prevalence of carbapenem-resistant Acinetobacter isolates has increased, and the production of oxacillinase (OXA)-type carbapenemases is the main mechanism underlying resistance. We evaluated OXA production from 114 Acinetobacter isolates collected between March and December 2013 from different clinical specimens of patients in two hospitals (Hospital 1 [n = 61] and Hospital 2 [n = 53]) located in Niterói, Rio de Janeiro, Brazil. We also evaluated the genetic diversity of OXA-producing isolates. METHODS All the isolates were identified through the automated system Vitek II and matrix-assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF MS as belonging to the A. baumannii-A. calcoaceticuscomplex. Antimicrobial susceptibility profiles were verified through agar diffusion tests. The presence of OXA-encoding genes was confirmed by PCR. The genetic diversity of isolates positive for carbapenemase production was analyzed through pulsed-field gel electrophoresis. RESULTS There was a high rate of resistance to carbapenems in the isolates (imipenem: 96%; meropenem: 92%) from both hospitals. Moreover, a high percentage (95.6%) of OXA-23-positive isolates was observed for both hospitals, indicating that this was the main mechanism of carbapenem-resistance among the studied population. In addition, most isolates (96.5%) were positive for bla OXA-51. A high genetic diversity and a few major genotypes were found among the OXA-23-positive isolates analyzed. Only intra-hospital dissemination was observed. CONCLUSIONS The elevated dissemination of bla OXA-23-like observed among Acinetobacter isolates from both the studied hospitals highlights the need for continuous epidemiological surveillance in these institutions.

Carbapenem-resistant Acinetobacter pittii strain harboring blaOXA-72 from Brazil.

In this study, we report the isolation of OXA-72-producing Acinetobacter pittii in Brazil. A carbapenem-resistant A. pittii strain was recovered from a hospitalized female patient from Espírito Santo, Southeastern Brazil. PCR screening and DNA sequencing allowed us to identify the presence of blaOXA-72. We observed blaOXA-72 in a ~11kb plasmid and flanked by XerC/XerD-binding sites.

Multiclonal Expansion of Klebsiella pneumoniae Isolates Producing NDM-1 in Rio de Janeiro, Brazil.

We characterized NDM-1-producing Klebsiella isolates from Rio de Janeiro, Brazil. PCR was applied for resistance and virulence determinants. The genetic context of blaNDM was determined by S1 nuclease pulsed-field gel electrophoresis (PFGE) and hybridization. Genotyping was performed by PFGE and multilocus sequence typing (MLST). Most isolates carried multiple resistance genes and remained susceptible to amikacin, fosfomycin-trometamol, polymyxin B, and tigecycline. The spread of NDM-1-producing Klebsiella pneumoniae was not associated with clonal expansion and appears to be associated with Tn3000.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) applications in bacteriology: brazilian contributions / Aplicações da técnica de espectrometria de massa por ionização e dessorção de matriz com laser em tempo de voo (MALDI-TOF MS) em bacteriologia: contribuições brasileiras

Among its innumerous applications in Bacteriology, the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique is evolving as a powerful tool for bacterial identification and antimicrobial resistance investigation. Publications have evaluated the MALDI-TOF MS performance in the identification of a series of bacterial pathogens, including the most common severe infectious agents, emergent pathogens involved with outbreaks of healthcare-associated infections, rare pathogens, and those whose isolation in culture media is difficult. As compared to conventional methods of bacterial identification, MALDI-TOF MS has proven to be a fast, accurate and cost-effective technique. Currently, MALDI-TOF MS has been used in antimicrobial resistance studies, since it has shown to be an efficient tool in detecting specific resistance mechanisms in bacteria, such as beta-lactamases production, for example. Here, we describe the advances in this growing field of mass spectrometry applied to Bacteriology, including Brazilian contributions.

Dentre as suas inúmeras aplicações em Bacteriologia, a técnica de "Espectrometria de Massa por Ionização e Dessorção de Matriz com Laser em Tempo de Voo [Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS)]" tem evoluído como uma poderosa ferramenta para a identificação bacteriana e a investigação da resistência bacteriana aos antimicrobianos. Publicações tem avaliado o desempenho de MALDI-TOF na identificação de uma série de patógenos bacterianos, incluindo os agentes mais comuns de infecções graves, patógenos emergentes envolvidos com surtos de infecções associadas à saúde, patógenos raros, e aqueles de difícil isolamento em meios de cultura. Em comparação aos métodos convencionais de identificação bacteriana, MALDI-TOF MS provou ser uma técnica rápida, precisa e rentável. Atualmente, MALDI-TOF MS tem sido utilizado em estudos de resistência antimicrobiana, uma vez que tem mostrado ser uma ferramenta eficiente na detecção de mecanismos especificos de resistência em bactérias, como a produção beta-lactamases, por exemplo. Aqui, nós descrevemos os avanços neste crescente campo da espectrometria de massa aplicada à Bacteriologia, incluindo as contribuições brasileiras.

Draft genome sequence of a multidrug-resistant Acinetobacter baumannii ST15 (CC15) isolated from Brazil

Acinetobacter baumannii is an important pathogen frequently associated with nosocomial outbreaks around the world. In Brazil, A. baumannii has become particularly problematic because of its prevalence and the carbapenems resistance. Here, we report the draft genome sequence of a multidrug-resistant A. baumannii(ST15/CC15) isolated in 2009 from the state of Espírito Santo (Southeast Brazil). We observed important resistance determinant genes in an estimated genome size of 4,102,788 bp with 3,862 predicted coding regions. A detailed report of the genomic data analysis might help to understand the specific features of highly successful strains belonged to a relevant complex clonal in different Brazilian geographical regions.

Spread of multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa clones in patients with ventilator-associated pneumonia in an adult intensive care unit at a university hospital

Background:In Brazil, ventilator-associated pneumonia (VAP) caused by carbapenem resis- tant Acinetobacter baumanniiand Pseudomonas aeruginosaisolates are associated with significant mortality, morbidity and costs. Studies on the clonal relatedness of these isolates could lay the foundation for effective infection prevention and control programs.Objectives: We sought to study the epidemiological and molecular characteristics of A. baumannii vs. P. aeruginosaVAP in an adult intensive care unit (ICU).Methods: It was conducted a cohort study of patients with VAP caused by carbapenem resistant A. baumanniiand P'. aeruginosaduring 14 months in an adult ICU. Genomic studies were used to investigate the clonal relatedness of carbapenem resistant OXA-23-producing A. baumanniiand P. aeruginosaclinical isolates. The risk factors for acquisition of VAP were also evaluated. Clinical isolates were collected for analysis as were samples from the environment and were typed using pulsed field gel electrophoresis.Results: Multivariate logistic regression analysis identified trauma diagnosed at admission and inappropriate antimicrobial therapy as independent variables associated with the development of A. baumanniiVAP and hemodialysis as independent variable associated with P. aeruginosaVAP. All carbapenem resistant clinical and environmental isolates of A. baumanniiwere OXA-23 producers. No MBL-producer P. aeruginosawas detected. Molecular typing revealed a polyclonal pattern; however, clone A (clinical) and H (surface) were the most frequent among isolates of A. baumanniitested, with a greater pattern of resistance than other isolates. In P. aeruginosathe most frequent clone I was multi-sensitive.Conclusion: These findings suggest the requirement of constant monitoring of these microor- ganisms in order to control the spread of these clones in the hospital environment.

Draft genome sequence of a multidrug-resistant Acinetobacter baumannii ST15 (CC15) isolated from Brazil.

Acinetobacter baumannii is an important pathogen frequently associated with nosocomial outbreaks around the world. In Brazil, A. baumannii has become particularly problematic because of its prevalence and the carbapenems resistance. Here, we report the draft genome sequence of a multidrug-resistant A. baumannii(ST15/CC15) isolated in 2009 from the state of Espírito Santo (Southeast Brazil). We observed important resistance determinant genes in an estimated genome size of 4,102,788 bp with 3,862 predicted coding regions. A detailed report of the genomic data analysis might help to understand the specific features of highly successful strains belonged to a relevant complex clonal in different Brazilian geographical regions.

Spread of multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa clones in patients with ventilator-associated pneumonia in an adult intensive care unit at a university hospital.

BACKGROUND: In Brazil, ventilator-associated pneumonia (VAP) caused by carbapenem resistant Acinetobacter baumannii and Pseudomonas aeruginosa isolates are associated with significant mortality, morbidity and costs. Studies on the clonal relatedness of these isolates could lay the foundation for effective infection prevention and control programs. OBJECTIVES: We sought to study the epidemiological and molecular characteristics of A. baumannii vs. P. aeruginosa VAP in an adult intensive care unit (ICU). METHODS: It was conducted a cohort study of patients with VAP caused by carbapenem resistant A. baumannii and P. aeruginosa during 14 months in an adult ICU. Genomic studies were used to investigate the clonal relatedness of carbapenem resistant OXA-23-producing A. baumannii and P. aeruginosa clinical isolates. The risk factors for acquisition of VAP were also evaluated. Clinical isolates were collected for analysis as were samples from the environment and were typed using pulsed field gel electrophoresis. RESULTS: Multivariate logistic regression analysis identified trauma diagnosed at admission and inappropriate antimicrobial therapy as independent variables associated with the development of A. baumannii VAP and hemodialysis as independent variable associated with P. aeruginosa VAP. All carbapenem resistant clinical and environmental isolates of A. baumannii were OXA-23 producers. No MBL-producer P. aeruginosa was detected. Molecular typing revealed a polyclonal pattern; however, clone A (clinical) and H (surface) were the most frequent among isolates of A. baumannii tested, with a greater pattern of resistance than other isolates. In P. aeruginosa the most frequent clone I was multi-sensitive. CONCLUSION: These findings suggest the requirement of constant monitoring of these microorganisms in order to control the spread of these clones in the hospital environment.

First report of NDM-1-producing Acinetobacter baumannii sequence type 25 in Brazil.

New Delhi metallo-ß-lactamase 1 (NDM-1) was first identified in Brazil in Enterobacter hormaechei and Providencia rettgeri in 2013. Here, we describe the first case of NDM-1-producing Acinetobacter baumannii sequence type 25 isolated from the urinary tract of a 71-year-old man who died of multiple complications, including A. baumannii infection. The NDM-1 gene was detected by quantitative PCR, and its sequence confirmed its presence in an ∼ 100-kb plasmid.

Characterization of carbapenem-resistant Acinetobacter baumannii in Brazil (2008-2011): countrywide spread of OXA-23-producing clones (CC15 and CC79).

The study investigated the genetic relationship of carbapenem-resistant Acinetobacter baumannii clinical isolated from inpatients during 2008-2011 from 11 Brazilian states. Antimicrobial susceptibility profile was determined by disc diffusion method and Etest. Polymerase chain reaction was applied for carbapenemase genes, and ISAba1. Isolates were subjected to pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for molecular typing. Most of the isolates showed high resistance rates to antibiotics tested. The blaOXA-51-like gene was found in all isolates, and 146 (94.2%) isolates were positive for blaOXA-23-like. In the most OXA-23-producing isolates, the blaOXA-23-like gene was accompanied by ISAba1. A total of 146 OXA-23-producing isolates were clustered into 28 genotypes by PFGE. Molecular analysis by MLST identified 13 sequence types (STs). The most prevalent PFGE profiles were designated as ST15 (CC15), ST1 (CC1), and ST79 (CC79). This study showed the widespread of clonal complexes of A. baumannii harboring the blaOXA-23-like gene in different Brazilian states.

Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil

OBJECTIVE: The present study was undertaken to characterize CTX-M ESBL-producing Klebsiella pneumoniae collected from hospitals in different cities of Brazil. MATERIAL AND METHODS: Eighty-five K. pneumoniae strains isolated from hospitalized patients in six different hospitals of three cities of Brazil were analyzed. ESBL production was confirmed by the standard double-disk synergy test and the Etest®. The MIC50 and MIC90 for ESBL-producing isolates were determined by the Etest® method. The antimicrobial susceptibilities of bacterial isolates were determined using the agar diffusion method according to the CLSI. Screening for blaTEM, blaSHV, blaCTX-M genes and class 1 integron was performed by PCR amplification. To determine the genomic diversity of CTX-M-producers, isolates were analyzed by macrorestriction profile analysis following PFGE. RESULTS AND DISCUSSION: Seventy-one K. pneumoniae isolates were ESBL-producing. PCR and sequencing experiments detected 38 CTX-M-producing K. pneumoniae belonged to groups CTX-M 1, CTX-M 2, CTX-M 8 and CTX-M 9. The association of different types ESBL (CTX-M, SHV and TEM) was frequent. All K. pneumoniae isolates carried class 1 integron. PFGE analysis revealed thirty-one clonal types among CTX-M-producing isolates. The data presented herein illustrate the diversity of genotypes of CTX-M producing K. pneumoniae among Brazilians hospitals.

Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil.

OBJECTIVE: The present study was undertaken to characterize CTX-M ESBL-producing Klebsiella pneumoniae collected from hospitals in different cities of Brazil. MATERIAL AND METHODS: Eighty-five K. pneumoniae strains isolated from hospitalized patients in six different hospitals of three cities of Brazil were analyzed. ESBL production was confirmed by the standard double-disk synergy test and the Etest®. The MIC50 and MIC90 for ESBL-producing isolates were determined by the Etest® method. The antimicrobial susceptibilities of bacterial isolates were determined using the agar diffusion method according to the CLSI. Screening for blaTEM, blaSHV, blaCTX-M genes and class 1 integron was performed by PCR amplification. To determine the genomic diversity of CTX-M-producers, isolates were analyzed by macrorestriction profile analysis following PFGE. RESULTS AND DISCUSSION: Seventy-one K. pneumoniae isolates were ESBL-producing. PCR and sequencing experiments detected 38 CTX-M-producing K. pneumoniae belonged to groups CTX-M 1, CTX-M 2, CTX-M 8 and CTX-M 9. The association of different types ESBL (CTX-M, SHV and TEM) was frequent. All K. pneumoniae isolates carried class 1 integron. PFGE analysis revealed thirty-one clonal types among CTX-M-producing isolates. The data presented herein illustrate the diversity of genotypes of CTX-M producing K. pneumoniae among Brazilians hospitals.

Detecção de bactérias multirresistentes aos antimicrobianos em esgoto hospitalar no Rio de Janeiro / Detection of multidrug-resistant bacteria to antibiotics in hospital sewage in Rio de Janeiro

Drogas antimicrobianas e bactérias resistentes aos antimicrobianos estão disseminadas em grandes quantidades no ambiente, como resultado do aumento e freqüente uso indiscriminado dos antibióticos. Bactérias e seus genes de resistência tem sido detectados em diferentes ambientes, tais como esgoto hospitalar, esgoto doméstico e águas de rios contaminados. O esgoto hospitalar é um importante poluente, representando riscos para a saúde publica se chegar aos sistemas de distribuição. Ambientes fortemente seletivos, como os hospitais, permitem a geração bactérias resistentes, as quais podem ser lançadas no esgoto hospitalar. O presente trabalho tem como objetivo investigar a presença bactérias resistentes aos antimicrobianos em efluentes de uma estação de tratamento de esgoto hospitalar no Rio de Janeiro, avaliando o potencial do sistema de tratamento para a eliminação de micro-organismos. A estação de tratamento de esgoto fica localizada na região metropolitana. O sistema de lodo ativado por aeração prolongada é constituído por três partes básicas: o tanque de aeração, o decantados e o tanque de cloração. Vinte e quatro amostras de esgoto foram coletadas no período de Julho a Dezembro de 2008. oito amostras (1000 ml) foram coletadas a partir de diferentes pontos: afluente, efluente do tanque decantador e efluente clorado. Micro-organismos indicadores também foram investigados. Os isolados bacterianos foram identificados a partir de provas bioquímicas convencionais. A sensibilidade aos antimicrobianos das bactérias isoladas foi determinada através do método fenotípico de difusão em ágar, de acordo com as orientações do Clincial and Laboratory Standarts Institute (CLSI). A identificação da produção fenotípica de beta-lactamases de espectro estendido e de carbapenemases entre os isolados também seguiram as recomendações do CLSI. Ensaios de PCR foram processados para a identificação dos genes blaKPC,blaTEM blaSHV e blaCTX-M. A genotipagem das amostras bacterianas foi realizada por eletroforese em gel de campo pulsado. Concentrações significativas de coliformes totais e fecais foram detectadas nos efluentes hospitalares. Um total de 226 isolados foi identificado, entre os quais 213 (94 porcento) pertenciam à família Enterobacteriaceae. Outros grupos de micro-organismos, como Pseudomonas aeruginosa, Acinetobacter baumannii e Aeromonas spp., foram também observados. A maioria das cepas era sensível ao imipenem e ao meropenem; e resistente àcefalotina, à cefotaxima e ao sulfametoxazol-trimetoprim. O fenótipo de ESBL foi caracterizado em 97 (43 porcento) isolados. Os produtores de ESBL mais comuns foram: Klebsiella pneumoniae, Enterobacter cloacae e Escherichia coli. Micro-organismos patogênicos e altas taxas de resistência ainda puderam ser observados nos efluentes clorados. Os genes blaTEM blaSHV e blaCTX-M foram detectados em 82 porcento, 48 porcento e 67 porcento dos isolados do efluente hospitalar, respectivamente. Em muitos isolados, a ocorrência de mais de um tipo de ESBL foi observada, sendo a associação dos tipos TEM e CTX-M a mais freqüente. O gene blaKPC foi detectado em dois isolados do efluente. Foi possível observar isolados clínicos e do esgoto geneticamente relacionados. Concluímos que, apesar do tratamento, o esgoto hospitalar pode ser considerado um veículo ambiental de disseminação de bactérias multirresistentes. A ocorrência destes micro-organismos nos efluentes é preocupante e tem impacto sobre a saúde pública. Medidas urgentes são necessárias para enfrentar este problema. Vale ressaltar que, em muitos países em desenvolvimento, os efluentes hospitalares não recebem tratamento adequado.