RESUMEN
Acinetobacter baumannii is a successful nosocomial pathogen due to its genomic plasticity. Homologous recombination allows genetic exchange and allelic variation among different clonal lineages and is one of the mechanisms associated with horizontal gene transfer (HGT) of resistance determinants. The main mechanism of colistin resistance in A. baumannii is mediated through mutations in the pmrCAB operon. Here, we describe two A. baumannii clinical isolates belonging to International Clone 7 (IC7) that have undergone recombination in the pmrCAB operon and evaluate the contribution of mobile genetic elements (MGE) to this phenomenon. Isolates 67569 and 72554 were colistin susceptible and resistant, respectively, and were submitted for short- and long-read genome sequencing using Illumina MiSeq and MinION platforms. Hybrid assemblies were built with Unicycler, and the assembled genomes were compared to reference genomes using NUCmer, Cortex, and SplitsTree. Genomes were annotated using Prokka, and MGEs were identified with ISfinder and repeat match. Both isolates presented a 21.5-kb recombining region encompassing pmrCAB. In isolate 67659, this region originated from IC5, while in isolate 72554 multiple recombination events might have happened, with the 5-kb recombining region encompassing pmrCAB associated with an isolate representing IC4. We could not identify MGEs involved in the mobilization of pmrCAB in these isolates. In summary, A. baumannii belonging to IC7 can present additional sequence divergence due to homologous recombination across clonal lineages. Such variation does not seem to be driven by antibiotic pressure but could contribute to HGT mediating colistin resistance. IMPORTANCE Colistin resistance rates among Acinetobacter baumannii clinical isolates have increased over the last 20 years. Despite reports of the spread of plasmid-mediated colistin resistance among Enterobacterales, the presence of mcr-type genes in Acinetobacter spp. remains rare, and reduced colistin susceptibility is mainly associated with the acquisition of nonsynonymous mutations in pmrCAB. We have recently demonstrated that distinct pmrCAB sequences are associated with different A. baumannii International Clones (IC). In this study, we identified the presence of homologous recombination as an additional cause of genetic variation in this operon, which, to the best of our knowledge, was not mediated by mobile genetic elements. Even though this phenomenon was observed in both colistin-susceptible and -resistant isolates, it has the potential to contribute to the spread of resistance-conferring alleles, leading to reduced susceptibility to this last-resort antimicrobial agent.
Asunto(s)
Acinetobacter baumannii/genética , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Colistina/farmacología , Genoma Bacteriano , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/efectos de los fármacos , Brasil , Células Clonales/metabolismo , Farmacorresistencia Bacteriana/genética , Transferencia de Gen Horizontal , Humanos , Pruebas de Sensibilidad Microbiana , MutaciónRESUMEN
Carbapenem-resistant Acinetobacter baumannii (CRAB) are emerging worldwide. In South America, clinical isolates presenting such a phenotype usually do not belong to the globally distributed international clone 2 (IC2). The majority of these isolates are also resistant to multiple other antimicrobials and are often designated extremely drug-resistant (XDR). The aim of this study was to characterize the resistance mechanisms presented by 18 carbapenem-resistant A. baumannii isolates from five different Brazilian hospitals. Species identification was determined by rpoB sequencing, and antimicrobial susceptibility was determined by broth microdilution. Isolates were submitted to whole genome sequencing using Illumina platform and genetic similarity was determined by PFGE, MLST, and cgMLST. Genome analysis was used to identify intrinsic and acquired resistance determinants, including mutations in the AdeRSABC efflux system and in outer membrane proteins (OMPs). All isolates were identified as A. baumannii and grouped into 4 pulsotypes by PFGE, which belonged to clonal complexes (CC) 15 Pas /103 Ox (n = 4) and 79 Pas /113 Ox (n = 14), corresponding to IC4 and IC5, respectively. High MIC values to carbapenems, broad-spectrum cephalosporins, amikacin, and ciprofloxacin were observed in all isolates, while MICs of ampicillin/sulbactam, gentamicin, and tigecycline varied among the isolates. Minocycline was the most active antimicrobial agent tested. Moreover, 12 isolates (66.7%) were considered resistant to polymyxins. Besides intrinsic OXA-51 and ADC variants, all isolates harbored an acquired carbapenem-hydrolyzing class D ß-lactamase (CHDL) encoding gene, either bla OXA- 23 or bla OXA- 72. A diversity of aminoglycoside modifying enzymes and resistance determinants to other antimicrobial classes were found, as well as mutations in gyrA and parC. Non-synonymous mutations have also been identified in the AdeRSABC efflux system and in most OMPs, but they were considered natural polymorphisms. Moreover, resistance to polymyxins among isolates belonging to IC5 were associated to non-synonymous mutations in pmrB, but no known polymyxin resistance mechanism was identified in isolates belonging to IC4. In conclusion, A. baumannii clinical isolates belonging to South America's major clones present a myriad of antimicrobial resistance determinants. Special attention should be paid to natural polymorphisms observed in each clonal lineage, especially regarding non-synonymous mutations in constitutive genes associated with distinct resistance phenotypes.
RESUMEN
Using a combination of short- and long-read DNA sequencing, we have investigated the location of antibiotic resistance genes and characterized mobile genetic elements (MGEs) in three clinical multi-drug resistant Acinetobacter baumannii. The isolates, collected in Bolivia, clustered separately with three different international clonal lineages. We found a diverse array of transposons, plasmids and resistance islands related to different insertion sequence (IS) elements, which were located in both the chromosome and in plasmids, which conferred resistance to multiple antimicrobials, including carbapenems. Carbapenem resistance might be caused by a Tn2008 carrying the bla OXA-23 gene. Some plasmids were shared between the isolates. Larger plasmids were less conserved than smaller ones and they shared some homologous regions, while others were more diverse, suggesting that these big plasmids are more plastic than the smaller ones. The genetic basis of antimicrobial resistance in Bolivia has not been deeply studied until now, and the mobilome of these A. baumannii isolates, combined with their multi-drug resistant phenotype, mirror the transfer and prevalence of MGEs contributing to the spread of antibiotic resistance worldwide and require special attention. These findings could be useful to understand the antimicrobial resistance genetics of A. baumannii in Bolivia and the difficulty in tackling these infections.
RESUMEN
While antibiotic-resistant bacteria have been detected in extreme environments, including Antarctica, to date there are no reports of Acinetobacter species isolated from this region. Here, we characterized by whole-genome sequencing (WGS) the genetic content of a single antibiotic-resistant Acinetobacter spp. isolate (A154) collected in Antarctica. The isolate was recovered in 2013 from soil samples at Fildes Peninsula, Antarctica, and was identified by detection of the intrinsic OXA-23 gene, and confirmed by Tetra Correlation Search (TCS) and WGS. The antibiotic susceptibility profile was determined by disc diffusion, E-test, and broth microdilution methods. From WGS data, the acquired resistome and insertion sequence (IS) content were identified by in silico analyses. Plasmids were studied by the alkaline lysis method followed by pulsed-field gel electrophoresis and conventional PCR. The A154 isolate was identified as A. radioresistens by WGS analysis and displayed >99.9 of similarity by TCS in relation with the databases. Moreover, it was resistant to ampicillin, ceftriaxone, ceftazidime, cefepime, cefotaxime, streptomycin, and kanamycin. Likewise, in addition to the intrinsic blaOXA-23-like gene, A154 harbored the plasmid-encoded antibiotic-resistance genes blaPER-2, tet(B), aph(3')-Vla, strA, and strB, as well as a large diversity of ISs. This is the first report of antibiotic-resistant A. radioresistens in Antarctica. Our findings show the presence of several resistance genes which could be either intrinsic or acquired in the region.
Asunto(s)
Acinetobacter/genética , Acinetobacter/aislamiento & purificación , Farmacorresistencia Bacteriana Múltiple , Genes Bacterianos , Acinetobacter/efectos de los fármacos , Regiones Antárticas , Antibacterianos/farmacología , Biología Computacional , Pruebas de Sensibilidad Microbiana , Plásmidos/análisis , Microbiología del Suelo , Secuenciación Completa del GenomaRESUMEN
In total, 95 Acinetobacter baumannii isolates recovered from patients from two hospitals in Cochabamba, Bolivia were studied. The presence of class D and B ß-lactamases was investigated using polymerase chain reaction, and antimicrobial susceptibility testing was performed by agar dilution and broth microdilution. The resistance rate to carbapenems was 53.7%. All carbapenem-resistant A. baumannii (CRAb, n=51) and four carbapenem-susceptible isolates were further analysed by whole-genome sequencing. The resulting genome assemblies were used to identify the acquired resistome, and core genome multi-locus sequence typing (cgMLST) was used to determine their molecular epidemiology. All but one of the CRAb isolates (n=50) belonged to international clone (IC) 7 and they clustered into five sequence types; on cgMLST, they were found to be separated by ≥40 alleles. All CRAb isolates carried blaOXA-23 on transposon Tn2008. Metallo-ß-lactamases were not detected. These data show that dissemination of several IC7 A. baumannii clones harbouring the carbapenem resistance determinant blaOXA-23 is occurring in these two hospitals in Cochambamba.
Asunto(s)
Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/genética , Enfermedades Endémicas , Genoma Bacteriano , Genotipo , Tipificación de Secuencias Multilocus , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/aislamiento & purificación , Antibacterianos/farmacología , Bolivia/epidemiología , Análisis por Conglomerados , Hospitales , Humanos , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Reacción en Cadena de la Polimerasa , beta-Lactamasas/genéticaRESUMEN
BACKGROUND: Acinetobacter calcoaceticus-A. baumannii (Acb) complex and Stenotrophomonas maltophilia represent frequent causes of hospital-acquired infections. We evaluated the frequency and resistance rates of Acb complex and S. maltophilia isolates from medical centers enrolled in the SENTRY Program. METHODS: A total of 13 752 Acb complex and 6467 S. maltophilia isolates were forwarded to a monitoring laboratory by 259 participating sites from the Asia-Pacific region, Latin America, Europe, and North America between 1997 and 2016. Confirmation of species identification and antimicrobial susceptibility testing were performed using conventional methods and/or matrix-assisted laser desorption ionization-time of flight mass spectrometry and the broth microdilution method, respectively. Antimicrobial susceptibility results were interpreted by CLSI and EUCAST 2018 criteria. RESULTS: Acb complex and S. maltophilia were most frequently isolated from patients hospitalized with pneumonia (42.9% and 55.8%, respectively) and bloodstream infections (37.3% and 33.8%, respectively). Colistin and minocycline were the most active agents against Acb complex (colistin MIC50/90, ≤0.5/2 mg/L; 95.9% susceptible) and S. maltophilia (minocycline MIC50/90, ≤1/2 mg/L; 99.5% susceptible) isolates, respectively. Important temporal decreases in susceptibility rates among Acb complex isolates were observed for all antimicrobial agents in all regions. Rates of extensively drug-resistant Acb complex rates were highest in Europe (66.4%), followed by Latin America (61.5%), Asia-Pacific (56.9%), and North America (38.8%). Among S. maltophilia isolates, overall trimethoprim-sulfamethoxazole (TMP-SMX) susceptibility rates decreased from 97.2% in 2001-2004 to 95.7% in 2013-2016, but varied according to the geographic region. CONCLUSIONS: We observed important reductions of susceptibility rates to all antimicrobial agents among Acb complex isolates obtained from all geographic regions. In contrast, resistance rates to TMP-SMX among S. maltophilia isolates remained low and relatively stable during the study period.
RESUMEN
We report contemporary (2014-2016) Tigecycline Evaluation and Surveillance Trial (T.E.S.T.) global data on activity of tigecycline and comparators against WHO 'priority pathogens', and global trends (2004-2016) in antimicrobial resistance. MICs were determined using CLSI broth microdilution methodology. Antimicrobial resistance was determined using CLSI breakpoints (FDA breakpoints for tigecycline). Data are reported for Africa, Asia, Europe, North America and South America. From 2014-2016, Africa, Asia and South America reported highest resistance rates among Acinetobacter baumannii; North America lowest (all antimicrobials tested). The tigecycline MIC90 against A. baumannii was 2 mg/L in all regions except South America (1 mg/L). Among Enterobacteriaceae, meropenem resistance was low and tigecycline resistance was ≤1.3% in all regions (Escherichia coli, 0.0-0.3%; Klebsiella pneumoniae 0.0-1.3%; Enterobacter spp. 0.5-1.1%; Serratia marcescens 0.0-1.3%). Ceftriaxone resistance among E. coli ranged from 14.5% (North America) to 54.7% (Asia), and among K. pneumoniae from 9.1% (North America) to 54.0% (South America). North America reported highest rates of vancomycin-resistant Enterococcus faecium (64.6%); Europe lowest (17.7%). The tigecycline MIC90 against methicillin-resistant Staphylococcus aureus (MRSA) ranged from 0.12 mg/L (Africa and North America) to 0.5 mg/L (Asia). From 2004-2016, carbapenem resistance increased among A. baumannii (all regions), reaching 92.3% in Africa and 85.7% in South America (2016). Rates of ceftriaxone-resistant E. coli increased in all regions except Asia. Ceftriaxone resistance in K. pneumoniae increased in Europe. Rates of vancomycin-resistant E. faecium and MRSA were highest in North America and South America (and Asia for MRSA); lowest in Europe.
Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana Múltiple , Monitoreo Epidemiológico , Infecciones por Bacterias Gramnegativas/epidemiología , Infecciones por Bacterias Grampositivas/epidemiología , Tigeciclina/farmacología , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/crecimiento & desarrollo , África/epidemiología , Asia/epidemiología , Carbapenémicos/farmacología , Ceftriaxona/farmacología , Enterobacter/efectos de los fármacos , Enterobacter/crecimiento & desarrollo , Enterococcus faecium/efectos de los fármacos , Enterococcus faecium/crecimiento & desarrollo , Escherichia coli/efectos de los fármacos , Escherichia coli/crecimiento & desarrollo , Europa (Continente)/epidemiología , Infecciones por Bacterias Gramnegativas/tratamiento farmacológico , Infecciones por Bacterias Gramnegativas/microbiología , Infecciones por Bacterias Grampositivas/tratamiento farmacológico , Infecciones por Bacterias Grampositivas/microbiología , Humanos , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/crecimiento & desarrollo , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Staphylococcus aureus Resistente a Meticilina/crecimiento & desarrollo , Pruebas de Sensibilidad Microbiana , América del Norte/epidemiología , Serratia marcescens/efectos de los fármacos , Serratia marcescens/crecimiento & desarrollo , América del Sur/epidemiologíaRESUMEN
Acinetobacter seifertii is a recently described species that belongs to the Acinetobacter calcoaceticus-Acinetobacter baumannii complex. It has been recovered from clinical samples and is sometimes associated with antimicrobial resistance determinants. We present here the case of three A. seifertii clinical isolates which were initially identified as Acinetobacter sp. by phenotypic methods but no identification at the species level was achieved using semi-automated identification methods. The isolates were further analysed by whole genome sequencing and identified as A. seifertii. Due to the fact that A. seifertii has been isolated from serious infections such as respiratory tract and bloodstream infections, we emphasize the importance of correctly identifying isolates of the genus Acinetobacter at the species level to gain a deeper knowledge of their prevalence and clinical impact.
Asunto(s)
Infecciones por Acinetobacter/microbiología , Acinetobacter/genética , Acinetobacter/aislamiento & purificación , Acinetobacter/clasificación , Acinetobacter/efectos de los fármacos , Infecciones por Acinetobacter/sangre , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Bolivia/epidemiología , Infecciones Relacionadas con Catéteres/microbiología , Girasa de ADN/genética , ADN Bacteriano/genética , Genoma Bacteriano , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Reacción en Cadena de la Polimerasa , ARN Ribosómico 16S/genética , Espectrometría de Masa por Láser de Matriz Asistida de Ionización DesorciónRESUMEN
The typing of multidrug-resistant Acinetobacter baumannii isolates is important for the control and prevention of hospital outbreaks. This study aimed to analyze the molecular epidemiology of 46 OXA-23 carbapenemase-producing A. baumannii strains and compare them to previously described local and international clones (ICs). Isolates were recovered during May 2009-August 2011, from 8 different hospitals in the state of Parana (Brazil). The molecular profiles were determined by repetitive extragenic palindromic PCR. Seven different clusters were identified (A to G). Thirty-two isolates were clustered in the same pattern (clone A), which belong to IC 4.