RESUMEN

Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages (4,152 prophages + 122 virulent phages, distributed in 46 countries in the world), we show that 91% (875 out of 963) of the prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are not only cosmopolitan but also the most abundant species. We also noted that polylysogens had very divergent prophages, belonging to different prophage species, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. Our study highlights how integrating the host population structure and a solid operational definition of phage species allows us to better appreciate phage diversity and its transmission dynamics. IMPORTANCE: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.

Asunto(s)

Especificidad del Huésped , Profagos , Profagos/genética , Profagos/fisiología , Profagos/clasificación , Acinetobacter baumannii/virología , Acinetobacter baumannii/genética , Acinetobacter baumannii/clasificación , Metagenómica , Filogenia , Genoma Viral , Bacteriófagos/genética , Bacteriófagos/fisiología , Bacteriófagos/clasificación , Bacteriófagos/aislamiento & purificación

RESUMEN

Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of Acinetobacter baumannii, a very important nosocomial pathogen. Here we analyse 1450+ genomes (covering >40 countries and >4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii. We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae. Despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Our results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genomic epidemiology (and surveillance) of bacterial pathogens.

Asunto(s)

Acinetobacter baumannii/clasificación , Proteínas Bacterianas/genética , Biología Computacional/métodos , Farmacorresistencia Bacteriana Múltiple , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Bases de Datos Genéticas , Flujo Génico , Transferencia de Gen Horizontal , Filogenia , Secuenciación Completa del Genoma

RESUMEN

OBJECTIVES: To analyze the relationship of ribosomal protein mutations and clonality of high-risk clones Acinetobacter baumannii. METHODS: Seventy-nine carbapenem-resistant A. baumannii were subjected to whole-genome sequencing (Illumina NextSeq), and codifying sequences of ribosomal proteins were extracted and screened for mutations. MALDI-TOF MS analysis (Bruker Biotyper) and Spectra data from MALDI-TOF was employed to generate a dendrogram based on principal component analysis (PCA) data. Clones were identified by Multilocus sequencing typing (MLST) based on WGS. RESULTS: Ribosomal RNA protein sequences extracted from the genomes identified mutations that were associated with clonal complexes, but most of them were silent. PCA did not cluster the isolates according to their clonality identified by MLST. CONCLUSIONS: By comparing the nucleotide and amino acid sequences of diversified A. baumannii, and Bruker Biotyper profiles, we showed that silent mutations in ribosomal RNA nucleotides are associated with clonal complexes, but since most of the mutations were silent, MALDI-TOF MS raw data was not a useful tool for typing the high-risk clones of this species.

Asunto(s)

Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/genética , Proteínas Ribosómicas/genética , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Antibacterianos/farmacología , Brasil/epidemiología , Carbapenémicos/farmacología , ADN Bacteriano , Farmacorresistencia Bacteriana , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Mutación Silenciosa , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Secuenciación Completa del Genoma

RESUMEN

Acinetobacter baumannii is nowadays a relevant nosocomial pathogen characterized by multidrug resistance (MDR) and concomitant difficulties to treat infections. OmpA is the most abundant A. baumannii outer membrane (OM) protein, and is involved in virulence, host-cell recognition, biofilm formation, regulation of OM stability, permeability and antibiotic resistance. OmpA members are two-domain proteins with an N-terminal eight-stranded ß-barrel domain with four external loops (ELs) interacting with the environment, and a C-terminal periplasmic domain binding non-covalently to the peptidoglycan. Here, we combined data from genome sequencing, phylogenetic and multilocus sequence analyses from 975 strains/isolates of the Acinetobacter calcoaceticus/Acinetobacter baumannii complex (ACB), 946 from A. baumannii, to explore ompA microevolutionary divergence. Five major ompA variant groups were identified (V1 to V5) in A. baumannii, encompassing 52 different alleles coding for 23 different proteins. Polymorphisms were concentrated in five regions corresponding to the four ELs and the C-terminal end, and provided evidence for intra-genic recombination. ompA variants were not randomly distributed across the A. baumannii phylogeny, with the most frequent V1(lct)a1 allele found in most clonal complex 2 (CC2) strains and the second most frequent V2(lct)a1 allele in the majority of CC1 strains. Evidence was found for assortative exchanges of ompA alleles not only between separate A. baumannii lineages, but also different ACB species. The overall results have implications for A. baumannii evolution, epidemiology, virulence and vaccine design.

Asunto(s)

Acinetobacter baumannii/clasificación , Proteínas de la Membrana Bacteriana Externa/genética , Variación Genética , Acinetobacter baumannii/genética , Acinetobacter baumannii/patogenicidad , Bases de Datos Genéticas , Evolución Molecular , Tipificación de Secuencias Multilocus , Filogenia , Secuenciación Completa del Genoma

RESUMEN

Acinetobacter baumannii (Aba) is an emerging opportunistic pathogen associated to nosocomial infections. The rapid increase in multidrug resistance (MDR) among Aba strains underscores the urgency of understanding how this pathogen evolves in the clinical environment. We conducted here a whole-genome sequence comparative analysis of three phylogenetically and epidemiologically related MDR Aba strains from Argentinean hospitals, assigned to the CC104O/CC15P clonal complex. While the Ab244 strain was carbapenem-susceptible, Ab242 and Ab825, isolated after the introduction of carbapenem therapy, displayed resistance to these last resource ß-lactams. We found a high chromosomal synteny among the three strains, but significant differences at their accessory genomes. Most importantly, carbapenem resistance in Ab242 and Ab825 was attributed to the acquisition of a Rep_3 family plasmid carrying a blaOXA-58 gene. Other differences involved a genomic island carrying resistance to toxic compounds and a Tn10 element exclusive to Ab244 and Ab825, respectively. Also remarkably, 44 insertion sequences (ISs) were uncovered in Ab825, in contrast with the 14 and 11 detected in Ab242 and Ab244, respectively. Moreover, Ab825 showed a higher killing capacity as compared to the other two strains in the Galleria mellonella infection model. A search for virulence and persistence determinants indicated the loss or IS-mediated interruption of genes encoding many surface-exposed macromolecules in Ab825, suggesting that these events are responsible for its higher relative virulence. The comparative genomic analyses of the CC104O/CC15P strains conducted here revealed the contribution of acquired mobile genetic elements such as ISs and plasmids to the adaptation of A. baumannii to the clinical setting.

Asunto(s)

Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Farmacorresistencia Bacteriana , Plásmidos/genética , Secuenciación Completa del Genoma/métodos , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Adaptación Fisiológica , Aminoglicósidos/farmacología , Animales , Argentina , Composición de Base , Carbenicilina/farmacología , Elementos Transponibles de ADN , Modelos Animales de Enfermedad , Genómica , Humanos , Filogenia , Sintenía

RESUMEN

Over the last few decades, carbapenemase-producing Acinetobacter baumannii has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach considering the whole genomes of 148 isolates (almost 40 from Mexico and Honduras), we describe the recent emergence of the lineage sequence type 758 (ST758), which belongs to the international clone V and has spread out to Canada, Mexico, Honduras, and Colombia. Notably, this lineage was found to coexist with other A. baumannii lineages in hospitals in Mexico and Honduras. Isolates from this lineage show considerable variation in antibiotic resistance profiles, but most of them are resistant to carbapenems. Moreover, we found a variety of acquired oxacillinase (OXA) families within this lineage and tracked the very recent inception, and subsequent horizontal transmission, of the OXA-239 carbapenemase. This work highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.IMPORTANCEA. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.

Asunto(s)

Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/enzimología , Genoma Bacteriano , beta-Lactamasas/genética , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Antibacterianos/farmacología , Carbapenémicos/farmacología , Infección Hospitalaria/microbiología , Farmacorresistencia Bacteriana Múltiple/genética , Genómica , Honduras , Humanos , México , Pruebas de Sensibilidad Microbiana

RESUMEN

OBJECTIVES: The extensively drug-resistant (XDR) Acinetobacter baumannii international clone VI (IC-6) has been identified worldwide since 2006. This study reports the emergence of IC-6 in the Brazilian Amazon region and reveals the particular genomic features considering its mobilome and resistome. METHODS: A total of 32 carbapenem-resistant A. baumannii strains recovered from Boa Vista city (Roraima, Brazil) in 2016 were characterised by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The whole genome sequences of the Brazilian IC-6 strains were obtained. The mobilome and resistome were assessed by in silico analyses. RESULTS: PFGE and MLST demonstrated that the 32 A. baumannii strains belonged to four clones. One XDR clone corresponded to the high-risk pandemic IC-6 lineage from ST944Oxf/78Pas. The IC-6 resistome was composed of aadA5, aac(3'')-IIa, aph(3')-Ia, armA, aadB, msrE, blaTEM-1, IS15DIV-blaCTX-M-115-IS15DIV, blaOXA-90, ISAba1-blaADC-152, blaOXA-72, qacEΔ1 and sul1. Mobilome prediction revealed that blaOXA-72 was embedded in a 15.5-kb plasmid and that it was flanked by putative XerC/D-binding sites, possibly involved in blaOXA-72 mobilisation. Several resistance genes were in a 48-kb multidrug resistance genomic island inserted in the chromosome, which also harboured genes involved in host pathogenicity and adaptive traits. Interestingly, the Brazilian strains shared the blaOXA-72 and blaCTX-M-115 with IC-6/ST944Oxf/78Pas recovered in a distinct spatiotemporal context, pointing to an epidemiological link among them. CONCLUSION: This study highlights the importance of surveillance of XDR A. baumannii strains, even outside of densely populated cosmopolitan regions, to reveal the epidemiology of pandemic lineages, stressing their threat to public health.

Asunto(s)

Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/clasificación , Secuenciación Completa del Genoma/métodos , beta-Lactamasas/genética , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Acinetobacter baumannii/aislamiento & purificación , Antibacterianos/farmacología , Brasil/epidemiología , Cromosomas Bacterianos/genética , Farmacorresistencia Bacteriana Múltiple , Electroforesis en Gel de Campo Pulsado , Evolución Molecular , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Filogenia , Plásmidos/genética , Vigilancia de la Población

RESUMEN

BACKGROUND: Acinetobacter baumannii is a leading cause of nosocomial infections. This species is characterised by the presence of pandemic lineages (International Clones) that present a broad antimicrobial resistance profile. OBJECTIVE: To perform the molecular epidemiology of carbapenem-resistant A. baumannii from a clinical setting in the Amazon Basin, and to characterise their antimicrobial resistance determinants. METHODS: The genetic relationship of carbapenem-resistant A. baumannii were assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Class A, B and D ß-lactamase genes were screened by polymerase chain reaction (PCR) and sequencing. The antimicrobial susceptibility profile was obtained by Disc-diffusion method and minimum inhibitory concentration (MIC) determination. FINDINGS: All carbapenem-resistant A. baumannii strains belonged to three international clones, IC-1, IC-5 and IC-6, the latter recently reported by the first time in Brazil. The major determinant of carbapenem resistance in IC-1 and IC-5 strains was bla OXA-23, associated with ISAba1 and ISAba3, respectively, while IC-6 harboured the bla OXA-72. CONCLUSIONS: The A. baumannii epidemiology in Brazilian Amazon Region was unknown. It was demonstrated that A. baumannii XDR international clones were responsible for nosocomial infections in Boa Vista during 2016-2018, revealing that the epidemiological scenario of A. baumannii infections in Amazon Region resembles those from the cosmopolitan regions worldwide.

Asunto(s)

Infecciones por Acinetobacter/virología , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , beta-Lactamasas/genética , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Brasil , Pruebas Antimicrobianas de Difusión por Disco , Electroforesis en Gel de Campo Pulsado , Genotipo , Humanos , Tipificación de Secuencias Multilocus , Fenotipo

RESUMEN

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/genética

RESUMEN

We analyze the evolutionary dynamics of ninety carbapenem-resistant Acinetobacter baumannii (CRAB) isolates collected between 1990 and 2015 in Chile. CRAB were identified at first in an isolate collected in 2005, which harbored the ISAba1-blaOXA-69 arrangement. Later, OXA-58- and OXA-23-producing A. baumannii strains emerged in 2007 and 2009, respectively. This phenomenon was associated with variations in the epidemiology of OXA-type carbapenemases, linked to nosocomial lineages belonging to ST109, ST162, ST15 (CC15) and ST318 (CC15).

Asunto(s)

Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Carbapenémicos/farmacología , Infección Hospitalaria/microbiología , Hospitales Pediátricos , Resistencia betalactámica , Acinetobacter baumannii/clasificación , Evolución Molecular , Humanos , Filogenia

RESUMEN

Although Acinetobacter baumannii has become one of the most important nosocomial pathogens worldwide, very little is known about the genetic identity of isolates from less developed countries in Latin America. To alleviate this, we sequenced the genomes of 16 A. baumannii isolates from Honduras. Whole-genome sequencing was conducted on 16 isolates from five Honduran Hospitals. With the sequences of these Honduran isolates and other 42 publically available genomes, a maximum likelihood phylogeny was constructed to establish the relationship between the Honduran isolates and those belonging to the International Clones (ICs). In addition, sequence type (ST) assignation was conducted by the PubMLST, and antibiotic resistance genes were identified using ResFinder. The Honduran isolates are highly diverse and contain new allele combinations under the Bartual multilocus sequence typing scheme. The most common STs were STB447/STP10 and STB758/STP156. Furthermore, none of these isolates belongs to clonal complexes related to the ICs. Antibiotic susceptibility profiles of these isolates showed that they are multidrug resistant (MDR) or extensively drug resistant (XDR). In addition, the Honduran isolates had genes involved in resistance to seven antibiotic families. For instance, several blaOXA alleles were found, including blaOXA-23 and a gene encoding the metallo-beta-lactamase NDM-1. Notably, nine of the Honduran isolates have antibiotic resistance genes to three or more antibiotic families. In summary, in this study, we unveiled an untapped source of genetic diversity of MDR and XDR isolates; notably, these isolates did not belong to the well-known ICs.

Asunto(s)

Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/genética , Farmacorresistencia Bacteriana Múltiple/genética , Genes Bacterianos , Genoma Bacteriano , beta-Lactamasas/genética , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/aislamiento & purificación , Antibacterianos/farmacología , Células Clonales , Monitoreo Epidemiológico , Expresión Génica , Variación Genética , Honduras/epidemiología , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Filogenia , Plásmidos/química , Plásmidos/metabolismo , Centros de Atención Terciaria , Secuenciación Completa del Genoma , beta-Lactamasas/metabolismo

RESUMEN

Carbapenem-resistant Acinetobacter baumannii is the top-ranked pathogen in the World Health Organization priority list of antibiotic-resistant bacteria. It emerged as a global pathogen due to the successful expansion of a few epidemic lineages, or international clones (ICs), producing acquired class D carbapenemases (OXA-type). During the past decade, however, reports regarding IC-I isolates in Latin America are scarce and are non-existent for IC-II and IC-III isolates. This study evaluates the molecular mechanisms of carbapenem resistance and the epidemiology of 80 non-duplicate clinical samples of A. baumannii collected from February 2014 through April 2016 at two tertiary care hospitals in Lima. Almost all isolates were carbapenem-resistant (97.5%), and susceptibility only remained high for colistin (95%). Pulsed-field gel electrophoresis showed two main clusters spread between both hospitals: cluster D containing 51 isolates (63.8%) associated with sequence type 2 (ST2) and carrying OXA-72, and cluster F containing 13 isolates (16.3%) associated with ST79 and also carrying OXA-72. ST2 and ST79 were endemic in at least one of the hospitals. ST1 and ST3 OXA-23-producing isolates were also identified. They accounted for sporadic hospital isolates. Interestingly, two isolates carried the novel OXA-253 variant of OXA-143 together with an upstream novel insertion sequence (ISAba47). While the predominant A. baumannii lineages in Latin America are linked to ST79, ST25, ST15, and ST1 producing OXA-23 enzymes, we report the emergence of highly resistant ST2 (IC-II) isolates in Peru producing OXA-72 and the first identification of ST3 isolates (IC-III) in Latin America, both considered a serious threat to public health worldwide.

Asunto(s)

Infecciones por Acinetobacter/epidemiología , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Carbapenémicos/farmacología , Resistencia betalactámica , Infecciones por Acinetobacter/transmisión , Acinetobacter baumannii/genética , Acinetobacter baumannii/aislamiento & purificación , Enfermedades Transmisibles Emergentes/epidemiología , Enfermedades Transmisibles Emergentes/microbiología , Electroforesis en Gel de Campo Pulsado , Genes Bacterianos , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Perú/epidemiología

Asunto(s)

Infecciones por Acinetobacter/epidemiología , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/genética , Tipificación de Secuencias Multilocus , Humanos , Epidemiología Molecular , Reacción en Cadena de la Polimerasa Multiplex , Filogenia

RESUMEN

The global success of multidrug-resistant Acinetobacter baumannii has been associated with the dissemination of a high-risk clone designated clonal complex (CC) 92B (Bartual scheme)/CC2P (Pasteur scheme), which is the most frequent genetic lineage in European, Asian, and North American carbapenem-resistant Acinetobacter isolates. In these isolates, carbapenem resistance is mainly mediated by ß-lactamases encoded by blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, and/or blaOXA-58-like genes. In this study, we characterized the population genetics of 121 carbapenem-resistant A. baumannii complex isolates recovered from 14 hospitals in seven cities in Colombia (2008-2010). Multiplex PCR was used to detect blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, and blaOXA-58-like genes. Molecular typing was performed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). PCR showed that 118 (97.5%) of the isolates were positive for both blaOXA-23-like and blaOXA-51-like genes, and three other isolates were only positive for blaOXA-51-like. PFGE identified 18 different pulsotypes, while MLST identified 11 different sequence types (STs), seven of which had not been previously described in Acinetobacter. None of the STs found in this study was associated with CC92B/CC2P. The most widespread STs in our isolates belonged to ST636 and their single-locus variants ST121/ST124/ST634 (CC636B) followed by STs belonging to CC110B. Our observations suggest a wide distribution of diverse A. baumannii complex clones containing blaOXA-23-like in Colombian hospitals (especially CC636B and CC110B) that differ from the high-risk clones commonly found in other regions of the world, indicating a distinct molecular epidemiology of carbapenem-resistant Acinetobacter spp. in Colombia.

Asunto(s)

Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Carbapenémicos/farmacología , Regulación Bacteriana de la Expresión Génica , Resistencia betalactámica/genética , beta-Lactamasas/genética , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/crecimiento & desarrollo , Células Clonales , Colombia/epidemiología , Electroforesis en Gel de Campo Pulsado , Variación Genética , Hospitales , Humanos , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Tipificación de Secuencias Multilocus , Reacción en Cadena de la Polimerasa Multiplex , Serogrupo , beta-Lactamasas/clasificación , beta-Lactamasas/metabolismo

RESUMEN

Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-ß-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.

Asunto(s)

Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/enzimología , Proteínas Bacterianas/genética , Infecciones por Enterobacteriaceae/microbiología , Enterobacteriaceae/enzimología , Plásmidos/genética , beta-Lactamasas/genética , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/genética , Antibacterianos/farmacología , Proteínas Bacterianas/metabolismo , Colombia/epidemiología , Farmacorresistencia Bacteriana , Enterobacteriaceae/clasificación , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/genética , Infecciones por Enterobacteriaceae/epidemiología , Humanos , México/epidemiología , Filogenia , Plásmidos/metabolismo , beta-Lactamasas/metabolismo

RESUMEN

Nonfermenting Gram-negative bacteria such as Pseudomonas aeruginosa and Acinetobacter baumannii are widespread in the environment and are increasingly associated with nosocomial infections, often associated with multidrug-resistance phenotypes. This study aimed to evaluate epidemiological, physiological, and molecular characteristics of carbapenem resistance in P. aeruginosa and A. baumannii. In total, 63 nonreplicated strains (44 A. baumannii and 19 P. aeruginosa) were isolated from hospitalized patients. Antimicrobial resistance patterns, biocide tolerance, oxidative stress, hemolytic activity, and biofilm formation were assessed. Genetic markers related to ß-lactamase synthesis, efflux systems, and porin loss were screened by PCR. Epidemiological data of patients were analyzed. Advanced age, intensive care unit admission, invasive medical devices, treatment with fluoroquinolones or ß-lactams/ß-lactamase inhibitor combinations, and prolonged hospital stay were predisposing factors for infection. Colistin showed to be active in vitro against these bacteria. Carbapenem-resistant P. aeruginosa strains did not show hemolytic activity and were less tolerant to oxidative stress and biocides. However, increased ability of biofilm formation was observed, comparing to the carbapenem-susceptible isolates. Genetic markers related to oxacillinases synthesis (OXA-23 and OXA-143), oprD absence, and efflux pump (adeB) were detected in carbapenem-resistant A. baumannii. Screening for OXA-51-like gene was performed as confirmatory test for A. baumannii identification. In P. aeruginosa genes encoding efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM) and SPM-1 were found; besides, oprD absence was also observed. Our results suggest that these organisms are well adapted to different environments and confirm the difficulty of therapeutic management of patients with infections associated with multidrug-resistant microorganisms, with direct impact on mortality and epidemiological control of these strains in health centers.

Asunto(s)

Acinetobacter baumannii/genética , Farmacorresistencia Bacteriana Múltiple/genética , Genes MDR , Porinas/genética , Pseudomonas aeruginosa/genética , beta-Lactamasas/genética , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/epidemiología , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/aislamiento & purificación , Adolescente , Adulto , Antibacterianos/farmacología , Biopelículas/efectos de los fármacos , Biopelículas/crecimiento & desarrollo , Brasil/epidemiología , Carbapenémicos/farmacología , Niño , Preescolar , Estudios Transversales , Femenino , Fluoroquinolonas/farmacología , Expresión Génica , Hospitales , Humanos , Lactante , Recién Nacido , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Epidemiología Molecular , Estrés Oxidativo , Porinas/metabolismo , Infecciones por Pseudomonas/tratamiento farmacológico , Infecciones por Pseudomonas/epidemiología , Infecciones por Pseudomonas/microbiología , Pseudomonas aeruginosa/clasificación , Pseudomonas aeruginosa/efectos de los fármacos , Pseudomonas aeruginosa/aislamiento & purificación , beta-Lactamasas/metabolismo

Asunto(s)

Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/enzimología , Farmacorresistencia Bacteriana Múltiple , Genotipo , Neumonía Asociada al Ventilador/microbiología , beta-Lactamasas/análisis , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/aislamiento & purificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Brasil , Femenino , Hospitales Universitarios , Humanos , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Tipificación de Secuencias Multilocus , Neumonía Asociada al Ventilador/epidemiología , Adulto Joven , beta-Lactamasas/genética

RESUMEN

BACKGROUND: The genus Acinetobacter sp. comprises more than 50 species, and four are closely related and difficult to be distinguished by either phenotypic or genotypic methods: the Acinetobacter calcoaceticus-baumannii complex (ABC). The correct identification at species level is necessary mainly due to the epidemiological aspects. METHODS: We evaluated a multiplex PCR for gyrB gene to identify the species of the ABC using the sequencing of the ITS 16S-23S fragment as a gold standard. Isolates identified as Acinetobacter calcoaceticus-baumannii from three hospitals at southern Brazil in 2011 were included in this study. RESULTS: A total of 117 isolates were obtained and 106 (90.6%) were confirmed as A. baumannii, 6 (5.1%) as A. nosocomialis and 4 (3.4%) as A. pittii by PCR for gyrB gene. Only one isolate did not present a product of the PCR for the gyrB gene; this isolate was identified as Acinetobacter genospecie 10 by sequencing of ITS. We also noted that the non-A. baumannii isolates were recovered from respiratory tract (8/72.7%), blood (2/18.2%) and urine (1/9.1%), suggesting that these species can cause serious infection. CONCLUSION: These findings evidenced that the multiplex PCR of the gyrB is a feasible and simple method to identify isolates of the ABC at the species level.

Asunto(s)

Infecciones por Acinetobacter , Acinetobacter baumannii/genética , Girasa de ADN/genética , ADN Bacteriano/análisis , Reacción en Cadena de la Polimerasa Multiplex/métodos , Infecciones por Acinetobacter/diagnóstico , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , ADN Bacteriano/química , ADN Bacteriano/genética , Humanos

RESUMEN

One hundred and twenty-six epidemiologically sequential, unrelated, carbapenem-resistant Acinetobacter baumannii isolates from nine hospitals in six countries of South America were collected between July 2013 and June 2014. Genes coding for Ambler class D and B carbapenemases were sought by PCR. All isolates were typed using the 3-locus sequence typing and blaOXA-51-like sequence-based typing techniques. The blaOXA-23 gene was recovered in all the participating hospitals and in all the isolates of seven of nine medical centres. The blaOXA-72 gene was only recovered in the two medical centres from Guayaquil city, Ecuador. Trilocus sequence typing revealed the presence of sequence groups SG2, SG4 and SG5. blaOXA-51-like sequence-based typing revealed the presence of blaOXA-132, blaOXA-65, blaOXA-69 and blaOXA-64. Our results showed that the population of carbapenem-resistant A. baumannii in South America was principally associated with ST79, ST25 and ST15 (92 %) and harboured the blaOXA-23 gene mainly. CC2 was not detected.

Asunto(s)

Infecciones por Acinetobacter/epidemiología , Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/efectos de los fármacos , Antibacterianos/farmacología , Carbapenémicos/farmacología , Resistencia betalactámica , Acinetobacter baumannii/genética , Acinetobacter baumannii/aislamiento & purificación , Proteínas Bacterianas/genética , Genotipo , Hospitales , Humanos , Epidemiología Molecular , Tipificación de Secuencias Multilocus , Reacción en Cadena de la Polimerasa , América del Sur/epidemiología , beta-Lactamasas/genética

RESUMEN

This study reports the presence of hospital-associated high-risk lineages of OXA-23-producing ST79 Acinetobacter baumannii and SPM-1-producing ST277 Pseudomonas aeruginosa in urban rivers in Brazil. These findings indicate that urban rivers can act as reservoirs of clinically important multidrug-resistant bacteria, which constitute a potential risk to human and animal health.

Asunto(s)

Acinetobacter baumannii/enzimología , Pseudomonas aeruginosa/enzimología , Ríos/microbiología , beta-Lactamasas/análisis , Acinetobacter baumannii/clasificación , Acinetobacter baumannii/genética , Acinetobacter baumannii/aislamiento & purificación , Animales , Brasil , Ciudades , Genotipo , Humanos , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Pseudomonas aeruginosa/clasificación , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/aislamiento & purificación , beta-Lactamasas/genética