Imported and intensive care unit-born Acinetobacter baumannii clonal complexes: one-year prospective cohort study in intensive care patients

Contamination of healthcare environment by carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii is frequently found on floors, devices, and environmental sites in hospitals and can survive for prolonged periods and accumulate resistance determinants. The infection and presence of carbapenem-resistant A. baumannii (CRAB) in patients is associated with increased mortality, severe clinical outcomes, and longer lengths of stay at hospitals. This review addresses contamination by CRAB in corporal surfaces of patients and healthcare workers and environmental sites at healthcare-related settings. We summarized published data during the last decade on potential reservoirs for CRAB, including contamination frequency and the involved resistance mechanisms, and some measures associated with the elimination of CRAB from hospital surfaces.

Surveillance cultures following a regional outbreak of carbapenem-resistant Acinetobacter baumannii

OBJECTIVES

The primary aim of this study was to assess the epidemiology of carbapenem-resistant Acinetobacter baumannii (CRAB) for 9 months following a regional outbreak with this organism. We also aimed to determine the differential positivity rate from different body sites and characterize the longitudinal changes of surveillance test results among CRAB patients.

DESIGN

Observational study.

SETTING

A 607-bed tertiary-care teaching hospital in Milwaukee, Wisconsin.

PATIENTS

Any patient admitted from postacute care facilities and any patient housed in the same inpatient unit as a positive CRAB patient.

METHODS

Participants underwent CRAB surveillance cultures from tracheostomy secretions, skin, and stool from December 5, 2018, to September 6, 2019. Cultures were performed using a validated, qualitative culture method, and final bacterial identification was performed using mass spectrometry.

RESULTS

In total, 682 patients were tested for CRAB, of whom 16 (2.3%) were positive. Of the 16 CRAB-positive patients, 14 (87.5%) were residents from postacute care facilities and 11 (68.8%) were African American. Among positive patients, the positivity rates by body site were 38% (6 of 16) for tracheal aspirations, 56% (9 of 16) for skin, and 82% (13 of 16) for stool.

CONCLUSIONS

Residents from postacute care facilities were more frequently colonized by CRAB than patients admitted from home. Stool had the highest yield for identification of CRAB.

Multidrug-resistant Acinetobacter baumannii outbreaks: a global problem in healthcare settings

INTRODUCTION

The increase in the prevalence of multidrug-resistant Acinetobacter baumannii infections in hospital settings has rapidly emerged worldwide as a serious health problem.

METHODS

This review synthetizes the epidemiology of multidrug-resistant A. baumannii, highlighting resistance mechanisms.

CONCLUSIONS

Understanding the genetic mechanisms of resistance as well as the associated risk factors is critical to develop and implement adequate measures to control and prevent acquisition of nosocomial infections, especially in an intensive care unit setting.

Molecular characterization and clonal dynamics of nosocomial blaOXA-23 producing XDR Acinetobacter baumannii

The emergence of infections associated to new antimicrobial resistance in Acinetobacter baumannii (Ab) genotypes represents a major challenge. In this context, this study aimed to determine the diversity of resistance mechanisms and investigate clonal dissemination and predominant sequence types (STs) in multidrug-resistant Ab strains of clinical (tracheal aspirate, n = 17) and environmental (surface, n = 6) origins. Additionally, the major clones found in clinical (A) and environmental (H) strains had their complete genomes sequenced. All strains were submitted to polymerase chain reactions (PCR) for the detection of the ISAba1/blaOXA-51-like and ISAba1/blaOXA-23-like genes, while the expression of genes encoding the carO porin, AdeABC (adeB), AdeFGH (adeG), and AdeIJK (adeJ) efflux pumps was determined by real time PCR (qPCR). Most of the strains were characterized as extensively drug-resistant (XDR) with high minimal inhibitory concentrations (MICs) detected for tigecycline and carbapenems. Associations between ISAba1/OXA-51 and ISAba1/OXA-23 were observed in 91.3% and 52.2% of the strains, respectively. Only the adeB gene was considered hyper-expressed. Furthermore, most of the strains analyzed by the MuLtilocus Sequence-Typing (MLST) were found to belong to the clonal complex 113 (CC113). In addition, a new ST, ST1399, belonging to CC229, was also discovered herein. Strains analyzed by whole genome sequencing presented resistance genes linked to multidrug-resistance phenotypes and confirmed the presence of Tn2008, which provides high levels carbapenem-resistance.

Distinct Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii from Colombian Hospitals

The global success of multidrug-resistant Acinetobacter baumannii has been associated with the dissemination of a high-risk clone designated clonal complex (CC) 92^B (Bartual scheme)/CC2^P (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 β-lactamases encoded by bla_OXA-23-like, bla_OXA-24-like, bla_OXA-51-like, and/or bla_OXA-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 bla_OXA-23-like, bla_OXA-24-like, bla_OXA-51-like, and bla_OXA-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 bla_OXA-23-like and bla_OXA-51-like genes, and three other isolates were only positive for bla_OXA-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 CC92^B/CC2^P. The most widespread STs in our isolates belonged to ST636 and their single-locus variants ST121/ST124/ST634 (CC636^B) followed by STs belonging to CC110^B. Our observations suggest a wide distribution of diverse A. baumannii complex clones containing bla_OXA-23-like in Colombian hospitals (especially CC636^B and CC110^B) 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.

The epidemiology of carbapenemases in Latin America and the Caribbean

INTRODUCTION

Enterobacteriaceae, Pseudomonas spp., and Acinetobacter spp. infections are major causes of morbidity and mortality, especially due to the emergence and spread of β-lactamases. Carbapenemases, which are β-lactamases with the capacity to hydrolyze or inactivate carbapenems, have become a serious concern as they have the largest hydrolytic spectrum and therefore limit the utility of most β-lactam antibiotics. Areas covered: Here, we present an update of the current status of carbapenemases in Latin America and the Caribbean. Expert commentary: The increased frequency of reports on carbapenemases in Latin America and the Caribbean shows that they have successfully spread and have even become endemic in some countries. Countries such as Brazil, Colombia, Argentina, and Mexico account for the majority of these reports. Early suspicion and detection along with implementation of antimicrobial stewardship programs in all healthcare settings are crucial for the control and prevention of carbapenemase-producing bacteria.

A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones

A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings.

Population Structure Analysis of Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates from Brazil Reveals Predominance of Clonal Complexes 1, 15, and 79

The population structure of 71 carbapenem-resistantAcinetobacter baumanniiclinical isolates from several hospitals in Brazil was investigated by ApaI pulsed-field gel electrophoresis,blaOXA-51-like subtyping, and multilocus sequence typing (Institute Pasteur scheme). In addition to the predominance of strains carryingblaOXA-23, we detected the presence ofblaOXA-72andblaOXA-231 We observed a predominance of clonal complex 1 (CC1), CC15, and CC79 and representative strains of the worldwide-disseminated international clone I.

Antimicrobial Combinations against Pan-Resistant Acinetobacter baumannii Isolates with Different Resistance Mechanisms

The study investigated the effect of antibiotic combinations against 20 clinical isolates of A. baumannii (seven colistin-resistant and 13 colistin-susceptible) with different resistance mechanisms. Clinical data, treatment, and patient mortality were evaluated. The following methods were used: MIC, PCRs, and outer membrane protein (OMP) analysis. Synergy was investigated using the checkerboard and time-kill methods. Clonality was evaluated by PFGE. Based on clonality, the whole genome sequence of six A. baumannii isolates was analyzed. All isolates were resistant to meropenem, rifampicin, and fosfomycin. OXA-23 and OXA-143 were the most frequent carbapenemases found. Four isolates showed loss of a 43kDa OMP_. The colistin-susceptible isolates belonged to different clones and showed the highest synergistic effect with fosfomycin-amikacin. Among colistin-resistant isolates, the highest synergistic effect was observed with the combinations of colistin-rifampicin followed by colistin-vancomycin. All colistin-resistant isolates harbored bla_OXA-23-like and belonged to CC113. Clinical and demographic data were available for 18 of 20 patients. Fourteen received treatment and eight patients died during treatment. The most frequent site of infection was the blood in 13 of 14 patients. Seven patients received vancomycin plus an active drug against A. baumannii; however, mortality did not differ in this group. The synergistic effect was similar for colistin-susceptible isolates of distinct clonal origin presenting with the same resistance mechanism. Overall mortality and death during treatment was high, and despite the high synergism in vitro with vancomycin, death did not differ comparing the use or not of vancomycin plus an active drug against A. baumannii.

Association of class 1 and 2 integrons with multidrug-resistant Acinetobacter baumannii international clones and Acinetobacter nosocomialis isolates

The Acinetobacter baumannii clonal complex 113/79 (CC113/79) and class 2 integrons predominate in Latin America; a relationship between these characteristics was explored. The presence of integrases was determined in successive hospital Acinetobacter isolates (163 A. baumannii isolates and 72 Acinetobacter nosocomialis isolates). Most isolates had integrons, but class 1 and 2 integrons were present significantly more often in CC109/1 and CC113/79, respectively. The high prevalence of CC113/79 in Latin America may account for the predominance of class 2 integrons.

Carbapenem resistance in Pseudomonas aeruginosa and Acinetobacter baumannii in the nosocomial setting in Latin America

Increasing prevalence of carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter baumannii strains in the nosocomial setting in Latin America represents an emerging challenge to public health, as the range of therapeutic agents active against these pathogens becomes increasingly constrained. We review published reports from 2002 to 2013, compiling data from throughout the region on prevalence, mechanisms of resistance and molecular epidemiology of carbapenem-resistant strains of P. aeruginosa and A. baumannii. We find rates of carbapenem resistance up to 66% for P. aeruginosa and as high as 90% for A. baumannii isolates across the different countries of Latin America, with the resistance rate of A. baumannii isolates greater than 50% in many countries. An outbreak of the SPM-1 carbapenemase is a chief cause of resistance in P. aeruginosa strains in Brazil. Elsewhere in Latin America, members of the VIM family are the most important carbapenemases among P. aeruginosa strains. Carbapenem resistance in A. baumannii in Latin America is predominantly due to the oxacillinases OXA-23, OXA-58 and (in Brazil) OXA-143. Susceptibility of P. aeruginosa and A. baumannii to colistin remains high, however, development of resistance has already been detected in some countries. Better epidemiological data are needed to design effective infection control interventions.

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.

Emergence of Acinetobacter baumannii international clone II in Brazil: reflection of a global expansion

The aim of this study was to investigate the occurrence of carbapenem-resistant Acinetobacter baumannii international clones (IC) in Curitiba, Brazil, using multilocus sequence typing and trilocus PCR-based typing schemes. IC2 was the first emerging clone. This IC was detected in an isolate from 2003 of a PFGE type spread in at least two hospitals since 1999. Subsequently, IC2 waned while IC1 and clonal complex 15/104 prevailed. This is the first description of IC2 in Brazil and Latin America.

Clonal complexes 104, 109 and 113 playing a major role in the dissemination of OXA-carbapenemase-producing Acinetobacter baumannii in Southeast Brazil

Carbapenem resistance among Acinetobacter baumannii strains isolated from clinical settings in Brazil has increased dramatically in the last 10 years due to the emergence and dissemination of OXA-type carbapenemase encoding genes. This study aimed to characterize the presence of carbapenem-hydrolyzing class D β-lactamases (CHDL)-encoding genes and clonal complexes playing a major role in the dissemination of OXA-carbapenemase-producing A. baumannii in Southeast Brazil. A total of 74 A. baumannii strains isolated from patients admitted to 4 hospitals in Southeast Brazil were analyzed. Molecular characterization of strains revealed that 67 strains carried blaOXA-23 (72%), blaOXA-143 (25%) or both genes (3%). PFGE analysis identified 12 PFGE clusters, grouping 26 pulsotypes. Two PFGE clusters were predominant, comprising more than 66% of OXA-producing A. baumannii isolates. Among 23 representative strains characterized by MLST-UO (Multilocus Sequence Typing Scheme - University of Oxford, http://pubmlst.org/abaumannii/), 14 different STs were identified, of which six were confirmed as novel sequence types (designated as STs 402-407). Most of these isolates belonged to clonal complexes CC104,CC109 or CC113, whereas three STs were singletons (ST339, 403 and 407). In conclusion, the presence of blaOXA-23- and blaOXA-143-like genes was not related to specific ST/CC, suggesting that the dissemination of OXA-carbapenemase-encoding genes may involve different STs, in which the spread of OXA-23-like is most likely due to mobile elements (i.e., plasmids). In this regard, CC104, CC109 and CC113 played a major role as predominant CDHL-carrying clones, instead of CC92, which was not identified.

Dissemination of Acinetobacter nosocomialis clone among critically ill patients and the environment

We examined the environmental dissemination of Acinetobacter nosocomialis multilocus sequence typing clonal complex 260/71 in Rio de Janeiro, Brazil, including water from a dam and food samples. The increasing use of sequence based methods has demonstrated a large, previously unpredicted, dissemination of bacteria that may serve as opportunistic pathogens.