Molecular epidemiology of multidrug-resistant Acinetobacter baumannii in a single institution over a 10-year period

Genetic diversity and clonal evolution of carbapenem-resistant Acinetobacter baumannii isolates from Portugal and the dissemination of ST118

In this study, 116 multidrug-resistant Acinetobacter baumannii (MDR-Ab) isolates recovered in various regions of Portugal were studied. All isolates were non-susceptible to tigecycline; one isolate was also non-susceptible to colistin, making it a step closer to pandrug resistance. Among 72 isolates tested by PFGE, 98.6% carried bla(OXA-66), 1.4% bla(OXA-104), 77.8% bla(OXA-23), 23.6% bla(OXA-24), 18.1% bla(TEM-1) and 1.4% bla(CTX-M-15-like) genes. No OXA-58 or metallo-β-lactamase-encoding genes were detected. ISAba1 was found in 58/72 isolates (80.6%). Among these, ISAba1 was found upstream of bla(OXA-51-like) in 54 isolates. All but two of these isolates also carried ISAba1-bla(OXA-23), highlighting the coexistence of ISAba1-bla(OXA-51-like) and ISAba1-bla(OXA-23) genetic platforms, emphasising the importance of mobile genetic elements in the dissemination of carbapenem-hydrolysing class D β-lactamase genes. Tn2006-like and Tn2008-like, found within ST92 and ST118, may reflect either multiple genetic structures in the origin of bla(OXA-23) acquisition or interclonal complex evolution. These results indicate that there may exist different genetic origins for carbapenem resistance among MDR-Ab isolates. Six PFGE profiles were associated with three major sequence types, with ST118 (OXA-23- or OXA-24-producer) being widely disseminated since 2009. ST98 (described so far as endemic in Portugal) and ST92 (which co-existed with ST98 before 2009) appeared to have been gradually replaced by ST118. The new ST188 (OXA-104-producer) was detected for the first time in this country. Identification of an extensively drug-resistant ST118 and carbapenem-resistant ST92, ST98 and ST118 isolates, both in community and healthcare facilities, demonstrates the menace of A. baumannii-associated infections.

Insights into the global molecular epidemiology of carbapenem non-susceptible clones of Acinetobacter baumannii

The global emergence of multidrug resistance (MDR) among Gram-negative bacteria has dramatically limited the therapeutic options. During the last two decades, Acinetobacter baumannii has become a pathogen of increased clinical importance due to its remarkable ability to cause outbreaks of infections and to acquire resistance to almost all currently used antibiotics, including the carbapenems. This review considers the literature on A. baumannii and data from multilocus sequence typing studies to explore the global population structure of A. baumannii and detect the occurrence of clonality, with the focus on the presence of specific resistance mechanisms such as the OXA-carbapenemases. The worldwide dissemination of MDR and carbapenem non-susceptible A. baumannii is associated with diverse genetic backgrounds, but predominated by a number of extensively distributed clones, such as CC92(B)/CC2(P) and CC109(B)/CC1(P), which have frequently been supplemented by acquired OXA-type carbapenemase genes.

Longitudinal analysis of the temporal evolution of Acinetobacter baumannii strains in Ohio, USA, by using rapid automated typing methods

Genotyping methods are essential to understand the transmission dynamics of Acinetobacter baumannii. We examined the representative genotypes of A. baumannii at different time periods in select locations in Ohio, using two rapid automated typing methods: PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS), a form of multi-locus sequence typing (MLST), and repetitive-sequence-based-PCR (rep-PCR). Our analysis included 122 isolates from 4 referral hospital systems, in 2 urban areas of Ohio. These isolates were associated with outbreaks at 3 different time periods (1996, 2000 and 2005–2007). Type assignments of PCR/ESI-MS and rep-PCR were compared to each other and to worldwide (WW) clone types. The discriminatory power of each method was determined using the Simpson's index of diversity (DI). We observed that PCR/ESI-MS sequence type (ST) 14, corresponding to WW clone 3, predominated in 1996, whereas ST 12 and 14 co-existed in the intermediate period (2000) and ST 10 and 12, belonging to WW clone 2, predominated more recently in 2007. The shift from WW clone 3 to WW clone 2 was accompanied by an increase in carbapenem resistance. The DI was approximately 0.74 for PCR/ESI-MS, 0.88 for rep-PCR and 0.90 for the combination of both typing methods. We conclude that combining rapid automated typing methods such as PCR/ESI-MS and rep-PCR serves to optimally characterize the regional molecular epidemiology of A. baumannii. Our data also sheds light on the changing sequence types in an 11 year period in Northeast Ohio.

Molecular characterization of carbapenem-non-susceptible Acinetobacter spp. in Japan: predominance of multidrug-resistant Acinetobacter baumannii clonal complex 92 and IMP-type metallo-β-lactamase-producing non-baumannii Acinetobacter species

We conducted an epidemiological study concerning carbapenem-non-susceptible clinical isolates of Acinetobacter spp. in Japan by molecular procedures including carbapenemase gene identification and amplified ribosomal DNA restriction analysis. Among 598 clinically isolated Acinetobacter spp. in 2007, 27 (4.5%) were non-susceptible to carbapenems. Most carbapenem-non-susceptible Acinetobacter baumannii (13/14) belonged to clonal complex (CC) 92, harbored bla (OXA-51-like) genes, including novel bla (OXA-206), downstream of ISAba1, and were recovered mainly from the Kanto region. Carbapenem-non-susceptible A. baumannii CC92 isolates were further divided by pulsed-field gel electrophoresis into two groups, one of which was characterized by the presence of bla (OXA-23). One A. baumannii CC276 isolate carried bla (IMP-1) and bla (OXA-58). Almost all non-baumannii Acinetobacter isolates (12/13), including Acinetobacter pittii (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis (formerly Acinetobacter genomic species 13TU), produced IMP-type metallo-β-lactamases, and were recovered from various regions in Japan. This is the first report describing the nationwide molecular epidemiology of carbapenem-non-susceptible Acinetobacter spp. with genomic species-level identification in Japan.

Endemic Acinetobacter baumannii in a New York hospital

Background

Acinetobacter baumannii is an increasingly multidrug-resistant (MDR) cause of hospital-acquired infections, often associated with limited therapeutic options. We investigated A. baumannii isolates at a New York hospital to characterize genetic relatedness.

Methods

Thirty A. baumannii isolates from geographically-dispersed nursing units within the hospital were studied. Isolate relatedness was assessed by repetitive sequence polymerase chain reaction (rep-PCR). The presence and characteristics of integrons were assessed by PCR. Metabolomic profiles of a subset of a prevalent strain isolates and sporadic isolates were characterized and compared.

Results

We detected a hospital-wide group of closely related carbapenem resistant MDR A. baumannii isolates. Compared with sporadic isolates, the prevalent strain isolates were more likely to be MDR (p = 0.001). Isolates from the prevalent strain carried a novel Class I integron sequence. Metabolomic profiles of selected prevalent strain isolates and sporadic isolates were similar.

Conclusion

The A. baumannii population at our hospital represents a prevalent strain of related MDR isolates that contain a novel integron cassette. Prevalent strain and sporadic isolates did not segregate by metabolomic profiles. Further study of environmental, host, and bacterial factors associated with the persistence of prevalent endemic A. baumannii strains is needed to develop effective prevention strategies.

Use of adherence monitors as part of a team approach to control clonal spread of multidrug-resistant Acinetobacter baumannii in a research hospital

BACKGROUND

Multidrug-resistant Acinetobacter baumannii (MDRAB) is difficult to treat and eradicate. Several reports describe isolation and environmental cleaning strategies that controlled hospital MDRAB outbreaks. Such interventions were insufficient to interrupt MDRAB transmission in 2 intensive care unit-based outbreaks in our hospital. We describe strategies that were associated with termination of MDRAB outbreaks at the National Institutes of Health Clinical Center.

METHODS

In response to MDRAB outbreaks in 2007 and 2009, we implemented multiple interventions, including stakeholder meetings, enhanced isolation precautions, active microbial surveillance, cohorting, and extensive environmental cleaning. We conducted a case-control study to analyze risk factors for acquiring MDRAB. In each outbreak, infection control adherence monitors were placed in MDRAB cohort areas to observe and correct staff infection control behavior.

RESULTS

Between May 2007 and December 2009, 63 patients acquired nosocomial MDRAB; 57 (90%) acquired 1 or more of 4 outbreak strains. Of 347 environmental cultures, only 2 grew outbreak strains of MDRAB from areas other than MDRAB patient rooms. Adherence monitors recorded 1,330 isolation room entries in 2007, of which 8% required interventions. In 2009, around-the-clock monitors recorded 4,892 staff observations, including 127 (2.6%) instances of nonadherence with precautions, requiring 68 interventions (1.4%). Physicians were responsible for more violations than other staff (58% of hand hygiene violations and 37% of violations relating to gown and glove use). Each outbreak terminated in temporal association with initiation of adherence monitoring.

CONCLUSIONS

Although labor intensive, adherence monitoring may be useful as part of a multifaceted strategy to limit nosocomial transmission of MDRAB.

Evolution of multidrug-resistant Acinetobacter baumannii clonal lineages: a 10 year study in Greece (2000-09)

OBJECTIVES

To analyse the evolution and genetic relatedness of Acinetobacter baumannii clonal lineages in Greece during a 10 year period.

METHODS

The study included 94 randomly selected A. baumannii clinical isolates recovered from 2000 to 2009 in eight tertiary Greek hospitals. Carbapenem MICs were determined by agar dilution. PCR was applied for carbapenemase genes. Isolates were typed by PFGE and tri-locus sequence typing (3LST), and 25 were also typed by multilocus sequence typing (MLST) developed by the Institut Pasteur, followed by e-Burst analysis.

RESULTS

All isolates were multidrug-resistant (MDR); 54 (57.4%) were non-susceptible to imipenem and/or meropenem. The bla(OXA-58) gene was identified in 51 (94.4%) carbapenem-non-susceptible and 15 (37.5%) carbapenem-susceptible isolates; other carbapenemase genes were not detected. Eight different PFGE types were identified. Sequence typing revealed previously characterized 3LST groups (1, 2, 4 and 5) and MLST types (STs) (1, 2, 15, 45 and 54) and the novel STs 85 (in two distant hospitals) and 86. Eight novel 3LST alleles were identified. Fifty-two (55.3%) isolates were assigned to 3LST group 1 and ST2 or ST45, both corresponding to international clonal complex 2 (CC2). Thirty-one (33.0%) isolates were assigned to 3LST group 2 and ST1 (CC1). From 2000 to 2004 63% of isolates belonged to 3LST group 2, but from 2005 to 2009 87.5% of isolates belonged to 3LST group 1; this shift was accompanied by an increase in carbapenem resistance from 43.5% to 64.6% of isolates.

CONCLUSIONS

The emergence of MDR A. baumannii in Greece was associated with CC1 and CC2, which are disseminated worldwide, often harbouring the bla(OXA-58) gene. Novel 3LST alleles and STs were also detected, underlining an evolutionary divergence in Greece.

Molecular epidemiology of carbapenem-nonsusceptible Acinetobacter baumannii in the United States

Acinetobacter baumannii is emerging as an important nosocomial pathogen worldwide. We report molecular epidemiology of 65 carbapenem-nonsusceptible A. baumannii isolates identified from hospitals in New York, Pennsylvania, Florida, Missouri, Nevada, and California between 2008 and 2009. All isolates were subjected to pulsed-field gel electrophoresis (PFGE). Select isolates then underwent multilocus sequence typing (MLST). While the PFGE patterns tended to cluster within each hospital, sequence types (STs) belonging to the clonal complex 92 (CC92) and the pan-European clonal lineage II (EUII; worldwide clonal lineage 2) were predominant in all hospitals. Of them, ST122 and ST208 were the most common and were found in four of the six hospitals. Isolates belonging to the pan-European clonal lineages I and III were identified in one hospital each. Carbapenemase-encoding genes bla(OXA-23) and/or ISAba1-bla(OXA-51-like) were present among the majority of isolates. These findings suggest that carbapenem-nonsusceptible A. baumannii isolates found in U.S. hospitals constitute part of the global epidemic driven by CC92, but have unique STs other than ST92, which may be spreading by means of patient transfer between health care facilities within the United States.

Adherence and motility characteristics of clinical Acinetobacter baumannii isolates

Acinetobacter baumannii continues to be a major health problem especially in hospital settings. Herein, features that may play a role in persistence and disease potential were investigated in a collection of clinical A. baumannii strains from Australia. Twitching motility was found to be a common trait in A. baumannii international clone I strains and in abundant biofilm formers, whereas swarming motility was only observed in isolates not classified within the international clone lineages. Bioinformatic analysis of the type IV fimbriae revealed a correlation between PilA sequence homology and motility. A high level of variability in adherence to both abiotic surfaces and epithelial cells was found. We report for the first time the motility characteristics of a large number of A. baumannii isolates and present a direct comparison of A. baumannii binding to nasopharyngeal and lung epithelial cells.

Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii

Acinetobacter baumannii is an emerging human pathogen and a significant cause of nosocomial infections among hospital patients worldwide. The enormous increase in multidrug resistance among hospital isolates and the recent emergence of pan-drug-resistant strains underscores the urgency to understand how A. baumannii evolves in hospital environments. To this end, we undertook a genomic study of a polyclonal outbreak of multidrug-resistant A. baumannii at the research-based National Institutes of Health Clinical Center. Comparing the complete genome sequences of the three dominant outbreak strain types enabled us to conclude that, despite all belonging to the same epidemic lineage, the three strains diverged before their arrival at the National Institutes of Health. The simultaneous presence of three divergent strains from this lineage supports its increasing prevalence in international hospitals and suggests an ongoing adaptation to the hospital environment. Further genomic comparisons uncovered that much of the diversification that occurred since the divergence of the three outbreak strains was mediated by homologous recombination across 20% of their genomes. Inspection of recombinant regions revealed that several regions were associated with either the loss or swapping out of genes encoding proteins that are exposed to the cell surface or that synthesize cell-surface molecules. Extending our analysis to a larger set of international clinical isolates revealed a previously unappreciated ability of A. baumannii to vary surface molecules through horizontal gene transfer, with subsequent intraspecies dissemination by homologous recombination. These findings have immediate implications in surveillance, prevention, and treatment of A. baumannii infections.

Extended-spectrum AmpC cephalosporinase in Acinetobacter baumannii: ADC-56 confers resistance to cefepime

ADC-56, a novel extended-spectrum AmpC (ESAC) β-lactamase, was identified in an Acinetobacter baumannii clinical isolate. ADC-56 possessed an R148Q change compared with its putative progenitor, ADC-30, which enabled it to hydrolyze cefepime. Molecular modeling suggested that R148 interacted with Q267, E272, and I291 through a hydrogen bond network which constrained the H-10 helix. This permitted cefepime to undergo conformational changes in the active site, with the carboxyl interacting with R340, likely allowing for better binding and turnover.

Aminoglycoside resistance in multiply antibiotic-resistant Acinetobacter baumannii belonging to global clone 2 from Australian hospitals

OBJECTIVES

To examine the distribution and context of aminoglycoside resistance genes in multiply antibiotic-resistant Acinetobacter baumannii isolates from Australia that are members of the global clone 2 and carry the bla(OXA-23) gene conferring resistance to carbapenems.

METHODS

Sixty-one multiply antibiotic-resistant A. baumannii strains isolated between 2000 and 2010 at six Australian hospitals that belonged to global clone 2 and carried the bla(OXA-23) gene were studied. Various molecular techniques were used to determine their relatedness and to detect antibiotic resistance genes and insertion sequences. Structures surrounding the aminoglycoside resistance genes were sequenced.

RESULTS

The isolates all shared several antibiotic resistance genes, including the sul2 sulphonamide resistance gene, but varied in their pattern of resistance to aminoglycosides. The aminoglycoside resistance profiles of isolates were accounted for by four resistance genes-aadB, aacC1, aphA1b and aphA6-in various combinations. The aadB gene cassette was located at a secondary site on a 6 kb plasmid similar to pRAY. The aphA6 gene was in a transposon, TnaphA6, bounded by directly oriented copies of ISAba125. The aacC1 gene cassette in a class 1 integron and Tn6020 carrying aphA1b were always present together, but were not linked.

CONCLUSIONS

Imipenem-resistant global clone 2 A. baumannii isolates containing bla(OXA-23) have been present in Australian hospitals for at least 10 years. Variation in this global clone 2 type has occurred with the introduction of various aminoglycoside resistance genes carried on a small plasmid or within transposons.