Suitable restriction enzyme for standardization of pulsed-field gel electrophoresis protocol and interlaboratory comparison of Acinetobacter baumannii

Molecular typing of multi-drug resistant Acinetobacter baumannii isolates from clinical and environmental specimens in three Iranian hospitals by pulsed field gel electrophoresis

BACKGROUND

Multi-drug resistant (MDR) Acinetobacter baumannii is one of the most important causes of nosocomial infections. The purpose of this study was to identify antibiotic resistance patterns, biofilm formation and the clonal relationship of clinical and environmental isolates of A. baumannii by Pulsed Field Gel Electrophoresis method. Forty-three clinical and 26 environmental isolates of the MDR A. baumannii were collected and recognized via API 20NE. Antibiotic resistance of the isolates was assessed by the disk diffusion method, and the biofilm formation test was done by the microtiter plate method. Pulsed Field Gel Electrophoresis (PFGE) was used to assess the genomic features of the bacterial isolates.

RESULTS

The resistance rate of clinical and environmental isolates against antibiotics were from 95 to 100%. The difference in antibiotic resistance rates between clinical and environmental isolates was not statistically significant (p > 0.05). Biofilm production capabilities revealed that 31 (44.9%), and 30 (43.5%) isolates had strong and moderate biofilm producer activity, respectively. PFGE typing exhibited eight different clusters (A, B, C, D, E, F, G, and H) with two significant clusters included A and G with 21 (30.4%) and 16 (23.2%) members respectively, which comprises up to 53.6% of all isolates. There was no relationship between biofilm formation and antibiotic resistance patterns with PFGE pulsotypes.

CONCLUSIONS

The results show that there is a close relationship between environmental and clinical isolates of A. baumannii. Cross-contamination is also very important that occurs through daily clinical activities between environmental and clinical isolates. Therefore, in order to reduce the clonal contamination of MDR A. baumannii environmental and clinical isolates, it is necessary to use strict infection control strategies.

Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives

Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.

Characterization of a Novel blaKLUC Variant With Reduced β-Lactam Resistance From an IncA/C Group Plasmid in a Clinical Klebsiella pneumoniae Isolate

Similar to other CTX-M family enzymes, KLUC is a recently identified and emerging determinant of cefotaxime resistance that has been recovered from at least three Enterobacteriaceae species, including Kluyvera cryocrescens, Escherichia coli, and Enterobacter cloacae. Whether this extended-spectrum β-lactamase (ESBL) has been disseminated among commonly isolated Enterobacteriaceae is worthy of further investigation. In this study, we screened 739 nosocomial Enterobacteriaceae isolates (240 Klebsiella pneumoniae and 499 E. coli strains) and found that one K. pneumoniae and four E. coli isolates harbored the bla_KLUC gene. Three bla_KLUC determinants isolated from E. coli were entirely identical to a bla_KLUC-3 gene previously recovered in the same hospital. PFGE of four bla_KLUC-harboring E. coli strains showed that prevalence of these determinants was most likely mediated by horizontal gene transfer but not clonal dissemination. However, the variant isolated from K. pneumoniae belonged to a novel member of the KLUC enzyme group. This newly identified enzyme (KLUC-5) has an amino acid substitution compared with previously identified KLUC-1 (G18S) and KLUC-3 (G240D). Antimicrobial susceptibility tests showed that KLUC-5 significantly reduced resistance activity to almost all the selected antimicrobials compared to previously identified KLUC-3. Site-directed mutagenesis showed that bla_KLUC-5-D240G and bla_KLUC-5-S18G significantly enhanced the MIC against its best substrate. Conjugation and S1-PFGE indicated that bla_KLUC-5 was located on a transferable plasmid, which was further decoded by single-molecule, real-time sequencing. Comparative genome analysis showed that its backbone exhibited genetic homology to the IncA/C incompatibility group plasmids. A transposable element, ISEcp1, was detected 256-bp upstream of the bla_KLUC-5 gene; this location was inconsistent with the previously identified bla_KLUC-1 but congruent with the variants recovered from E. coli in the same hospital. These data provide evidence of the increasingly emerging KLUC group of ESBLs in China.

Lettuce and fruits as a source of multidrug resistant Acinetobacter spp

The role of ready-to-eat products as a reservoir of pathogenic species of Acinetobacter remains unclear. The objective of the present study was to evaluate the presence of Acinetobacter species in lettuces and fruits marketed in Portugal, and their susceptibility to antimicrobials. Acinetobacter spp. were isolated from 77.9% of the samples and these microorganisms were also found as endophytes (i.e. present within the plant tissue) in 12 of 20 samples of lettuces analysed. Among 253 isolates that were identified as belonging to this genus, 181 presented different PFGE profiles, representing different strains. Based on the analysis of the partial sequence of rpoB, 175 strains were identified as members of eighteen distinct species and the remaining six strains may represent five new candidate species since their rpoB sequence similarities with type strains were less than 95%. Acinetobacter calcoaceticus and Acinetobacter johnsonii were the most common species, both with the frequency of 26.5%; and 11% of the strains belong to the Acinetobacter baumannii group (i.e. A. baumannii, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter nosocomialis), which is most frequently associated with nosocomial infections. Overall, the strains were least susceptible to piperacillin (80.1%), piperacillin-tazobactam (64.1%), ceftazidime (43.1%), ciprofloxacin (16.6%), trimethoprim-sulfamethoxazole (14.9%), imipenem (14.4%) and colistin (13.3%). The most active antimicrobials were minocycline and tetracycline, with 0.6% and 3.9% of strains resistant, respectively. About 29.8% of the strains were classified as multidrug-resistant (MDR), 4.4% as extensively drug-resistant (XDR) and the prevalence of MDR strains within the A. baumannii group (25%) was similar to other species (30.4%). The presence of clinically important species as well as MDR strains in lettuces and fruits may be a threat to public health considering that they may transmit these pathogens to environments such as the community and hospital settings.

Molecular analysis of Acinetobacter baumannii strains isolated in Lebanon using four different typing methods

This study analyzed 42 Acinetobacter baumannii strains collected between 2009-2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), repetitive sequence-based PCR (rep-PCR) and blaOXA-51 sequence-based typing (SBT). Among 31 carbapenem resistant strains, we have detected three carbapenem resistance genes: 28 carried the blaOXA-23 gene, 1 the blaOXA-24 gene and 2 strains the blaOXA-58 gene. This is the first detection of blaOXA-23 and blaOXA-24 in Lebanon. PFGE identified 11 types and was the most discriminating technique followed by rep-PCR (9 types), blaOXA-51 SBT (8 types) and MLST (7 types). The PFGE type A'/ST2 was the dominant genotype in our collection present in Beyrouth and North Lebanon. The clustering agreement between all techniques was measured by adjust Wallace coefficient. An overall agreement has been demonstrated. High values of adjust Wallace coefficient were found with followed combinations: PFGE to predict MLST types  = 100%, PFGE to predict blaOXA-51 SBT = 100%, blaOXA-51 SBT to predict MLST = 100%, MLST to predict blaOXA-51 SBT = 84.7%, rep-PCR to predict MLST = 81.5%, PFGE to predict rep-PCR = 69% and rep-PCR to predict blaOXA-51 SBT = 67.2%. PFGE and MLST are gold standard methods for outbreaks investigation and population structure studies respectively. Otherwise, these two techniques are technically, time and cost demanding. We recommend the use of blaOXA-51 SBT as first typing method to screen isolates and assign them to their corresponding clonal lineages. Repetitive sequence-based PCR is a rapid tool to access outbreaks but careful interpretation of results must be always performed.

Current molecular methods in epidemiological typing of Acinetobacter baumannii

ABSTRACT 

The emergence of Acinetobacter baumannii during recent decades as an important nosocomial pathogen responsible of worldwide, intensively documented, outbreaks has resulted in a need for effective epidemiological typing methods. Throughout the years, many typing methods for A. baumannii epidemiological studies have been proposed from phenotypic to molecular methods. Currently, the use of phenotypic typing methods have declined considerably and been progressively replaced by molecular methods. In this review, we introduce the current molecular methods available for A. baumannii typing. Each method has its own advantages and disadvantages, and the selection of an appropriate genotyping method depends on studied objectives. This review sheds light on questions in different epidemiological settings and most molecular methods used to fit these objectives.