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

International Clones of High Risk of Acinetobacter Baumannii-Definitions, History, Properties and Perspectives

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named 'international clones of high risk' (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic blaOXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed.

Antimicrobial resistance and biofilm formation capacity among Acinetobacter baumannii strains isolated from patients with burns and ventilator-associated pneumonia

BACKGROUND

Acinetobacter baumannii is a pathogen responsible for nosocomial infections, especially in patients with burns and ventilator-associated pneumonia (VAP). The aims of this study was to compare the biofilm formation capacity, antimicrobial resistance patterns and molecular typing based on PFGE (Pulsed-Field Gel Electrophoresis) in A. baumannii isolated from burn and VAP patients.

MATERIALS AND METHODS

A total of 50 A. baumannii isolates were obtained from burn and VAP patients. In this study, we assessed antimicrobial susceptibility, biofilm formation capacity, PFGE fingerprinting, and the distribution of biofilm-related genes (csuD, csuE, ptk, ataA, and ompA).

RESULTS

Overall, 74% of the strains were multidrug resistant (MDR), and 26% were extensively drug-resistant (XDR). Regarding biofilm formation capacity, 52%, 36%, and 12% of the isolates were strong, moderate, and weak biofilm producers. Strong biofilm formation capacity significantly correlated with XDR phenotype (12/13, 92.3%). All the isolates harbored at least one biofilm-related gene. The most prevalent gene was csuD (98%), followed by ptk (90%), ataA (88%), ompA (86%), and csuE (86%). Harboring all the biofilm-related genes was significantly associated with XDR phenotype. Finally, PFGE clustering revealed 6 clusters, among which cluster No. 2 showed a significant correlation with strong biofilm formation and XDR phenotype.

CONCLUSION

Our findings revealed the variable distribution of biofilm-related genes among MDR and XDR A. baumannii isolates from burn and VAP patients. A significant correlation was found between strong biofilm formation capacity and XDR phenotype. Finally, our results suggested that XDR phenotype was predominant among strong-biofilm producer A. baumannii in our region.

The association between Acinetobacter baumannii infections and the COVID-19 pandemic in an intensive care unit

We aimed to describe the increased rate of Acinetobacter baumannii infections during the COVID-19 pandemic and define its significance within the last five years. This study was performed in a tertiary hospital with 280 beds and included all patients infected with A. baumannii in the intensive care unit between January 1, 2018, and June 30, 2022. A. baumannii-infected patients in the intensive care unit 27 months before the pandemic and 27 months during the pandemic were included. Pulsed-field gel electrophoresis was performed to assess clonal relatedness. The infection control measures were specified based on the findings and targeted elimination. In total, 5718 patients were admitted to the intensive care unit from January 1st, 2018, to June 30th, 2022. A. baumannii infection was detected in 81 patients. Compared to the pre-pandemic era, the rate of A. baumannii infection during the pandemic was 1.90 times higher (OR: 1.90, 95% CI: [1.197, 3.033]). Clonality assessment of multidrug-resistant A. baumannii samples revealed eight clusters with one main cluster comprising 14/27 isolates between 2021 and 2022. The case fatality rate of the pre-pandemic and pandemic era was not different statistically (83.33% vs. 81.48%, p = 0.835). Univariate analysis revealed the association of mechanical ventilation (p = 0.002) and bacterial growth in tracheal aspirate (p = 0.001) with fatality. During the COVID-19 pandemic, potential deficits in infection control measures may lead to persistent nosocomial outbreaks. In this study, the introduction of enhanced and customized infection control measures has resulted in the containment of an A. baumannii outbreak.

Molecular typing and antibiotic resistance patterns among clinical isolates of Acinetobacter baumannii recovered from burn patients in Tehran, Iran

Acinetobacter baumannii (A. baumannii) is now considered a highly resistant pathogen to various types of antibiotics. Therefore, tracking the source of its prevalence and continuous control is crucial. This study aimed to determine antibiotic resistance and perform various molecular typing methods on clinical isolates of A. baumannii isolated from hospitalized burn patients in Shahid Motahari Burn Hospital, Tehran, Iran. Hospital isolates were confirmed by phenotypic and molecular methods. Then the sensitivity to different antibiotics was determined using the minimum inhibitory concentration (MIC) method. In order to perform molecular typing, three-locus dual assay multiplex polymerase chain reaction (PCR), multiple-locus variable-number tandem repeat analysis (MLVA), and multilocus sequence typing (MLST) methods were used. Among the 60 isolates collected, the frequencies of multidrug-resistant (MDR) and extensively drug-resistant (XDR) isolates were 90 and 10%, respectively. The most effective antibiotics were colistin with 100% and tigecycline with 83.33% sensitivity. Isolates were 100% resistant to piperacillin/tazobactam and cephalosporins, and 68.3% were resistant to carbapenem. The results of multiplex PCR showed five groups that international clone I (IC I) and IC II were the most common. The MLVA method identified 34 MLVA types (MTs), 5 clusters, and 25 singletons. Multilocus sequence typing results for tigecycline-resistant isolates showed seven different sequence types (STs). Increasing antibiotic resistance in A. baumannii isolates requires careful management to control and prevent the occurrence of the pre-antibiotic era. The results of this study confirm that the population structure of A. baumannii isolates has a high diversity. More extensive studies are needed in Iran to better understand the epidemiology of A. baumannii.

Genotypic and phenotypic comparison of clinical and environmental Acinetobacter baumannii strains

The genotypic and phenotypic characteristics and antibiotic resistance (antibiogram) profiles of clinical (n = 13) and environmental (n = 7) Acinetobacter baumannii isolates were compared. Based on the Repetitive Extragenic Palindromic Sequence-based PCR (REP-PCR) analysis, the clinical and environmental A. baumannii isolates shared low genetic relatedness (∼60%). Multilocus sequence typing (MLST, Oxford scheme) indicated that the clinical A. baumannii were assigned to three sequence types (ST231, ST945 and ST848), while the environmental A. baumannii (excluding AB 14) were categorised into the novel ST2520. The majority of the clinical (excluding AB 5, CAB 11, CAC 37) and environmental (excluding AB 14 and AB 16) A. baumannii strains were then capable of phase variation with both the translucent (71.4%; 15/21) and opaque (95.2%; 20/21) colony phenotypes detected. The clinical isolates however, exhibited significantly (p < 0.05) higher biofilm formation capabilities (OD₅₇₀: 2.094 ± 0.497). Moreover, the clinical isolates exhibited significantly (p < 0.05) higher resistance to first line antibiotics, with 92.3% (12/13) characterised as extensively drug resistant (XDR), whereas environmental A. baumannii exhibited increased antibiotic susceptibility with only 57.1% (4/7) characterised as multidrug resistant (MDR). The environmental isolate AB 14 was however, characterised as XDR. In addition, only five clinical A. baumannii isolates exhibited colistin resistance (38.5%; 5/13). The current study highlighted the differences in the genotypic, phenotypic, and antibiotic resistance profiles of clinical and environmental A. baumannii. Moreover, the environmental strains were assigned to the novel ST2520, which substantiates the existence of this opportunistic pathogen in extra-hospital reservoirs.

Phylogenetic analysis of carbapenem-resistant Acinetobacter baumannii isolated from different sources using Multilocus Sequence Typing Scheme

The emergence and worldwide distribution of carbapenem-resistant Acinetobacter baumannii strains has become a major public health threat. The objective of this study was to investigate the clonal relatedness of A. baumannii isolates collected from clinical and extra-hospital environments in Mthatha, South Africa. Forty carbapenem-resistant isolates comprising of clinical (20) and extra-hospital (20) were identified and tested for antimicrobial susceptibility. Detection of carbapenemase encoding genes was performed by Real-time PCR. The clonal relationship of clinical isolates relative to extra-hospital isolates was determined via multilocus sequence typing (MLST). All isolates (clinical and extra-hospital) were resistant to most common antibiotics including carbapenems (imipenem; MIC ≥32 μg/mL and meropenem; MIC ≥32 μg/mL) with the only exception being amikacin (with 3 isolates susceptible), tigecycline (14 isolates susceptible) and colistin (all isolates susceptible). The bla OXA-23-like and the intrinsic bla OXA-51 -like genes were detected in all the isolates tested. The bla OXA-58-like and bla IMP-type genes were detected in 2 clinical isolates whilst the bla OXA-24-like, bla VIM-type, bla NDM-1, bla SIM, and bla AmpC were not detected. The bla OXA-24-like, bla OXA-58-like, bla IMP-type, bla VIM-type, bla NDM-1, bla SIM, and bla AmpC were negative in the extra-hospital isolates. Co-occurrence of bla OXA-23 -like, bla OXA-58-like and bla IMP-type was observed in 2 clinical isolates. The MLST performed on 33 isolates identified 5 existing sequence types (ST) (ST1, ST2, ST25, ST85 and ST215) in clinical isolates and 2 existing STs (ST1 and ST2) in extra-hospital isolates. The most dominant ST was ST2 accounting for 68.8% of the clinical isolates and 82.4% of the extra-hospital isolates. The study demonstrated high prevalence and potential clonal spread of globally-disseminated clonal complex 2 carrying bla OXA-23-like within our local settings. However, ST25 might be an emerging lineage carrying the bla OXA-23-like . Continuous monitoring is important in limiting the spread of these strains in other healthcare settings and the community.

Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017-2019

Acinetobacter baumannii is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and to rapidly acquire the resistance to a broad spectrum of antibiotics. Thus, the epidemiological surveillance of A. baumannii within a particular hospital, region, and across the world is an important healthcare task that currently usually includes performing whole-genome sequencing (WGS) of representative isolates. During the past years, the dissemination of A. baumannii across the world was mainly driven by the strains belonging to two major groups called the global clones or international clones (ICs) of high risk (IC1 and IC2). However, currently nine ICs are already considered. Although some clones were previously thought to spread in particular regions of the world, in recent years this is usually not the case. In this study, we determined five ICs, as well as three isolates not belonging to the major ICs, in one multidisciplinary medical center within the period 2017-2019. We performed WGS using both short- and long-read sequencing technologies of nine representative clinical A. baumannii isolates, which allowed us to determine the antibiotic resistance and virulence genomic determinants, reveal the CRISPR/Cas systems, and obtain the plasmid structures. The phenotypic and genotypic antibiotic resistance profiles are compared, and the possible ways of isolate and resistance spreading are discussed. We believe that the data obtained will provide a better understanding of the spreading and resistance acquisition of the ICs of A. baumannii and further stress the necessity for continuous genomic epidemiology surveillance of this problem-causing bacterial species.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii From Khartoum State, Sudan

Carbapenem resistant Acinetobacter baumannii (CRAb) is an important global pathogen contributing to increased morbidity and mortality in hospitalized patients, due to limited alternative treatment options. Nine international clonal (IC) lineages have been identified in many countries worldwide, however, data still lacks from some parts of the world, particularly in Africa. We hereby present the molecular epidemiology of MDR A. baumannii from four hospitals in Khartoum, Sudan, collected from 2017 to 2018. Forty-two isolates were whole-genome sequenced, and subsequent molecular epidemiology was determined by core genome MLST (cgMLST), and their resistomes identified. All isolates had an array of diverse antibiotic resistance mechanisms conferring resistance to multiple classes of antibiotics. We found a predominance (88%) of IC2 (with the intrinsic OXA-66 and acquired OXA-23), and some with NDM-1. IC2 isolates were sub-divided into 4 STs separated by 5 to 431 allelic differences, and with evidence of seven transmission clusters. Isolates belonging to IC1, IC5, and IC9 were also identified. These data illustrate that MDR IC2 A. baumannii are widely distributed in Khartoum hospitals and are in possession of multiple antibiotic resistance determinants.

Molecular Epidemiology and Mechanisms of Carbapenem-Resistant Acinetobacter baumannii Isolates from ICU and Respiratory Department Patients of a Chinese University Hospital

Background

The objective of our study is to estimate the differences in molecular epidemiology and resistance mechanisms in carbapenem-resistant Acinetobacter baumannii (CRAB) isolates from the ICU and respiratory department(RD) in Fourth Affiliated Hospital of Harbin Medical University.

Methods

Carbapenemase genes associated with carbapenem resistance were studied by polymerase chain reaction(PCR). Genotyping was analyzed using multi-locus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE).

Results

Sixty non-duplicate CRAB isolates from the ICU and RD (n=30, respectively) were collected. All of CRAB strains were not resistant to colistin (0%). The CRAB strains from the ICU were significantly more resistant to tigecycline and cefoperazone/sulbactam compared with the RD (23.3% vs 0%, P=0.03; 53.3% % vs 23.3%, P=0.01, respectively). PCR detection of genes associated with CRAB revealed that the ratio in both the ICU and the RD of blaVIM-2, blaIMP-4, blaNDM-1, blaOXA-23, ampC, and mutation of CarO were present in 23.3% vs 0% (P=0.01), 40% vs 10% (P=0.02), 20% vs 0% (P=0.02), 80% vs 56.7%, 16.7% vs 13.3% and 86.7% vs 60% (P=0.04), respectively. Seven genotypes were detected by the PFGE in the RD and the ICU, respectively. Genotype I was significantly more frequent in the ICU compared with the RD (63.3% vs 36.6%, P=0.03). MLST showed that there were 10 ST genotypes in the RD and four in the ICU, but ST92 in both groups was 33.3% vs 63.3% (P=0.03), respectively.

Conclusion

There are differences in molecular epidemiology and resistance mechanisms in the CRAB isolates between the ICU and RD.

Investigation of an XDR-Acinetobacter baumannii ST2 outbreak in an intensive care unit of a Lebanese tertiary care hospital

Aim: We sought to investigate the genetic epidemiological relatedness of carbapenem-resistant Acinetobacter baumannii (CRAB) strains of a suspected outbreak in a Lebanese tertiary care hospital to implement necessary infection prevention and control measures. Methods: Twenty-eight nonduplicate CRAB isolates detected among hospitalized patients between January 2016 and July 2017 were studied by real-time polymerase chain reaction (PCR), pulsed-field gel electrophoresis and multilocus sequence typing analyses. Results: Twenty-seven isolates harbored blaOXA-23, of which one also carried blaNDM-1. The isolates distributed temporally in two presumably episodes were stratified by pulsed-field gel electrophoresis into many clusters. Although several clones have become endemic in the hospital, we have rapidly implemented appropriate infection prevention and control measures, achieving full eradication from August 2017 to November 2019. Conclusion: We have successfully investigated and controlled a polyclonal outbreak of OXA-23 producing ST2 CRAB.

Survey on Genetic Diversity, Biofilm Formation, and Detection of Colistin Resistance Genes in Clinical Isolates of Acinetobacter baumannii

Introduction

Acinetobacter baumannii is an opportunistic pathogen responsible for nosocomial infections. The emergence of colistin-resistant A. baumannii is a significant threat to public health. The aim of this study was to investigate the molecular characterization and genotyping of clinical A. baumannii isolates in Southwestern Iran.

Methods

A total of 70 A. baumannii isolates were collected from patients admitted to Imam Khomeini Hospital in Ahvaz, Southwestern Iran. Minimum inhibitory concentration test was conducted by using Vitek 2 system. The presence of biofilm-forming genes and colistin resistance-related genes were evaluated by PCR. The isolates were also examined for their biofilm formation ability and the expression of pmrA and pmrB genes. Finally, multilocus sequence typing (MLST) and PCR-based sequence group were used to determine the genetic relationships of the isolates.

Results

Overall, 61 (87.1%) and 9 (12.8%) isolates were multidrug-resistant (MDR) and extensively drug-resistant (XDR), respectively. Colistin and tigecycline with 2 (2.8%) and 32 (45.7%) resistance rates had the highest effect. Among all the isolates, 55 (78.5%), 7 (10%), and 3 (4.3%) were strong, moderate, and weak biofilm producers, respectively. The frequency rates of biofilm-related genes were 64 (91.4%), 70 (100%), 56 (80%), and 22 (31.42%) for bap, ompA, csuE, and bla_PER1, respectively. Overexpression of pmrA and pmrB genes was observed in two colistin-resistance isolates, but the expression of these genes did not change in colistin-sensitive isolates. Additionally, 37 (52.8%) and 8 (11.4%) isolates belonged to groups 1 (ICII) and 2 (IC I), respectively. MLST analysis revealed a total of nine different sequence types that six isolates belonged to clonal complex 92 (corresponding to ST801, ST118, ST138, ST 421, and ST735). Other isolates were belonging to ST133 and ST216, and two colistin-resistant (Ab4 and Ab41) isolates were belonging to ST387 and ST1812.

Conclusion

The present study revealed the presence of MDR and XDR A. baumannii isolates harboring biofilm genes and emergence of colistin-resistant isolates in Southwestern Iran. These isolates had high diversity, which was affirmed by typing techniques. The control measures and regular surveillance are urgently needed to preclude the spread of these isolates.

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.

Genetic relatedness of serial rectal isolates of Acinetobacter baumannii in an adult intensive care unit of a tertiary hospital in Kuwait

Acinetobacter baumannii is an opportunistic pathogen of intensive care unit (ICU) patients. A. baumannii colonizes many parts of the body including the gastrointestinal tract. Endemic and epidemic strains are polyclonal. There is no clarity on the origin of polyclonality of A. baumannii. The objective of the study was to define the genetic relatedness of serial isolates and the origin of polyclonality. Serial rectal isolates from ICU patients whose rectum was colonized on ≥5 sampling occasions were selected. From a total of 32 eligible colonized patients, isolates from a subgroup of 13 patients (a total of 108 isolates) showing different patterns of colonization as revealed by pulsed-field gel electrophoresis (PFGE) were studied. The isolates were analyzed by PFGE pulsotypes, sequence types (STs) by multi-locus sequence typing (MLST) and clonal complex (CC) by eBURST analysis. Serial isolates constituted a mixture of identical, related and unrelated pulsotypes. Analysis by STs and CCs were less discriminatory. The data suggest a combination of an initial colonizing isolate undergoing mutation as well as colonization by independent isolates. Further clarity on the origin of diversity should be better obtained by whole-genome sequencing.

Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach

In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.

Update on the epidemiological typing methods for Acinetobacter baumannii

The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.

Molecular Detection of Carbapenem Resistance in Acinetobacter Baumannii Isolated From Patients in Khorramabad City, Iran

BACKGROUND

Acinetobacter baumannii is an opportunistic pathogen, which causes a wide range of infections in hospitals, especially in intensive care units. Nowadays, due to the high resistance of Acinetobacter bumanni to antibiotics, this study, in addition to the phenotypic and genotypic investigations of drug resistance, focused on determining the molecular types of Acinetobacter baumannii isolated from patients in Khorramabad city by the pulsed-field gel electrophoresis (PFGE) method.

MATERIALS AND METHODS

In this cross-sectional study, 50 samples of Acinetobacter baumannii were collected from educational hospitals in Khorramabad city, Iran, from January to August 2015. They were identified in the laboratory using biochemical tests and culture methods. After determining the drug resistance pattern by the disc diffusion method and percentage of resistance genes to carbapenems, Acinetobacter baumannii isolates were analyzed using the PFGE method using the Apa1 enzyme.

RESULTS

The highest antibiotic resistance observed for Acinetobacter baumannii strains was against ampicillin-sulbactam (100%) and aztreonam (98%). The highest sensitivity was to polymixin B (100%) and colistin (94%), and also to the OXA-51-like gene present in all samples. The OXA-23-like gene was positive in 44 (88%) samples. PFGE results showed that Acinetobacterbaumannii strains had 33 different pulsotype patterns, of which 27 patterns had more than one strain and 23 had only one strain.

CONCLUSION

Due to the high resistance of Acinetobacter baumannii and its ease of spread and its ability to transfer resistance genes, resistance control methods should be used in the disinfection of hospital areas. Hospital staff should observe hygiene standards and there should also be a reduction in antibiotic use.

Seasonal Occurrence and Carbapenem Susceptibility of Bovine Acinetobacter baumannii in Germany

Acinetobacter baumannii is one of the leading causes of nosocomial infections in humans. To investigate its prevalence, distribution of sequence types (STs), and antimicrobial resistance in cattle, we sampled 422 cattle, including 280 dairy cows, 59 beef cattle, and 83 calves over a 14-month period. Metadata, such as the previous use of antimicrobial agents and feeding, were collected to identify putative determining factors. Bacterial isolates were identified via MALDI-TOF/MS and PCR, antimicrobial susceptibility was evaluated via VITEK2 and antibiotic gradient tests, resistance genes were identified by PCR. Overall, 15.6% of the cattle harbored A. baumannii, predominantly in the nose (60.3% of the A. baumannii isolates). It was more frequent in dairy cows (21.1%) than in beef cattle (6.8%) and calves (2.4%). A seasonal occurrence was shown with a peak between May and August. The rate of occurrence of A. baumannii was correlated with a history of use of 3rd generation cephalosporins in the last 6 months prior to sampling Multilocus sequence typing (Pasteur scheme) revealed 83 STs among 126 unique isolates. Nine of the bovine STs have previously been implicated in human infections. Besides known intrinsic resistance of the species, the isolates did not show additional resistance to the antimicrobial substances tested, including carbapenems. Our data suggest that cattle are not a reservoir for nosocomial A. baumannii but carry a highly diverse population of this species. Nevertheless, some STs seem to be able to colonize both cattle and humans.

Investigation of multidrug-resistant ST2 Acinetobacter baumannii isolated from Saint George hospital in Lebanon

BACKGROUND

Acinetobacter baumannii is an opportunistic pathogen causing various nosocomial infections. The spread of multidrug-resistant A. baumannii is a major public health problem. The aim of this study was to investigate the molecular epidemiology and the genetic support of multidrug-resistant A. baumannii isolates collected from Saint-Georges Hospital in Lebanon.

METHODS

Between January and August 2016, 31 A. baumannii isolates were collected from sputum samples of patients infected with ventilator-associated pneumonia (VAP) and treated with colistin-carbapenem combination therapy. Antibiotic susceptibility testing was performed using the disk diffusion method. Carbapenemases, extended spectrum β-lactamases encoding genes and mcr-1/2 genes were investigated by RT-PCR and standard PCR. The epidemiological relatedness of the strains was studied using MLST analysis.

RESULTS

Most of the isolates exhibited multidrug-resistant phenotypes. All the isolates were carbapenem-resistant and among them, 30 carried the class D carbapenemase bla_oxa-23 gene while one isolate carried bla_oxa-72 gene. MLST results revealed three sequence types, namely ST2, ST699, and ST627. Isolates having ST2 were the most prevalent clone (29/31, 93.5%).

CONCLUSIONS

This study shows a nosocomial spread of multidrug-resistant A. baumannii ST2 having bla_OXA-23 gene in Saint-George in Lebanon. Monitoring and control measures need to be adopted to avoid the spread of A. baumannii to patients.

Molecular mechanisms of antimicrobial resistance in Acinetobacter baumannii, with a special focus on its epidemiology in Lebanon

Acinetobacter baumannii is an opportunistic bacterium involved in several types of infection with high mortality and morbidity, especially in intensive care units. Treatment of these infections remains a challenge due to the worldwide emergence of broad-spectrum resistance to many antibiotics. Following the implementation of molecular techniques to study A. baumannii outbreaks, it has been shown that they are mainly caused by specific clones such as international clones I, II and III. The present work aims to review the available data on the mechanisms underlying antimicrobial resistance in A. baumannii, with a special focus on the molecular epidemiology of this species in Lebanon.

Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima, Peru

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.

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii in the Intensive Care Unit of Uruguay's University Hospital Identifies the First rmtC Gene in the Species

Carbapenem-resistant Acinetobacter baumannii (CRAB) infections are an increasing concern in intensive care units (ICUs) worldwide. The combination of carbapenemases and 16S rRNA-methyltransferases (16S-RMTases) further reduces the therapeutic options. OXA-carbapenemase/A. baumannii clone tandems in Latin America have already been described; however, no information exists in this region regarding the occurrence of 16S-RMTases in this microorganism. In addition, the epidemiology of A. baumannii in ICUs and its associated resistance profiles are poorly understood. Our objectives were as follows: to study the clonal relationship and antibiotic resistance profiles of clinical and digestive colonizing A. baumannii isolates in an ICU, to characterize the circulating carbapenemases, and to detect 16S-RMTases. Patients admitted between August 2010 and July 2011 with a clinically predicted hospital stay > 48 hr were included. Pharyngeal and rectal swabs were obtained during the first fortnight after hospitalization. Resistance profiles were determined with MicroScan^® and VITEK2 system. Carbapenemases and 16S-RMTases were identified by PCR and sequencing, and clonality was assessed by pulsed-field gel electrophoresis and multilocus sequence typing. Sixty-nine patients were studied and 63 were diagnosed with bacterial infections. Among these, 29 were CRAB isolates; 49 A. baumannii were isolated as digestive colonizers. These 78 isolates were clustered in 7 pulsetypes, mostly belonging to ST79. The only carbapenemase genes detected were bla_OXA-51 (n = 78), bla_OXA-23 (n = 62), and bla_OXA-58 (n = 3). Interestingly, two clinical isolates harbored the rmtC 16S-RMTase gene. To the best of our knowledge, this is the first description of the presence of rmtC in A. baumannii.

Database for the ampC alleles in Acinetobacter baumannii

Acinetobacter baumannii is a troublesome opportunistic pathogen with a high capacity for clonal dissemination. We announce the establishment of a database for the ampC locus in A. baumannii, in which novel ampC alleles are differentiated based on the occurrence of ≥ 1 nucleotide change, regardless of whether it is silent or missense. The database is openly accessible at the pubmlst platform for A. baumannii (http://pubmlst.org/abaumannii/). Forty-eight distinctive alleles of the ampC locus have so far been identified and deposited in the database. Isolates from clonal complex 1 (CC1), according to the Pasteur multilocus sequence typing scheme, had a variety of the ampC locus alleles, including alleles 1, 3, 4, 5, 6, 7, 8, 13, 14, 17, and 18. On the other hand, isolates from CC2 had the ampC alleles 2, 3, 19, 20, 21, 22, 23, 24, 26, 27, 28, and 46. Allele 3 was characteristic for sequence types ST3 or ST32. The ampC alleles 10, 16, and 25 were characteristic for CC10, ST16, and CC25, respectively. Our study points out that novel gene databases, in which alleles are numbered based on differences in their nucleotide identities, should replace traditional records that use amino acid substitutions to define new alleles.

Acinetobacter baumannii Isolated from Lebanese Patients: Phenotypes and Genotypes of Resistance, Clonality, and Determinants of Pathogenicity

Introduction:Acinetobacter baumannii is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR A. baumannii infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this organism possesses a wide range of virulence factors, whose expression is not yet fully understood. In this study, clinical A. baumannii isolates are characterized in terms of antibiotic resistance, mechanisms of carbapenem resistance, clonality, and virulence.

Materials and Methods:A. baumannii clinical isolates (n = 90) where obtained from a tertiary care center in Beirut, Lebanon. API 20NE strips in addition to the amplification of bla_{OXA−51−like} were used for identification. Antibiotic susceptibility testing by disk diffusion was then performed in addition to PCRs for the detection of the most commonly disseminated carbapenemases. Clonality was determined by tri-locus PCR typing and doubling times were determined for isolates with varying susceptibility profiles. Biofilm formation, hemolysis, siderophore production, proteolytic activity, and surface motility was then determined for all the isolates. Statistical analysis was then performed for the determination of associations.

Results and Discussion: 81 (90%) of the isolates were resistant to carbapenems. These high rates are similar to other multi-center studies in the country suggesting the need of intervention on a national level. 74 (91.3%) of the carbapenem resistant isolates harbored bla_{OXA−23−like} including two that also harbored bla_{OXA−24−like}. 88.9% of the A. baumannii isolates pertained to ICII and three other international clones were detected, showing the wide dissemination of clones into geographically distinct locations. Virulence profiles were highly diverse and no specific pattern was observed. Nevertheless, an association between motility, siderophore production, and biofilm formation was detected (p < 0.05).

Conclusions: A very high rate of carbapenem resistance was detected, showing the need for immediate intervention. IC II and OXA-23-like were the most disseminated, reflecting their international dissemination. No specific associations were made between virulence and resistance, but instead associations among certain virulence factors were found. Investigating a more clonally diverse pool of isolates could help in the determination of associations between virulence and resistance.

Wide spread of OXA-23-producing carbapenem-resistant Acinetobacter baumannii belonging to clonal complex II in different hospitals in Lebanon

OBJECTIVES

To investigate the molecular epidemiology of Acinetobacter baumannii strains isolated from different hospitals in Lebanon.

METHODS

A total of 119 non-duplicate Acinetobacter strains were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and partial rpoB gene sequencing. Antibiotic susceptibility testing was performed by disc diffusion method and all identified carbapenem-resistant isolates were investigated by PCR assays for the presence of the carbapenemase-encoding genes. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used for molecular typing.

RESULTS

Of the 119 A. baumannii isolates, 76.5% were resistant to carbapenems. The most common carbapenemase was the OXA-23-type, found in 82 isolates. The study of population structure using MLST revealed the presence of 30 sequence types (STs) including 18 new ones, with ST2 being the most commonly detected, accounting for 61% of the isolates typed. PFGE performed on all strains of ST2 identified a major cluster of 53 isolates, in addition to three other minor clusters and ten unique profiles.

CONCLUSIONS

This study highlights the wide dissemination of highly related OXA-23-producing carbapenem-resistant A. baumannii belonging to the international clone II in Lebanon. Thus, appropriate infection control measures are recommended in order to control the geographical spread of this clone in this country.

Molecular epidemiology and characterization of multiple drug-resistant (MDR) clinical isolates of Acinetobacter baumannii

OBJECTIVES

The aim of this study was to identify the genetic relatedness of multiple drug-resistant (MDR) Acinetobacter baumannii clinical isolates recovered from a hospital in Los Angeles.

METHODS

Twenty-one MDR A. baumannii isolates were collected and their antibiotic susceptibilities determined according to Clinical and Laboratory Standards Institute guidelines. Genes coding for antibiotic resistance were identified by PCR, and their identities were confirmed by DNA sequencing. Clonal relationships were studied by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

RESULTS

MDR consistently correlated with the presence of oxacillinases, mostly in the form of the plasmid-mediated OXA-23 enzyme, which was detected in 12 (57.1%) isolates. GES-type carbapenemases were found in 20 (95.2%) strains, AAC in all 21 (100%) strains, and PER in seven (33.3%) strains, and ISAba1 was detected in 16 (76.2%) isolates. The association between ISAba1 and resistance genes confirms insertion elements as a source of β-lactamase production. Of the 21 clinical isolates, five were found to be related to sequence type 1 (ST1) and 16 to ST2, as analyzed by MLST. PFGE demonstrated that the majority of clinical isolates were highly related (>85%).

CONCLUSIONS

This study supports a more complete understanding of genotyping of antibiotic resistance for better assessment of MDR strain transmission.

Infection Control Programs and Antibiotic Control Programs to Limit Transmission of Multi-Drug Resistant Acinetobacter baumannii Infections: Evolution of Old Problems and New Challenges for Institutes

Background: Acinetobacter baumannii complex (A. baumannii) has been isolated worldwide. The rapid spread of multidrug-resistant A. baumannii complex (MDRAB) in clinical settings has made choosing an appropriate antibiotic to treat these infections and executing contact precautions difficult for clinicians. Although controlling the transmission of MDRAB is a high priority for institutions, there is little information about MDRAB control. Therefore, this study evaluated infection control measures for A. baumannii infections, clusters and outbreaks in the literature. Methods: We performed a review of OVID Medline (from 1980 to 2015), and analyzed the literature. Results: We propose that both infection control programs and antibiotic control programs are essential for control of MDRAB. The first, effective control of MDRAB infections, requires compliance with a series of infection control methods including strict environmental cleaning, effective sterilization of reusable medical equipment, concentration on proper hand hygiene practices, and use of contact precautions, together with appropriate administrative guidance. The second strategy, effective antibiotic control programs to decrease A. baumannii, is also of paramount importance. Conclusion: We believe that both infection control programs and antibiotics stewardship programs are essential for control of MDRAB infections.

Molecular epidemiology of Acinetobacter baumannii in different hospitals in Tripoli, Lebanon using bla(OXA-51-like) sequence based typing

Background

A. baumannii has emerged as an important nosocomial pathogen with an outstanding ability to acquire multidrug resistant mechanisms. In this study, we investigate the molecular epidemiology and carbapenem resistance mechanisms of A. baumannii in Tripoli, Northern Lebanon.

Methods

One hundred sixteen non-duplicate isolates isolated between 2011 and 2013 in different hospitals in Tripoli, Lebanon from Lebanese patients and wounded Syrian patients during Syrian war were studied. Antibiotic susceptibility testing was determined by agar disc diffusion and Etest. Carbapenemase-encoding genes were investigated by PCR. All isolates were typed by bla_OXA-51-like sequence based typing (SBT) and 57 isolates were also analysed by MLST using Pasteur’s scheme followed by eBURST analysis.

Results

Of the 116 isolates, 70 (60 %) showed a carbapenem resistance phenotype. The bla_OXA-23 with an upstream insertion of ISAba1 was the major carbapenem resistance mechanism and detected in 65 isolates. Five isolates, including four from wounded Syrian patients and one from a Lebanese patient, were positive for bla_NDM-1. bla_OXA-51-like SBT revealed the presence of 14 variants, where bla_OXA-66 was the most common and present in 73 isolates, followed by bla_OXA-69 in 20 isolates. MLST analysis identified 17 sequence types (ST) and showed a concordance with bla_OXA-51-like SBT. Each clonal complex (CC) had a specific bla_OXA-51-like sequence such as CC2, which harboured bla_OXA-66 variant, and CC1 harbouring bla_OXA-69 variant. NDM-1 producing isolates belonged to ST85 (4 Syrian isolates) and ST25 (1 Lebanese isolate).

Conclusions

Our results showed a successful predominance of international clone 2 with a widespread occurrence of OXA-23 carbapenemase in Lebanese hospitals. These findings emphasise the urgent need of effective measures to control the spread of A. baumannii in this country.

Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives

Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.