Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents. 2013;41:11-19. [PMID: 23127486 DOI: 10.1016/j.ijantimicag.2012.09.008]

Emerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example

Whole-genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. However, it is still unexpectedly demanding to employ WGS for global epidemiological surveillance because of the high degree of similarity between the genomes of intercontinental isolates. The aim of this study was to utilize genomically derived bioinformatics analysis to identify globally distributed A. baumannii ST195 lineage and differentiation outbreaks to address this issue. The genomic sequences and their related epidemiological metadata of 2850 A. baumannii isolates were recruited from NCBI Genbank database. Assignment into sequence type (Oxford scheme) and lineage (global clone 2/CC92) were performed. A total of 91 ST195 A. baumannii isolates were subsequently classified to perform the bacterial source tracking analysis by implementing both core genome MLST (cgMLST) and core genome SNP (cgSNP) strategy that were integrated in our recently updated BacWGSTdb 2.0 server. Antibiotic resistance genes were identified using the ResFinder database. The ST195 A. baumannii isolates distributed widely in eight countries and harboured multiple antimicrobial resistance genes simultaneously. In most cases, the bacterial isolates recovered from geographically distant sources may present less genomic sequence similarity, i.e., the phylogenetic relationship between these ST195 isolates worldwide was roughly congruent with their country of isolation. However, a few isolates collected from distant geographic regions were revealed to possess smaller genetic distances (less than 8 loci or 20 SNPs) than the threshold without an observable epidemiological link. Our study highlights the emerging challenges entailed in the WGS-powered epidemiological surveillance of globally distributed clonal groups. Standardization is urgently required before WGS can be routinely applied to infectious diseases outbreak investigations.

Expansion of Salmonella Typhi clonal lineages with ampicillin resistance and reduced ciprofloxacin susceptibility in Eastern China

Purpose

This study was aimed to investigate the dynamics of antimicrobial resistance expansion among different lineages and isolates of S. Typhi.

Materials and methods

The S. Typhi isolates were collected from the patients clinically suspected of typhoid fever in Eastern China during 2005–2017. All isolates were tested retrospectively for susceptibility to eight antimicrobials and the genes related to quinolone and ampicillin resistance, including gyrA, ParC, qnrA, qnrB, qnrS, aac(6´)-Ib-cr, qepA and bla_TEM. The isolates were subtyped by PFGE.

Results

Of 140 isolates, all were susceptible to ciprofloxacin, cefotaxime, chloramphenicol, and trimethoprim-sulfamethoxazole, 95 (68%) were nalidixic acid resistant, and 74 (53%) were ampicillin resistant. The resistance to ampicillin and nalidixic acid was first observed in 2006. Among the 95 nalidixic acid-resistant S. Typhi isolates, 62 possessed S83F mutation in gyrA and 25 possessed D87Y mutation. All ampicillin-resistant isolates harbored gene bla_TEM-1. PFGE generated 47 distinguishable clonal lineages. Overall, 64% (89/140) belonged to seven prevalent lineages of clustering isolates. PFGE results illustrated the prevalence of nalidixic acid-resistant lineages increased steadily from 19% during 2005–2012 to 50% during 2013–2014, and thereafter to 74% during 2015–2017 and similar development of ampicillin-resistant lineages increased from 6% to 38%, and also to 39%.

Conclusion

The present study indicated the clonal expansion of S. Typhi with ampicillin resistance and reduced ciprofloxacin susceptibility. The findings also suggested that the differential development of antimicrobial resistance to various antimicrobial agents in S. Typhi, showing the rapid increase in ampicillin resistance and reduced ciprofloxacin susceptibility, and the high susceptibility to other traditional antimicrobial agents.

Counter Clinical Prognoses of Patients With Bloodstream Infections Between Causative Acinetobacter baumannii Clones ST191 and ST451 Belonging to the International Clonal Lineage II

This study was conducted to evaluate the possible clinical and bacteriologic features associated with 30-day mortality from Acinetobacter baumannii (A. baumannii) bloodstream infections (BSIs). We conducted a prospective, multicenter, observational study of 181 entire episodes of A. baumannii BSI from six general hospitals between May 2016 and April 2017 in South Korea. Cox proportional-hazards regression model was used to estimate risks of the primary endpoint, i.e., all-cause mortality within 30 days from the initial blood culture. Most (84.5%) of the A. baumannii blood isolates belonged to the international clonal lineage II (ICLII) and 89.5% of the isolates were either multidrug- or extensively-drug resistant. We identified three risk factors including the old age of patient {hazard ratio, 1.033; [95% Confidential Interval (CI), 1.010-1.056]}, the sequential organ failure assessment score [1.133 (1.041-1.233)], and causative A. baumannii sequence type (ST) 191 belonging to ICLII [1.918 (1.073-3.430)], and three protective factors including causative A. baumannii ST451 belonging to ICLII [0.228 (0.078-0.672)], platelet count [0.996 (0.993-0.999)], and definitive therapy within 72 h [0.255 (0.125-0.519)]. Differing 30-day mortality rate in the dominant ICLII was observed by ST, which was much high in ST191 and low in ST451 and it was likely associated with the molecular traits, rather than the drug resistance.

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 epidemiology of carbapenem-resistant Acinetobacter baumannii isolates reveals the emergence of blaOXA-23 and blaNDM-1 encoding international clones in India

Acinetobacter baumannii is a nosocomial pathogen increasingly affecting the critically ill patients and represents a major public health challenge. Carbapenem-resistant A. baumannii (CRAB) is found to be associated with International Clones (ICs) and different classes of carbapenemases. The objective of the present study was to investigate the prevalence of carbapenem resistance genes, clonal relationship and genetic structure of clinical isolates of A. baumannii. In the present study, multi-locus sequence typing (MLST^OX) and analysis were carried out using Oxford scheme for 86 clinical isolates of CRAB along with 11 carbapenem sensitive A. baumannii (CSAB) collected over a period of two years (2014-2016) from two tertiary care hospitals of North India. We observed a high prevalence of the bla_OXA-23-like (97.7%) among the CRAB followed by bla_NDM-1 (29.1%) and bla_OXA58-like (3.5%). Forty-seven Sequence Types (STs) were represented by all 97 isolates, out of which, 28 (59.6%) were novel STs that were assigned to 41 isolates. STs 451 (13%), 447 (7%), 195 (6%) and 848 (5%) were the most common STs. The majority of CRAB isolates (44.3%) belonged to the CC92, followed by the CC447 (15.1%), CC109 (9.3%) and CC110 (3.4%), which corresponds to the IC2, 8, 1 and 7 respectively. Phylogenetic and recombination analysis suggested two major and one minor lineage in the population. Further linkage disequilibrium analysis suggested clonal nature of the population as recombination was noticed at a low frequency, which was not enough to split the clonal relationship. The knowledge of genetic structure of CRAB from this study will be invaluable to illustrate epidemiology, surveillance and understanding its global diversity.

Methods for Natural Transformation in Acinetobacter baumannii

The genomes of Acinetobacter baumannii tell us stories about horizontal gene transfer (HGT) events that steadily drive the evolution of this nosocomial pathogen toward multidrug resistance. Natural transformation competence constitutes one of the several possible pathways that mediate HGT in A. baumannii. Here, we describe and discuss the methods for studying DNA uptake in A. baumannii via natural transformation.

Dissecting Colistin Resistance Mechanisms in Extensively Drug-Resistant Acinetobacter baumannii Clinical Isolates

The discovery of antibiotics revolutionized modern medicine and enabled us to cure previously deadly bacterial infections. However, a progressive increase in antibiotic resistance rates is a major and global threat for our health care system. Colistin represents one of our last-resort antibiotics that is still active against most Gram-negative bacterial pathogens, but increasing resistance is reported worldwide, in particular due to the plasmid-encoded protein MCR-1 present in pathogens such as Escherichia coli and Klebsiella pneumoniae. Here, we showed that colistin resistance in A. baumannii, a top-priority pathogen causing deadly nosocomial infections, is mediated through different avenues that result in increased activity of homologous phosphoethanolamine (PetN) transferases. Considering that MCR-1 is also a PetN transferase, our findings indicate that PetN transferases might be the Achilles heel of superbugs and that direct targeting of them may have the potential to preserve the activity of polymyxin antibiotics.

Nosocomial infections with Acinetobacter baumannii are a global problem in intensive care units with high mortality rates. Increasing resistance to first- and second-line antibiotics has forced the use of colistin as last-resort treatment, and increasing development of colistin resistance in A. baumannii has been reported. We evaluated the transcriptional regulator PmrA as potential drug target to restore colistin efficacy in A. baumannii. Deletion of pmrA restored colistin susceptibility in 10 of the 12 extensively drug-resistant A. baumannii clinical isolates studied, indicating the importance of PmrA in the drug resistance phenotype. However, two strains remained highly resistant, indicating that PmrA-mediated overexpression of the phosphoethanolamine (PetN) transferase PmrC is not the exclusive colistin resistance mechanism in A. baumannii. A detailed genetic characterization revealed a new colistin resistance mechanism mediated by genetic integration of the insertion element ISAbaI upstream of the PmrC homolog EptA (93% identity), leading to its overexpression. We found that eptA was ubiquitously present in clinical strains belonging to the international clone 2, and ISAbaI integration upstream of eptA was required to mediate the colistin-resistant phenotype. In addition, we found a duplicated ISAbaI-eptA cassette in one isolate, indicating that this colistin resistance determinant may be embedded in a mobile genetic element. Our data disprove PmrA as a drug target for adjuvant therapy but highlight the importance of PetN transferase-mediated colistin resistance in clinical strains. We suggest that direct targeting of the homologous PetN transferases PmrC/EptA may have the potential to overcome colistin resistance in A. baumannii.

Molecular epidemiology and decreased susceptibility to disinfectants in carbapenem-resistant Acinetobacter baumannii isolated from intensive care unit patients in central China

BACKGROUND

Infection with carbapenem-resistant Acinetobacter baumannii (CRAB) is an increasing problem for critically ill patients. The srains are frequently resistant to all antibiotics and disinfectants are often used to block the spread of these bacteria, playing an important role in infection control.

OBJECTIVES

The aim of this study was to investigate the antibiotic susceptibility, the clonal relationship, disinfectant resistance gene, β-lactamase genes and the disinfectant sensitivity of 82 A. baumannii isolates collected at a large hospital in Wuhan, China.

DESIGN

A retrospective basic study.

METHODS

Here we investigated 82 A. baumannii isolates from intensive care unit patients in a major teaching hospital in China for the distribution of resistance-associated genes and susceptibility to chlorine disinfectant (CLR), benzalkonium bromide (BB) and Chlorhexidine gluconate(CHG). Multi-locus sequence typing (MLST) was applied to explore their genetic evolution relationships.

RESULTS

qacE (30.48%, 25/82) and qac△E1 (76.82%, 63/82) genes were detected in our study, while none were positive for qacA/B, qacC/D or qacG. The MIC values of CLR were 250mg/L; The MIC values ranged from 32 to 128μg/mL for BB; The MIC values ranged from 0.0019% to 0.0078% for CHG. The presence or absence of qacE gene has a significant impact(p＜0.05) on MICs of BB or CHG. All isolates harboured bla_OXA-51/23 genes, and 98.78% of isolates contained the ISaba1 insertion sequence. All isolates were classified into 8 sequence types(STs) within clonal complex 92(CC92).

CONCLUSIONS

The predominant CRAB strains in our intensive care unit are bla_OXA-23-containing A. baumannii of CC92. The high prevalence of qac genes and reduced susceptibility to disinfectants confirm the need for continued vigilance against nosocomial infections.

Carbapenem-resistant Acinetobacter baumannii from Air and Patients of Intensive Care Units

To understand the molecular epidemiology and antibiotic resistance of air and clinical isolates of Acinetobacter baumannii, the intensive care unit settings of a hospital in Northern China were surveyed in 2014. Twenty non-duplicate A. baumannii isolates were obtained from patients and five isolates of airborne A. baumannii were obtained from the wards’ corridors. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to analyze the homology relationships of isolates. Resistance and resistance genes were detected by drug susceptibility test and PCR. The results demonstrated that all isolates can be classified into eight PFGE types and four sequence types (ST208, ST195, ST369 and ST530). A pair of isolates from patients (TAaba004) and from the air (TAaba012) that share 100% similarity in PFGE was identified, indicating that air might be a potential and important transmission route for A. baumannii. More than 80% of the isolates were resistant to carbapenems and aminoglycoside antibiotics. Twenty-four isolates, which were resistant to carbapenems, carried the bla_OXA-23-like gene. The data indicated that air might be an alternative way for the transmission of A. baumannii. Hospitals should pay more attention to this route, and design new measures accordingly.

Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania

BACKGROUND

Reliable phenotypic antimicrobial susceptibility testing can be a challenge in clinical settings in low- and middle-income countries. WGS is a promising approach to enhance current capabilities.

AIM

To study diversity and resistance determinants and to predict and compare resistance patterns from WGS data of Acinetobacter baumannii with phenotypic results from classical microbiological testing at a tertiary care hospital in Tanzania.

METHODS AND RESULTS

MLST using Pasteur/Oxford schemes yielded eight different STs from each scheme. Of the eight, two STs were identified to be global clones 1 (n = 4) and 2 (n = 1) as per the Pasteur scheme. Resistance testing using classical microbiology determined between 50% and 92.9% resistance across all drugs. Percentage agreement between phenotypic and genotypic prediction of resistance ranged between 57.1% and 100%, with coefficient of agreement (κ) between 0.05 and 1. Seven isolates harboured mutations at significant loci (S81L in gyrA and S84L in parC). A number of novel plasmids were detected, including pKCRI-309C-1 (219000 bp) carrying 10 resistance genes, pKCRI-43-1 (34935 bp) carrying two resistance genes and pKCRI-49-1 (11681 bp) and pKCRI-28-1 (29606 bp), each carrying three resistance genes. New ampC alleles detected included ampC-69, ampC-70 and ampC-71. Global clone 1 and 2 isolates were found to harbour ISAba1 directly upstream of the ampC gene. Finally, SNP-based phylogenetic analysis of the A. baumannii isolates revealed closely related isolates in three clusters.

CONCLUSIONS

The validity of the use of WGS in the prediction of phenotypic resistance can be appreciated, but at this stage is not sufficient for it to replace conventional antimicrobial susceptibility testing in our setting.

Outbreak of carbapenem-resistant Acinetobacter baumannii carrying the carbapenemase OXA-23 in ICU of the eastern Heilongjiang Province, China

Background

To investigate the carbapenem resistance mechanisms and clonal relationship of carbapenem-resistant Acinetobacter baumannii (CRAB) strains isolated in the intensive care unit (ICU) of the First Affiliated Hospital of Jiamusi University, management approaches to ICU clonal CRAB outbreaks were described.

Methods

The sensitivity of the antibiotic was determined using the VITEK-2 automated system. Carbapenemase genes (bla_TEM, bla_SHV, bla_KPC, bla_NDM, bla_IMP-4, bla_VIM, bla_OXA-23, bla_OXA-24, bla_OXA-51, and bla_OXA-58), AmpC enzyme genes (bla_ACC, bla_DHA, bla_ADC), and ISAba1 were assessed for all collected isolates using polymerase chain reaction (PCR). The transfer of resistance genes was investigated via conjugation experiments. The clonal relationship of isolates was determined via enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus sequence typing (MLST). When the detection rate of CRAB increased from 25% in 2010 to 92% in 2014, a number of actions were initiated, including enhanced infection control, staff education, and the cleaning of the hospital environment.

Results

Clinical isolates were positive for the following genes: bla_OXA23, bla_OXA51, bla_OXA24, bla_ADC, bla_TEM, ISAba1, ISA-23, and ISA-ADC; however, bla_OXA58, ISA-51, bla_NDM, bla_IMP, bla_KPC, bla_TEM, bla_SHV, bla_VIM, and bla_ACC were not detected. Four carbapenem-resistant isolates successfully transferred plasmids from A. baumannii isolates to E. coli J53. MLST showed that all strains belonged to ST2 except for one isolate, which belonged to the new genotype ST1199. The ERIC-PCR method found the following three genotypes: type A in 8, type B in 12, type C in 1, and two profiles (A, B) belonged to ST2. After taking control measures, the prevalence of CRAB isolates decreased, and the discovery rate of CRAB dropped to 11.4% in 2017.

Conclusion

The obtained result suggests that bla_OXA-23-producing CC2 isolates were prevalent in the ICU of the First Affiliated Hospital of Jiamusi University. Targeted surveillance was implemented to identify the current situation of the ICU and the further implementation of infection control effectively prevented the spread of nosocomial infection.

Circulation of imipenem-resistant Acinetobacter baumannii ST10, ST2 and ST3 in a university teaching hospital from Tehran, Iran

PURPOSE

Multi-drug resistant (MDR) Acinetobacter baumannii has introduced a worldwide health crisis. The purposes of this study were to characterize the clonal relatedness among MDR clinical strains and to introduce a new two-locus typing method confirmed by multi-locus sequence typing (MLST).

METHODOLOGY

In this study, we determined antimicrobial resistance, detected genes associated with carbapenem resistance and characterized clonal relatedness among 99 clinical isolates extracted from 82 hospitalized inpatients in a university hospital.

RESULTS

Of the 99 A. baumannii isolates, 92.9% (92/99) were resistant to imipenem and 97.9% (97/99) had an MDR profile. We found that the high prevalence of blaVIM [94.9% (94/99)] and blaOXA-23-like [93.93% (93/99)] is the main mechanism of carbapenem resistance. This study proposes a new two-locus typing (blaOXA-51-like and ampC) method for the rapid identification of clonal complexes (CCs). The results of this method and confirmation by MLST show that clinical isolates carry blaOXA-68 as well as ampC-10 or ampC-20 genes belonging to CC10 (ST10); blaOXA-66 and ampC-2 belonging to CC2 (ST2); and blaOXA-71 and ampC-3 belonging to CC3 (ST3). One isolate had blaOXA-90 with an undetermined allele number of ampC belonging to ST513.

CONCLUSION

The high prevalence of MDR strains and the circulation of four limited clones, including ST10 (45/99), ST2 (41/99), ST3 (12/99) and ST513 (1/99), in the clinical setting highlights the importance of a rigorous infection control programme. The two-locus typing method has more discrimination than the application of each method separately and it could be applied for the rapid determination of the CC without performing MLST.

Comparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes

Acinetobacter species assigned to the Acinetobacter calcoaceticus-baumannii (Acb) complex, are Gram-negative bacteria responsible for a large number of human infections. The population structure of Acb has been studied using two 7-gene MLST schemes, introduced by Bartual and coworkers (Oxford scheme) and by Diancourt and coworkers (Pasteur scheme). The schemes have three genes in common but underlie two coexisting nomenclatures of sequence types and clonal complexes, which complicates communication on A. baumannii genotypes. The aim of this study was to compare the characteristics of the two schemes to make a recommendation about their usage. Using genome sequences of 730 strains of the Acb complex, we evaluated the phylogenetic congruence of MLST schemes, the correspondence between sequence types, their discriminative power and genotyping reliability from genomic sequences. In silico ST re-assignments highlighted the presence of a second copy of the Oxford gdhB locus, present in 553/730 genomes that has led to the creation of artefactual profiles and STs. The reliability of the two MLST schemes was tested statistically comparing MLST-based phylogenies to two reference phylogenies (core-genome genes and genome-wide SNPs) using topology-based and likelihood-based tests. Additionally, each MLST gene fragment was evaluated by correlating the pairwise nucleotide distances between each pair of genomes calculated on the core-genome and on each single gene fragment. The Pasteur scheme appears to be less discriminant among closely related isolates, but less affected by homologous recombination and more appropriate for precise strain classification in clonal groups, which within this scheme are more often correctly monophyletic. Statistical tests evaluate the tree deriving from the Oxford scheme as more similar to the reference genome trees. Our results, together with previous work, indicate that the Oxford scheme has important issues: gdhB paralogy, recombination, primers sequences, position of the genes on the genome. While there is no complete agreement in all analyses, when considered as a whole the above results indicate that the Pasteur scheme is more appropriate for population biology and epidemiological studies of A. baumannii and related species and we propose that it should be the scheme of choice during the transition toward, and in parallel with, core genome MLST.

Reinventing the wheel: Impact of prolonged antibiotic exposure on multidrug-resistant ventilator-associated pneumonia in trauma patients

BACKGROUND

Multidrug-resistant (MDR) strains of both Acinetobacter baumannii (AB) and Pseudomonas aeruginosa (PA) as causative ventilator-associated pneumonia (VAP) pathogens are becoming increasingly common. Still, the risk factors associated with this increased resistance have yet to be elucidated. The purpose of this study was to examine the changing sensitivity patterns of these pathogens over time and determine which risk factors predict MDR in trauma patients with VAP.

METHODS

Patients with either AB or PA VAP over 10 years were stratified by pathogen sensitivity (sensitive [SEN] and MDR), age, severity of shock, and injury severity. Prophylactic and empiric antibiotic days, risk factors for severe VAP, and mortality were compared. Multivariable logistic regression was performed to determine which risk factors were independent predictors of MDR.

RESULTS

Three hundred ninety-seven patients were identified with AB or PA VAP. There were 173 episodes of AB (91 SEN and 82 MDR) and 224 episodes of PA (170 SEN and 54 MDR). The incidence of MDR VAP did not change over the study (p = 0.633). Groups were clinically similar with the exception of 24-hour transfusions (14 vs. 19 units, p = 0.009) and extremity Abbreviated Injury Scale (AIS) score (1 vs. 3, p < 0.001), both significantly increased in the MDR group. Antibiotic exposure as well as multiple episodes of inadequate empiric antibiotic therapy (mIEAT) (63% vs. 81%, p < 0.001) were significantly increased in the MDR group. Multivariable logistic regression identified prophylactic antibiotic days (odds ratio, 23.1; 95% confidence interval, 16.7-28, p < 0.001) and mIEAT (odds ratio, 18.1; 95% confidence interval, 12.2-26.1, p = 0.001) as independent predictors of MDR after adjusting for severity of shock, injury severity, severity of VAP, and antibiotic exposure.

CONCLUSION

Prolonged exposure to unnecessary antibiotics remains one of the strongest predictors for the development of antibiotic resistance. Multivariable logistic regression identified prophylactic antibiotic days and mIEAT an independent risk factors for MDR VAP. Thus, limiting prophylactic antibiotic days is the only potentially modifiable risk factor for the development of MDR VAP in trauma patients.

LEVEL OF EVIDENCE

Level IV Therapeutic; level III Prognostic.

Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens

The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.

Characterization of myophage AM24 infecting Acinetobacter baumannii of the K9 capsular type

In the present study, we investigate the biological properties and genomic organization of virulent bacteriophage AM24, which specifically infects multidrug-resistant clinical Acinetobacter baumannii strains with a K9 capsular polysaccharide structure. The phage was identified as a member of the family Myoviridae by transmission electron microscopy. The AM24 linear double-stranded DNA genome of 97,177 bp contains 167 open reading frames. Putative functions were assigned for products of 40 predicted genes, including proteins involved in nucleotide metabolism and DNA replication, packaging of DNA into the capsid, phage assembly and structural proteins, and bacterial cell lysis. The gene encoding the tailspike, which possesses depolymerase activity towards the corresponding capsular polysaccharides, is situated in the phage genome outside of the structural module, upstream of the genes responsible for packaging of DNA into the capsid. The data on characterization of depolymerase-carrying phage AM24 contributes to our knowledge of the diversity of viruses infecting different capsular types of A. baumannii.

Antimicrobial Susceptibility of Acinetobacter calcoaceticus-Acinetobacter baumannii Complex and Stenotrophomonas maltophilia Clinical Isolates: Results From the SENTRY Antimicrobial Surveillance Program (1997-2016)

Background

Acinetobacter calcoaceticus-A. baumannii (Acb) complex and Stenotrophomonas maltophilia represent frequent causes of hospital-acquired infections. We evaluated the frequency and resistance rates of Acb complex and S. maltophilia isolates from medical centers enrolled in the SENTRY Program.

Methods

A total of 13 752 Acb complex and 6467 S. maltophilia isolates were forwarded to a monitoring laboratory by 259 participating sites from the Asia-Pacific region, Latin America, Europe, and North America between 1997 and 2016. Confirmation of species identification and antimicrobial susceptibility testing were performed using conventional methods and/or matrix-assisted laser desorption ionization-time of flight mass spectrometry and the broth microdilution method, respectively. Antimicrobial susceptibility results were interpreted by CLSI and EUCAST 2018 criteria.

Results

Acb complex and S. maltophilia were most frequently isolated from patients hospitalized with pneumonia (42.9% and 55.8%, respectively) and bloodstream infections (37.3% and 33.8%, respectively). Colistin and minocycline were the most active agents against Acb complex (colistin MIC_50/90, ≤0.5/2 mg/L; 95.9% susceptible) and S. maltophilia (minocycline MIC_50/90, ≤1/2 mg/L; 99.5% susceptible) isolates, respectively. Important temporal decreases in susceptibility rates among Acb complex isolates were observed for all antimicrobial agents in all regions. Rates of extensively drug-resistant Acb complex rates were highest in Europe (66.4%), followed by Latin America (61.5%), Asia-Pacific (56.9%), and North America (38.8%). Among S. maltophilia isolates, overall trimethoprim-sulfamethoxazole (TMP-SMX) susceptibility rates decreased from 97.2% in 2001-2004 to 95.7% in 2013-2016, but varied according to the geographic region.

Conclusions

We observed important reductions of susceptibility rates to all antimicrobial agents among Acb complex isolates obtained from all geographic regions. In contrast, resistance rates to TMP-SMX among S. maltophilia isolates remained low and relatively stable during the study period.

Phenotypic and Genotypic Characterization of Clinical Isolates Belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) Complex Isolated From Animals Treated at a Veterinary Hospital in Switzerland

Objectives: We investigated a collection of strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex obtained from a veterinary clinic with regard to their genetic relatedness, presence of antibiotic resistance genes and antimicrobial susceptibility profiles.

Methods: Fifty-eight ACB-complex strains from animals treated at a veterinary clinic between 2006 and 2017, and seven strains collected from the hospital environment during 2012 were analyzed. Assignment to sequence types (ST) and international complexes (IC) was done by multilocus sequence typing (MLST) according to the Pasteur scheme. Genes encoding carbapenemases, aminoglycoside-modifying enzymes, macrolide-, quinolone- and co-trimoxazole resistance genes, the ISAba1 element, virulence associated intI1 genes and plasmid associated toxin-antitoxin markers were identified by microarray. Genes encoding bla_OXA−51-like carbapenemases were amplified by PCR and sequenced. Susceptibility profiles were determined by disc diffusion or by broth microdilution.

Results: Among 50 A. baumannii isolates from animals, two predominant clones were observed linked to CC1 (n = 27/54% of the isolates) and CC25 (n = 14/28%), respectively. Strains of IC I harbored bla_OXA−69, aac(3′)-la, aadA1, sul1, intI1, and splA/T genes. Isolates belonging to CC25 possessed bla_OXA−64. Six (12%) isolates belonging to CC2 and carrying bla_OXA−66 were also noted. One isolate belonged to CC10 (bla_OXA−68), one to CC149 (bla_OXA−104), the remaining isolate was assigned to ST1220 and possessed bla_OXA−116. Of six environmental A. baumannii, four (66.7%) belonged to CC25 (bla_OXA−64), one (16.7%) to CC2 (bla_OXA−66) and one to CC3 (bla_OXA−71). Nine isolates (eight from animals and one environmental strain) were non-baumannii strains and did not harbor bla_OXA−51-like genes. None of the isolates carried bla_OXA−23, bla_OXA−48, or bla_OXA−58, and none were resistant to carbapenems.

Conclusions: Clonal lineages of the veterinary A. baumannii isolates in our collection are identical to those globally emerging in humans but do not harbor bla_OXA−23. A. baumannii CC25 may be specific for this particular veterinary clinic environment.

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.

Contact-dependent growth inhibition systems in Acinetobacter

In bacterial contact-dependent growth inhibition (CDI) systems, CdiA proteins are exported to the outer membrane by cognate CdiB proteins. CdiA binds to receptors on susceptible bacteria and subsequently delivers its C-terminal toxin domain (CdiA-CT) into neighbouring target cells. Whereas self bacteria produce CdiI antitoxins, non-self bacteria lack antitoxins and are therefore inhibited in their growth by CdiA. In silico surveys of pathogenic Acinetobacter genomes have enabled us to identify >40 different CDI systems, which we sorted into two distinct groups. Type-II CdiAs are giant proteins (3711 to 5733 residues) with long arrays of 20-mer repeats. Type-I CdiAs are smaller (1900-2400 residues), lack repeats and feature central heterogeneity (HET) regions, that vary in size and sequence and can be exchanged between CdiA proteins. HET regions in most type-I proteins confer the ability to adopt a coiled-coil conformation. CdiA-CT and pretoxin modules differ significantly between type-I and type-II CdiAs. Moreover, type-II genes only have remnants of genes in their 3' end regions that have been displaced by the insertion of novel cdi sequences. Type-I and type-II CDI systems are equally abundant in A. baumannii, whereas A. pittii and A. nosocomialis predominantly feature type-I and type-II systems, respectively.

Surface-Related Features and Virulence Among Acinetobacter baumannii Clinical Isolates Belonging to International Clones I and II

Acinetobacter baumannii currently represents one of the most important nosocomial infection agent due to its multidrug-resistance and a propensity for the epidemic spread. The A. baumannii strains belonging to the international clonal lineages I (IC I) and II (IC II) are associated with the hospital outbreaks and a high virulence. However, the intra and inter lineage-specific features of strains belonging to these most worldwide spread A. baumannii clones are not thoroughly explored. In this study we have investigated a set of cell surface-related features of A. baumannii IC I (n = 20) and IC II (n = 16) lineage strains, representing 30 distinct pulsed-field gel electrophoresis types in the collection of clinical isolates obtained in Lithuanian tertiary care hospitals. We show that A. baumannii IC II strains are non-motile, do not form pellicle and display distinct capsular polysaccharide profile compared with the IC I strains. Moreover, in contrast to the overall highly hydrophobic IC I strains, IC II strains showed a greater variation in cell surface hydrophobicity. Within the IC II lineage, hydrophilic strains demonstrated reduced ability to form biofilm and adhere to the abiotic surfaces, also possessed twofold thicker cell wall and exhibited higher resistance to desiccation. Furthermore, these strains showed increased adherence to the lung epithelial cells and were more virulent in nematode and mouse infection model compared with the hydrophobic IC II strains. According to the polymerase chain reaction-based locus-typing, the reduction in hydrophobicity of IC II strains was not capsule or lipooligosaccharide locus type-dependent. Hence, this study shows that the most widespread A. baumannii clonal lineages I and II markedly differ in the series of cell surface-related phenotypes including the considerable phenotypic diversification of IC II strains at the intra-lineage level. These findings suggest that the genotypically related A. baumannii strains might evolve the features which could provide an advantage at the specific conditions outside or within the host.

Emergence and Persistence of High-Risk Clones Among MDR and XDR A. baumannii at a Brazilian Teaching Hospital

Dissemination of carbapenem-resistant Acinetobacter baumannii is currently one of the priority themes discussed around the world, including in Brazil, where this pathogen is considered endemic. A total of 107 carbapenem-resistant A. baumannii (CRAB) isolates were collected from patients with bacteraemia attended at a teaching hospital in Brazil from 2008 to 2014. From these samples, 104 (97.2%) carried bla_{OXA−23−like}, all of them associated with ISAba1 The bla_OXA−231 (1.9%) and bla_OXA−72 (0.9%) genes were also detected in low frequencies. All isolates were susceptible to minocycline, and 38.3% of isolates presented intermediate susceptibility to tigecycline (MIC = 4 μg/ml). Molecular typing assessed by multi-locus sequence typing demonstrated that the strains were mainly associated with clonal complexes CC79 (47.4%), followed by CC1 (16.9%), and CC317 (18.6%), belonging to different pulsotypes and in different prevalences over the years. Changes in the clones' prevalence reinforce the need of identifying and controlling CRAB in hospital settings to preserve the already scarce therapeutic options available.

Genomic epidemiology of multidrug-resistant Gram-negative organisms

The emergence and spread of antibiotic-resistant Gram-negative bacteria (rGNB) across global healthcare networks presents a significant threat to public health. As the number of effective antibiotics available to treat these resistant organisms dwindles, it is essential that we devise more effective strategies for controlling their proliferation. Recently, whole-genome sequencing has emerged as a disruptive technology that has transformed our understanding of the evolution and epidemiology of diverse rGNB species, and it has the potential to guide strategies for controlling the evolution and spread of resistance. Here, we review specific areas in which genomics has already made a significant impact, including outbreak investigations, regional epidemiology, clinical diagnostics, resistance evolution, and the study of epidemic lineages. While highlighting early successes, we also point to the next steps needed to translate this technology into strategies to improve public health and clinical medicine.

Acinetobacter baumannii - a neglected pathogen in veterinary and environmental health in Germany

The emergence and global spread of drug resistant Acinetobacter (A.) baumannii is a cause of great concern. The current knowledge on antibiotic resistance in A. baumannii from animal origin is mostly based on few internationally published case reports, investigations of strain collections and several whole genome analyses. This lack of data results in a somewhat sketchy picture on how to assess the possible impact of drug resistant A. baumannii strains on veterinary and public health in Germany. Consequently, there is an urgent need to intensify the surveillance of A. baumannii in pet animals, the farm animal population and wildlife.

An insight into the emergence of Acinetobacter baumannii as an oro-dental pathogen and its drug resistance gene profile - An in silico approach

Background

Acinetobacter baumannii, a potential nosocomial pathogen has stealthily gained entry into the oral cavity. Their association with other pathogens like Pseudomonas aeruginosa in chronic and aggressive periodontitis cases is well documented. The magnitude of problem caused by A . baumannii could be attributed to resistance genes acquired by the organism. Since the microbiome of oral cavity is heterogeneous and complex, the transfer of genes from multidrug resistant A . baumannii may be a serious threat in infection control and management. In view of this fact, the present study aims to categorize and characterize drug resistant genes present in each of the 19 genomes of Acinetobacter Sp. selected for the study.

Methods

About 19 genome sequences of Acinetobacter spp. with the predominance of different strains of A . baumannii was genotyped using in silico restriction digestion and pulse field gel electrophoresis (PFGE). Further, the prevalence of common drug resistant genes in the genome of various Acinetobacter spp. was recorded using in silico PCR analysis.

Results

Based on the PFGE pattern, phylogenetic tree was constructed and the genomes were clustered into 6 genotypes. Genotype 4 (n = 8; 42.10%) and 5 (n = 6; 31.57%) were predominant, followed by genotypes 2 (n = 2; 10.52%), 1, 3 and 6 (n = 1; 5.26%). Three species were excluded from the list since they were negative for most of the drug resistant genes tested. Prevalence of drug resistant genes in each of the 16 genomes analysed found oxa-51, ISAba 1 and ADC 1 to be the major genes found in A . baumannii. Acinetobacter spp. belonging to genotypes 4 and 5 were found to harbour 6-10 and 2-8 potential drug resistant genes respectively.

Conclusion

The present study showed cluster of multi-drug resistant genes in genomes analysed, thus, warranting the need for antibiotic surveillance, alternate therapeutic measures and development of novel antimicrobials. An extensive study on the genes conferring drug resistance in this pathogen will open new avenues for battling the entry and spread of this pathogen in vulnerable patient groups.

Epidemiological investigation of an Acinetobacter baumannii outbreak using core genome multilocus sequence typing

OBJECTIVES

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious nosocomial pathogen that causes a variety of serious, often life-threatening, infections and outbreaks. This study aimed to investigate the molecular epidemiology of clinical CRAB isolates from an outbreak that occurred in the intensive care unit (ICU) of an Italian hospital.

METHODS

From December 2016 to April 2017, 13 CRAB isolates were collected from seven patients treated in the ICU at 'L. Spallanzani' Hospital (Rome, Italy). Typing was performed by repetitive extragenic palindromic PCR (rep-PCR) using a DiversiLab^® system. Whole-genome sequencing (WGS) data were used for in silico analysis of traditional multilocus sequence typing (MLST) results, to identify resistance genes and for core genome MLST (cgMLST) analysis. Epidemiological data were obtained from hospital records.

RESULTS

All isolates showed a carbapenem-resistant profile and carried the bla_OXA-23 carbapenemase gene. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group, whilst the cgMLST approach, which uses 2390 gene targets to characterise the gene-by-gene allelic profile, highlighted the presence of two cluster types. These results allowed us to identify two patients who were likely to be the source of two separate transmission chains.

CONCLUSION

These results show that WGS by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.

The plasmid-encoded transcription factor ArdK contributes to the repression of the IMP-6 metallo-β-lactamase gene blaIMP-6, leading to a carbapenem-susceptible phenotype in the blaIMP-6-positive Escherichia coli strain A56-1S

Carbapenemase-producing Enterobacteriaceae (CPE) are a global concern because these bacteria are resistant to almost all β-lactams. Horizontal interspecies gene transfer via plasmid conjugation has increased the global dissemination of CPE. Recently, an Enterobacteriaceae strain positive for carbapenemase gene but showing a carbapenem-susceptible phenotype was identified, suggesting that these susceptible strains may be challenging to detect solely via antimicrobial susceptibility tests without molecular analysis. Here, we isolated a bla_IMP-6 carbapenemase-gene positive but imipenem- and meropenem-susceptible Escherichia coli (ISMS-E) strain A56-1S (imipenem and meropenem minimum inhibitory concentration, ≤ 0.125 mg/L), from a human urine specimen in Japan. A56-1S was carbapenemase negative by the Carba NP test, suggesting that IMP-6 production was low or undetectable. Thus, to characterize the mechanism of this phenotype, a meropenem-resistant E. coli A56-1R strain was obtained using meropenem-selection. A56-1R was positive for carbapenemase production by the Carba NP test, and bla_IMP-6 transcription in A56-1R was 53-fold higher than in A56-1S, indicating that bla_IMP-6 in A56-1S is negatively regulated at the transcriptional level. Comparative genomic analysis between the two strains revealed that the alleviation of restriction of DNA (ardK) gene encoding a putative transcription factor is disrupted by the IS26 insertion in A56-1R. A cotransformation assay of ardK and the regulatory element upstream of bla_IMP-6 showed repression of bla_IMP-6 transcription, indicating that ArdK negatively modulates bla_IMP-6 transcription. ArdK binding and affinity assays demonstrated that ArdK directly binds to the regulatory element upstream of bla_IMP-6 with dissociation constant values comparable to those of general transcription factors. The IMP-6 carbapenemase showed low hydrolytic activity against imipenem, resulting in an imipenem-susceptible and meropenem-resistant (ISMR) phenotype (previously reported as a stealth phenotype). However, the low expression of IMP-6 in the A56-1S strain could be a typical characteristic of ISMS-E due to gene repression, indicating that conventional antimicrobial susceptibility tests might be unable to detect such strains even when using both imipenem and meropenem. Bacteria that exhibit the ISMS phenotype could play a potential role as undetectable reservoirs and might facilitate gene transfer to other organisms while avoiding detection.

Quantitative Proteomics Reveals Antibiotics Resistance Function of Outer Membrane Proteins in Aeromonas hydrophila

Outer membrane proteins (OMPs) play essential roles in antibiotic resistance, particularly in Gram-negative bacteria; however, they still have many unidentified functions regarding their behavior in response to antibiotic stress. In the current work, quantitative tandem mass tag labeling-based mass spectrometry was used to compare the outer membrane related proteins between an oxytetracycline-resistant (OXY-R) and its original control stain (OXY-O) in Aeromonas hydrophila. Consequently, a total of 261 commonly altered proteins in two biological repeats were identified including 29 proteins that increased and 28 that decreased. Gene ontology analysis showed that the expression of transport proteins was significantly reduced, and translation-related proteins were downregulated in the OXY-R strain. After using western blotting to validate selected altered proteins, eight OMP-related genes were knocked out and their roles in antibiotic resistance were further evaluated. The survival assays showed that some mutants such as ΔAHA_4281, ΔAHA_2766, ΔAHA_2282, ΔAHA_1181, and ΔAHA_1280 affected the susceptibility of A. hydrophila to antimicrobials. Moreover, the minimum inhibitory concentration assay showed that these candidate mutants also respond differently to other types of antibiotics. Our results reveal several novel outer membrane related proteins of A. hydrophila that play important roles in antibiotic resistance, and as such, may be helpful for screening studies to identify novel drug targets.

The AbaR antibiotic resistance islands found in Acinetobacter baumannii global clone 1 - Structure, origin and evolution

In multiply resistant Acinetobacter baumannii, complex transposons located in the chromosomal comM gene carry antibiotic and heavy metal resistance determinants. For one type, known collectively as AbaR, the ancestral form, AbaR0, entered a member of global clone 1 (GC1) in the mid 1970s and continued to evolve in situ forming many variants. In AbaR0, antibiotic and mercuric ion resistance genes are located between copies of a cadmium-zinc resistance transposon, Tn6018, and this composite transposon is in a class III transposon, Tn6019, carrying arsenate/arsenite resistance genes and five tni transposition genes. The antibiotic resistance genes in the AbaR0 and derived AbaR3 configurations are aphA1b, bla_TEM, catA1, sul1, tetA(A), and cassette-associated aacC1 and aadA1 genes. These genes are in a specific arrangement of fragments from well-known transposons, e.g. Tn1, Tn1721, Tn1696 and Tn2670, that arose in an IncM1 plasmid. All known GC1 lineage 1 isolates carry AbaR0 or AbaR3, which arose around 1990, or a variant derived from one of them. Variants arose via deletions caused by one of three internal IS26s, by recombination between duplicate copies of sul1 or Tn6018, or by gene cassette addition or replacement. A few GC2 isolates also carry an AbaR island with different cassette-associated genes, aacA4 and oxa20.

Acinetobacter Infections in Neonates

PURPOSE OF REVIEW

MDR-Gram-negative bacteria are a great concern in the neonatal population, with a worldwide rise in the reported incidence and with very limited therapeutic options. Acinetobacter baumannii is responsible for many infections in neonates and outbreaks in neonatal intensive care unit (NICU); also, outbreaks caused by other Acinetobacter species have been reported. The aim of this review is to document the epidemiology of Acinetobacter spp. infections in neonates and risk factors for acquisition of Acinetobacter spp. in the NICU using data from published studies.

RECENT FINDINGS

Acinetobacter spp. infections are increasing in neonates in NICU. Outbreak caused by multidrug resistant (MDR) or extensively drug resistant (XDR) A. baumannii but also outbreak caused by susceptible A. soli and A. septicus sp. nov., were reported in neonates. Acinetobacter spp. were responsible for bloodstream infections and respiratory tract infections in neonates. Risk factors for A. baumannii acquisition in neonates were low birthweight, length of NICU stay, umbilical catheterization, central-venous catheterization, assisted ventilation, and prior antibiotic use. This review highlights the importance of surveillance of risk factors for healthcare-associated infections in NICU to control MDR and XDR A. baumannii infections in neonates.

Genetic structure of four plasmids found in Acinetobacter baumannii isolate D36 belonging to lineage 2 of global clone 1

Four plasmids ranging in size from 4.7 to 44.7 kb found in the extensively antibiotic resistant Acinetobacter baumannii isolate D36 that belongs to lineage 2 of global clone 1 were examined. D36 includes two cryptic plasmids and two carrying antibiotic resistance genes. The smallest plasmid pD36-1 (4.7 kb) carries no resistance genes but includes mobA and mobC mobilisation genes related to those found in pRAY* (pD36-2, 6,078 bp) that also carries the aadB gentamicin, kanamycin and tobramycin resistance gene cassette. These two plasmids do not encode a Rep protein. Plasmid pRAY* was found to be mobilised at high frequency by the large conjugative plasmid pA297-3 but a pRAY* derivative lacking the mobA and mobC genes was not. The two larger plasmids, pD36-3 and pD36-4, encode Rep_3 family proteins (Pfam1051). The cryptic plasmid pD36-3 (6.2 kb) has RepAci1 and pD36-4 (44.7 kb) encodes two novel Rep_3 family proteins suggesting a co-integrate. Plasmid pD36-4 includes the sul2 sulfonamide resistance gene, the aphA1a kanamycin/neomycin resistance gene in Tn4352::ISAba1 and a mer module in a hybrid Tn501/Tn1696 transposon conferring resistance to mercuric ions. New examples of dif modules flanked by pdif sites (XerC-XerD binding sites) that are part of many A. baumannii plasmids were also identified in pD36-3 and pD36-4 which carry three and two dif modules, respectively. Homologs of three dif modules, the sup sulphate permease module in pD36-3, and of the abkAB toxin-antitoxin module and the orf module in pD36-4, were found in different contexts in diverse Acinetobacter plasmids, consistent with module mobility. A novel insertion sequence named ISAba32 found next to the pdif site in the abkAB dif module is related to members of the ISAjo2 group which also are associated with the pdif sites of dif modules. Plasmids found in D36 were also found in some other members of GC1 lineage 2.

Acinetobacter in veterinary medicine, with an emphasis on Acinetobacter baumannii

Acinetobacter spp. are aerobic, rod-shaped, Gram-negative bacteria belonging to the Moraxellaceae family of the class Gammaproteobacteria and are considered ubiquitous organisms. Among them, Acinetobacter baumannii is the most clinically significant species with an extraordinary ability to accumulate antimicrobial resistance and to survive in the hospital environment. Recent reports indicate that A. baumannii has also evolved into a veterinary nosocomial pathogen. Although Acinetobacter spp. can be identified to species level using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) coupled with an updated database, molecular techniques are still necessary for genotyping and determination of clonal lineages. It appears that the majority of infections due to A. baumannii in veterinary medicine are nosocomial. Such isolates have been associated with several types of infection such as canine pyoderma, feline necrotizing fasciitis, urinary tract infection, equine thrombophlebitis and lower respiratory tract infection, foal sepsis, pneumonia in mink, and cutaneous lesions in hybrid falcons. Given the potential multidrug resistance of A. baumannii, treatment of diseased animals is often supportive and should preferably be based on in vitro antimicrobial susceptibility testing results. It should be noted that animal isolates show high genetic diversity and are in general distinct in their sequence types and resistance patterns from those found in humans. However, it cannot be excluded that animals may occasionally play a role as a reservoir of A. baumannii. Thus, it is of importance to implement infection control measures in veterinary hospitals to avoid nosocomial outbreaks with multidrug-resistant A. baumannii.

Carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa: characterization of carbapenemase genes and E-test evaluation of colistin-based combinations

Background

Carbapenamase producing Acinetobacter baumannii and Pseudomonas aeruginosa are emerging worldwide limiting the use of carbapenems as effective and safe drugs.

Purpose

To characterize different carbapenemase genes carried by carbapenem-resistant (CR) A. baumannii and P. aeruginosa isolates and to evaluate the in vitro effect of some colistin-based combinations by E-test method in Zagazig University Hospitals ICU isolates.

Methods

CR A. baumannii and P. aeruginosa isolated from the surgical intensive care unit (ICU) were tested for carbapenemase genes by polymerase chain reaction and the effect of colistin/meropenem and colistin/tigecycline combinations was evaluated by E-test.

Results

Genes coding for OXA-23, NDM and GES were detected in 90, 66.7 and 50% of CR A. baumannii, respectively, while genes coding for VIM, GES, NDM and IMP were detected in 50, 40.9, 27.3 and 18.2% of CR P. aeruginosa, respectively. Colistin/tigecycline combination showed synergistic and additive effect in 20% and 60% of A. baumannii isolates, respectively, while colistin/meropenem combination showed synergistic and additive effect in 63.6% and 36.4% of P. aeruginosa, respectively.

Conclusion

Carbapenemase genes carriage accounts for high level carbapenem resistance in our isolates. Colistin/tigecycline and colistin/meropenem combinations can be considered for treatment of severe infections by CR A. baumannii and P. aeruginosa, respectively.

Genomic mapping of ST85 blaNDM-1 and blaOXA-94 producing Acinetobacter baumannii isolates from Syrian Civil War Victims

OBJECTIVES

The rapid emergence of carbapenem-resistant Acinetobacter baumannii is a global health concern. A comparative genomic analysis was performed on two ST85 A. baumannii strains harboring bla_NDM-1 and bla_OXA-94 collected in Lebanon from Syrian Civil War victims.

METHODS

Genome sequencing data of ACMH-6200 and ACMH-6201 were used for in silico extraction of multilocus sequence types (MLST), resistance genes, and virulence factors. Plasmids were genetically mapped in silico and using PCR-based replicon typing (PBRT). The genetic environment of bla_NDM-1 and bla_OXA-94 was determined, and whole-genome single nucleotide polymorphism (wgSNP) analysis in comparison with 41 publicly available A. baumannii genomes was performed.

RESULTS

Tn125 carrying bla_NDM-1 was truncated by the insertion of ISAba14 downstream of dct, generating ΔTn125. bla_OXA-94 was upstream of ISAba13 and ISAba17. Resistance to ceftazidime could be attributed to AmpC cephalosporinase encoded by bla_ADC-25, and to bla_NDM-1 on plasmids_. GyrA (S83L) and ParC (S80L) substitutions conferred resistance to fluoroquinolones. wgSNP analysis separated the isolates based on their sequence types.

CONCLUSIONS

The role of refugees in the transmission of antimicrobial resistance in developing countries is understudied. As such, this study sheds light on the correlation between population mobility and the importation of drug-resistant pathogens. It also highlights the manifold mechanisms underlying antibiotic resistance in A. baumannii.

Identification of Novel Acinetobacter baumannii Type VI Secretion System Antibacterial Effector and Immunity Pairs

The type VI secretion system (T6SS) is a macromolecular machine that delivers protein effectors into host cells and/or competing bacteria. The effectors may be delivered as noncovalently bound cargo of T6SS needle proteins (VgrG/Hcp/PAAR) or as C-terminal extensions of these proteins. Many Acinetobacter baumannii strains produce a T6SS, but little is known about the specific effectors or how they are delivered. In this study, we show that A. baumannii AB307-0294 encodes three vgrG loci, each containing a vgrG gene, a T6SS toxic effector gene, and an antitoxin/immunity gene. Each of the T6SS toxic effectors could kill Escherichia coli when produced in trans unless the cognate immunity protein was coproduced. To determine the role of each VgrG in effector delivery, we performed interbacterial competitive killing assays using A. baumannii AB307-0294 vgrG mutants, together with Acinetobacter baylyi prey cells expressing pairs of immunity genes that protected against two toxic effectors but not a third. Using this approach, we showed that AB307-0294 produces only three T6SS toxic effectors capable of killing A. baylyi and that each VgrG protein is specific for the carriage of one effector. Finally, we analyzed a number of A. baumannii genomes and identified significant diversity in the range of encoded T6SS VgrG and effector proteins, with correlations between effector types and A. baumannii global clone lineages.

Temporal evolution of Acinetobacter baumannii ST107 clone: conversion of blaOXA-143 into blaOXA-231 coupled with mobilization of ISAba1 upstream occAB1

Nine carbapenem-resistant Acinetobacter baumannii isolates carrying bla_OXA-231 and an ISAba1 upstream occAB1 were evaluated. They were clonally related and belonged to ST107. An OXA-143-producing A. baumannii ST107 strain (Ac-148) that did not possess ISAba1 upstream occAB1 was included in the analysis. Reduction in the expression of occAB1 and a 4-fold increase of carbapenem MICs were observed for all isolates, except for the Ac-148 strain, probably due to the presence of ISAba1 upstream occAB1 but in the same transcriptional orientation. We reported an A. baumannii ST107 clone carrying bla_OXA-143 that acquired a mutation resulting into bla_OXA-231 and mobilized ISAba1 upstream occAB1.

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.

Evaluation of Polymyxin B Susceptibility Profile and Detection of Drug Resistance Genes among Acinetobacter Baumannii Clinical Isolates in Tehran, Iran during 2015-2016

Acinetobacter baumannii is an important opportunistic pathogen, responsible for approximately 10% of all gram-negative nosocomial infection. The aim of this study was to determine aminoglycoside and quinolone resistance genes and their antimicrobial susceptibility profile in the clinically A. baumannii. In this cross-sectional study, a total of 100 nonduplicative A. baumannii isolates were collected from different clinical samples. Antimicrobial susceptibility test was performed by disk diffusion method. QnrA, anrB, qnrS, aac(3)-IIa, and aac(6')-Ib genes were identified using PCR method. The results of antibiotic susceptibility test showed that polymyxin B was the most effective antimicrobial against A. baumannii. 97%, 95% and 82% of isolates were resistant to cefepime, ceftriaxone, and amikacin, respectively. The molecular distribution of aac(3)-IIa, aac(6')-Ib, and qnrA genes were 45%, 50%, and 50% of isolates, respectively. However, qnrB and qnrS genes could not be detected in any strain. This study showed that polymyxin B was the best drug against A. baumannii clinical isolates. This data is also valid for polymyxin E (colistin), which is mostly used in clinics. There is a high level of resistance genes among clinical A. baumannii isolates. This high prevalence rate highlights the necessity for the development of rapid diagnostic assays and continuous monitoring of antibiotic resistance.

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection. Comparative genomic analysis showed that many of them had conserved backbones. Plasmid coding sequences corresponding to plasmid specific functions were bioinformatically and functionally analyzed. Replication initiation protein analysis revealed the predominance of the Rep_3 superfamily. The phylogenetic tree constructed from all Acinetobacter Rep_3 superfamily plasmids showed 16 intermingled clades originating from nosocomial and environmental habitats. Phylogenetic analysis of relaxase proteins revealed the presence of a new sub-clade named MOBQAci, composed exclusively of Acinetobacter relaxases. Functional analysis of proteins belonging to this group showed that they behaved differently when mobilized using helper plasmids belonging to different incompatibility groups.

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing. All isolates were multidrug resistant, carrying two genomic islands that harboured several antibiotic-resistance genes. Most isolates were genetically identical and represented a single founder genotype. We identified three novel non-synonymous substitutions associated with meropenem resistance: F136L and G288S in AdeB (part of the AdeABC efflux pump) associated with an increase in meropenem MIC to ≥8 µg ml⁻¹; and A515V in FtsI (PBP3, a penicillin-binding protein) associated with a further increase in MIC to 32 µg ml⁻¹. Structural modelling of AdeB and FtsI showed that these mutations affected their drug-binding sites and revealed mechanisms for meropenem resistance. Notably, one of the adeB mutations arose prior to meropenem therapy but following ciprofloxacin therapy, suggesting exposure to one drug whose resistance is mediated by the efflux pump can induce collateral resistance to other drugs to which the bacterium has not yet been exposed.

Molecular Epidemiology of Emerging blaOXA-23-Like- and blaOXA-24-Like-Carrying Acinetobacter baumannii in Taiwan

The rate of recovery of carbapenem-resistant Acinetobacter baumannii (CRAB) isolates has increased significantly in recent decades in Taiwan. This study investigated the molecular epidemiology of CRAB with a focus on the mechanisms of resistance and spread in isolates with bla_OXA-23-like or bla_OXA-24-like All 555 CRAB isolates in our multicenter collection, which were recovered from 2002 to 2010, were tested for the presence of class A, B, and D carbapenemase genes. All isolates with bla_OXA-23-like or bla_OXA-24-like were subjected to pulsed-field gel electrophoresis, and 82 isolates (60 isolates with bla_OXA-23-like and 22 isolates with bla_OXA-24-like) were selected for multilocus sequence typing to determine the sequence type (ST) and clonal group (CG) and for detection of additional β-lactamase and aminoglycoside resistance genes. The flanking regions of carbapenem and aminoglycoside resistance genes were identified by PCR mapping and sequencing. The localization of bla_OXA was determined by S1 nuclease and I-CeuI assays. The numbers of CRAB isolates carrying bla_OXA-23-like or bla_OXA-24-like, especially those carrying bla_OXA-23-like, increased significantly from 2008 onward. The bla_OXA-23-like gene was carried by antibiotic resistance genomic island 1 (AbGRI1)-type structures located on plasmids and/or the chromosome in isolates of different STs (CG92 and novel CG786), whereas bla_OXA-24-like was carried on plasmids in CRAB isolates of limited STs (CG92). No class A or B carbapenemase genes were identified. Multiple aminoglycoside resistance genes coexisted in CRAB. Tn6180-borne armA was found in 74 (90.2%) CRAB isolates, and 58 (70.7%) isolates had Tn6179 upstream, constituting AbGRI3. bla_TEM was present in 38 (46.3%) of the CRAB isolates tested, with 35 (92.1%) isolates containing bla_TEM in AbGRI2-type structures, and 61% of ampC genes had ISAba1 upstream. We conclude that the dissemination and spread of a few dominant lineages of CRAB containing various resistance island structures occurred in Taiwan.

Comparative transcriptomics of multidrug-resistant Acinetobacter baumannii in response to antibiotic treatments

Multidrug-resistant Acinetobacter baumannii, a major hospital-acquired pathogen, is a serious health threat and poses a great challenge to healthcare providers. Although there have been many genomic studies on the evolution and antibiotic resistance of this species, there have been very limited transcriptome studies on its responses to antibiotics. We conducted a comparative transcriptomic study on 12 strains with different growth rates and antibiotic resistance profiles, including 3 fast-growing pan-drug-resistant strains, under separate treatment with 3 antibiotics, namely amikacin, imipenem, and meropenem. We performed deep sequencing using a strand-specific RNA-sequencing protocol, and used de novo transcriptome assembly to analyze gene expression in the form of polycistronic transcripts. Our results indicated that genes associated with transposable elements generally showed higher levels of expression under antibiotic-treated conditions, and many of these transposon-associated genes have previously been linked to drug resistance. Using co-expressed transposon genes as markers, we further identified and experimentally validated two novel genes of which overexpression conferred significant increases in amikacin resistance. To the best of our knowledge, this study represents the first comparative transcriptomic analysis of multidrug-resistant A. baumannii under different antibiotic treatments, and revealed a new relationship between transposons and antibiotic resistance.

Distribution and Molecular Characterization of Acinetobacter baumannii International Clone II Lineage in Japan

Multidrug-resistant (MDR) Acinetobacter spp. have been globally disseminated in association with the successful clonal lineage Acinetobacter baumannii international clone II (IC II). Because the prevalence of MDR Acinetobacter spp. in Japan remains very low, we characterized all Acinetobacter spp. (n = 866) from 76 hospitals between October 2012 and March 2013 to describe the entire molecular epidemiology of Acinetobacter spp. The most prevalent species was A. baumannii (n = 645; 74.5%), with A. baumannii IC II (n = 245) accounting for 28.3% of the total. Meropenem-resistant isolates accounted for 2.0% (n = 17) and carried ISAba1-bla_OXA-23-like (n = 10), bla_IMP (n = 4), or ISAba1-bla_OXA-51-like (n = 3). Multilocus sequence typing of 110 representative A. baumannii isolates revealed the considerable prevalence of domestic sequence types (STs). A. baumannii IC II isolates were divided into the domestic sequence type 469 (ST469) (n = 18) and the globally disseminated STs ST208 (n = 14) and ST219 (n = 4). ST469 isolates were susceptible to more antimicrobial agents, while ST208 and ST219 overproduced the intrinsic AmpC β-lactamase. A. baumannii IC II and some A. baumannii non-IC II STs (e.g., ST149 and ST246) were associated with fluoroquinolone resistance. This study revealed that carbapenem-susceptible A. baumannii IC II was moderately disseminated in Japan. The low prevalence of acquired carbapenemase genes and presence of domestic STs could contribute to the low prevalence of MDR A. baumannii A similar epidemiology might have appeared before the global dissemination of MDR epidemic lineages. In addition, fluoroquinolone resistance associated with A. baumannii IC II may provide insight into the significance of A. baumannii epidemic clones.

A multi-center study on the risk factors of infection caused by multi-drug resistant Acinetobacter baumannii

BACKGROUND

Acinetobacter baumannii (AB) is critical for healthcare-associated infections (HAI) with significant regional differences in the resistance rate, but its risk factors and infection trends has not been well studied. We aimed to explore the risk factors, epidemiological characteristics and resistance of multidrug-resistant Acinetobacter baumannii (MDR-AB) in intensive care unit inpatients.

METHODS

Data of patients with MDR-AB (195 cases), and with antibiotic-sensitive AB infection (294 cases, control) during January to December, 2015 in three medical centers in Xiamen, China were conducted and analyzed in the present retrospective study.

RESULTS

Lower respiratory tract infection with AB accounted for 68.71%. MDR-AB was detected in 39.88% of all cases. Univariate analysis suggested that mechanical ventilation, indwelling catheter, cancer patients, length of hospitalization in intensive care unit (ICU) ≥15 d, Acute Physiology and Chronic Health Evaluation (APACHE) II score, combined using antibiotic before isolation of AB and use of third-lines cephalosporins were associated with the development of MDR-AB healthcare-associated infections. Dose-response relationship analysis suggested that the age and the days of mechanical ventilation were associated with increased infection with MDR-AB. Logistic regression analysis suggested that, mechanical ventilation, combined using antibiotic before isolation of AB, and indwelling catheter, were associated with MDR-AB infection, with odds ratios (OR) and 95% confidence intervals (CI) of 3.93 (1.52-10.14), 4.11 (1.58-10.73), and 4.15 (1.32-12.99), respectively.

CONCLUSIONS

MDR-AB infection was associated with mechanical ventilation, combined using antibiotic before isolation of AB, and indwelling catheter. Furthermore, the age and the days of mechanical ventilation were associated with increased infection with MDR-AB.

Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology

Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii-calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987–2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008–2009 and thereafter, rates have remained fairly constant (e.g., 50–60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that bla_OXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates.