Clonal diversity of Acinetobacter baumannii clinical isolates revealed by a snapshot study

Acinetobacter baumannii from Samples of Commercially Reared Turkeys: Genomic Relationships, Antimicrobial and Biocide Susceptibility

Acinetobacter baumannii is especially known as a cause of nosocomial infections worldwide. It shows intrinsic and acquired resistances to numerous antimicrobial agents, which can render the treatment difficult. In contrast to the situation in human medicine, there are only few studies focusing on A. baumannii among livestock. In this study, we have examined 643 samples from turkeys reared for meat production, including 250 environmental and 393 diagnostic samples, for the presence of A. baumannii. In total, 99 isolates were identified, confirmed to species level via MALDI-TOF-MS and characterised with pulsed-field gel electrophoresis. Antimicrobial and biocide susceptibility was tested by broth microdilution methods. Based on the results, 26 representative isolates were selected and subjected to whole-genome sequencing (WGS). In general, A. baumannii was detected at a very low prevalence, except for a high prevalence of 79.7% in chick-box-papers (n = 118) of one-day-old turkey chicks. The distributions of the minimal inhibitory concentration values were unimodal for the four biocides and for most of the antimicrobial agents tested. WGS revealed 16 Pasteur and 18 Oxford sequence types, including new ones. Core genome MLST highlighted the diversity of most isolates. In conclusion, the isolates detected were highly diverse and still susceptible to many antimicrobial agents.

Local characteristics of molecular epidemiolgy of Acinetobacter baumannii in Jilin province (northeast China)

A. Baumannii is an opportunistic nosocomial pathogen which has severe antibiotic resistance. However, the epidemiology is less clearly understood in Jilin province and China. Thus, 89 A. baumannii isolates from a single hospital in Jilin province between 2013-2017 were performed by MLST. In order to better understanding of the epidemiology of Jilin isolates, Chinese strains originated from other domestic regions and worldwide isolates in MLST database were analyzed by silico phylogenetic tools together. A total of 22 STs in Jilin were identified, and 10 STs were found to be novel. The top three predominant sequence types are ST195 (n = 34, 38.2%), ST208 (n = 14, 15.7%) and ST540 (n = 13, 14.6%). ST369 is predicted to be group founder and ST195, ST540 are subgroup founders of the majority STs in Jilin Province. Some newly discovered singletons showed close relationship with strains from other countries, which suggest that nation-cross transmission is one of important origin of Jilin strains. The majority of Jilin STs showed clonality and close relationship with the majorities from other regions of China. But occupation of individual STs in Jilin were different from that of other domestic regions. The aggregation trend and genetic relationship proved that predominant Jilin STs continue to mutate during transmission. Drug resistance facilitated transmission of Jilin A.baumannii isolates because more than 94% of isolates are resistant to at least one carbapenem and the STs with strong resistance to carbapenems usually has more isolates. In conclusion, high diversity and different occupation of STs, and occupation of novel STs proved that epidemiology of A. baumannii in Jilin has special regional characteristics, and drug resistance facilitated transmission of domestic strains and foreign strains.

Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies.

The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.

Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase

Carbapenem-resistant Acinetobacter baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here, we characterize carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. Fifty-four carbapenem-resistant isolates from Alexandria Main University Hospital (AMUH), Alexandria, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. The core-gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. Multilocus sequence typing (MLST) sequence type (ST) and antibiotic-resistance genes were identified. The majority of Egyptian isolates belonged to one of three major clades, corresponding to Pasteur MLST clonal complex (CC^PAS) 1, CC^PAS2 and ST^PAS158. Strains belonging to ST^PAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried bla _NDM-1 and one carried bla _NDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CC^PAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 13 CC^PAS1 strains, the oxa23 gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CC^PAS1 clone from the USA military. The carbapenem-resistant A. baumannii population in AMUH is very diverse, and indicates an endemic circulating population, including a region-specific lineage. A major mechanism for oxa23 dissemination in CC^PAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.

Antibiotic induced biofilm formation of novel multidrug resistant Acinetobacter baumannii ST2121 clone

The aim of this study was to identify antimicrobial resistance and virulence factor genes exhibited by multidrug resistant (MDR) Acinetobacter baumannii, to analyze biofilm formation and to investigate clonal subtypes of isolate. Whole genome sequencing was done by Illumina NovaSeq 6,000 platform and multilocus sequence typing (MLST) was performed by Oxford and Pasteur typing schemes. Influence of imipenem and levofloxacin on biofilm formation was investigated in 96-well plates at 3 replicates. The strain was found to carry OXA-23, OXA-51-like, AmpC and TEM-1 beta-lactamases. The sequence of the blaOXA-51-like gene has been identified as a blaOXA-66. According to Pasteur MLST scheme the strain displayed ST2 allelic profile. However, based on Oxford MLST scheme this strain represents the new ST2121, as the gdhB gene has a single allelic mutation namely, the gdhB-227. It was determined that MDR isolate carried bap, basABCDFGHIJ, csuA/BABCDE, bauABCDEF, plcD, pgaABCD, entE, barAB, ompA, abaIR, piT2EAFTE/AUBl, fimADT, cvaC, bfmR, bfmS virulence genes. In our study imipenem induced the highest biofilm formation at a concentration of 32 µg/ml and levofloxacin at a concentration of 16 µg/ml. In conclusion, we detected a new MDR A. baumannii ST2121 clone harboring blaOXA-66 gene that has been reported for the first time in Turkey.

Outbreak of Multidrug-Resistant Acinetobacter baumannii ST208 Producing OXA-23-Like Carbapenemase in a Children's Hospital in Shanghai, China

Aims: Acinetobacter baumannii is notorious for acquiring antibiotic resistance and causing nosocomial infections worldwide. This study aimed to investigate the prevalence and molecular characteristics of A. baumannii isolates obtained from inpatients and the intensive care unit (ICU) environment of a pediatric hospital in Shanghai, China. Methods: Between July 2017 and January 2018, a total of 88 A. baumannii isolates, including three obtained from ICU environmental specimens, were characterized by antibiotic susceptibility, multilocus sequence typing, and resistance genes. Results: Carbapenem-resistant A. baumannii (CRAB) isolates, which were resistant to all the antibiotics tested except colistin, accounted for 69.3% (61/88) of all isolates. Three sequence types (STs) were identified among the CRAB isolates, and the predominant clone was ST208 (93.4%, 57/61), which included three environmental isolates and 54 clinical isolates collected from ICU patients. Carbapenem-susceptible isolates, none of which was multidrug resistant (MDR), showed a more diverse genetic background with three known STs and 21 novel STs identified. Intrinsic bla_OXA-51-like and bla_AmpC were detected in all isolates, while bla_OXA-23-like was only detected in all CRAB isolates. ISAba1-bla_OXA-23-like, ISAba1-bla_OXA-51-like, and ISAba1-bla_AmpC were identified in 69.3% (all CRAB isolates), 0%, and 65.9% (58 CRAB isolates) of all isolates, respectively. Conclusions: A nosocomial outbreak of MDR A. baumannii ST208 producing OXA-23-like carbapenemase occurred, highlighting the necessity for strict infection control interventions in the ICU.

Molecular Epidemiology of Acinetobacter calcoaceticus-Acinetobacter baumannii Complex Isolated From Children at the Hospital Infantil de México Federico Gómez

The Acinetobacter calcoaceticus-baumannii (Acb) complex is regarded as a group of phenotypically indistinguishable opportunistic pathogens responsible for mainly causing hospital-acquired pneumonia and bacteremia. The aim of this study was to determine the frequency of isolation of the species that constitute the Acb complex, as well as their susceptibility to antibiotics, and their distribution at the Hospital Infantil de Mexico Federico Gomez (HIMFG). A total of 88 strains previously identified by Vitek 2®, 40 as Acinetobacter baumannii and 48 as Acb complex were isolated from 52 children from 07, January 2015 to 28, September 2017. A. baumannii accounted for 89.77% (79/88) of the strains; Acinetobacter pittii, 6.82% (6/88); and Acinetobacter nosocomialis, 3.40% (3/88). Most strains were recovered mainly from patients in the intensive care unit (ICU) and emergency wards. Blood cultures (BC) provided 44.32% (39/88) of strains. The 13.63% (12/88) of strains were associated with primary bacteremia, 3.4% (3/88) with secondary bacteremia, and 2.3% (2/88) with pneumonia. In addition, 44.32% (39/88) were multidrug-resistant (MDR) strains and, 11.36% (10/88) were extensively drug-resistant (XDR). All strains amplified the bla_OXA-51 gene; 51.13% (45/88), the bla_OXA-23 gene; 4.54% (4/88), the bla_OXA-24 gene; and 2.27% (2/88), the bla_OXA-58 gene. Plasmid profiles showed that the strains had 1–6 plasmids. The strains were distributed in 52 pulsotypes, and 24 showed identical restriction patterns, with a correlation coefficient of 1.0. Notably, some strains with the same pulsotype were isolated from different patients, wards, or years, suggesting the persistence of more than one clone. Twenty-seven sequence types (STs) were determined for the strains based on a Pasteur multilocus sequence typing (MLST) scheme using massive sequencing; the most prevalent was ST 156 (27.27%, 24/88). The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas I-Fb system provided amplification in A. baumannii and A. pittii strains (22.73%, 20/88). This study identified an increased number of MDR strains and the relationship among strains through molecular typing. The data suggest that more than one strain could be causing an infection in some patient. The implementation of molecular epidemiology allowed the characterization of a set of strains and identification of different attributes associated with its distribution in a specific environment.

Genomic analysis of two Acinetobacter baumannii strains belonging to two different sequence types (ST172 and ST25)

OBJECTIVES

Acinetobacter baumannii is an opportunistic nosocomial pathogen that is the main focus of attention in clinical settings owing to its intrinsic ability to persist in the hospital environment and its capacity to acquire determinants of resistance and virulence. Here we present the genomic sequencing, molecular characterisation and genomic comparison of two A. baumannii strains belonging to two different sequence types (STs), one sporadic and one widely distributed in our region.

METHODS

Whole-genome sequencing (WGS) of Ab42 and Ab376 was performed using Illumina MiSeq-I and the genomes were assembled with SPAdes. ARG-ANNOT, CARD-RGI, ISfinder, PHAST, PlasmidFinder, plasmidSPAdes and IslandViewer were used to analyse both genomes.

RESULTS

Genome analysis revealed that Ab42 belongs to ST172, an uncommon ST, whilst Ab376 belongs to ST25, a widely distributed ST. Molecular characterisation showed the presence of two antibiotic resistance genes in Ab42 and nine in Ab376. No insertion sequences were detected in Ab42, however 22 were detected in Ab376. Moreover, two prophages were found in Ab42 and three in Ab376. In addition, a CRISPR-cas type I-Fb and two plasmids, one of which harboured an AbGRI1-like island, were found in Ab376.

CONCLUSIONS

We present WGS analysis of twoA. baumannii strains belonging to two different STs. These findings allowed us to characterise a previously undescribed ST (ST172) and provide new insights to the widely studied ST25.

Insight into Molecular Epidemiology, Antimicrobial Resistance, and Virulence Genes of Extensively Drug-Resistant Acinetobacter baumannii in Thailand

Extensively drug-resistant Acinetobacter baumannii (XDR-AB) is a major threat to public health worldwide. A retrospective study for 27 XDR-AB isolates from four tertiary hospitals in Thailand was conducted. Beta-lactamase and virulence genes were characterized by PCR. The bla_ADC, bla_OXA-51, and bla_OXA-23 were detected in all isolates, whereas bla_PER-1 and bla_NDM-1 genes were present in 7.4% and 3.7% of isolates. All isolates had virulence genes, including genes in iron acquisition system, biofilm formation and secretion systems. The plasmids in XDR-AB belonged to GR2 (100%), GR6 (40.7%), and GR1 (7.4%). Multilocus sequence typing sequence types (STs) were further investigated. The data demonstrated that XDR-AB isolates had nine STs: ST195 (n = 4), ST208 (n = 4), ST368 (n = 1), ST451 (n = 5), ST457 (n = 2), ST1947 (n = 1), ST1166 (n = 7), including two novel STs namely ST1682 (n = 2) and ST1684 (n = 1). We observed that the majority ST1166 (25.9%) was associated with the prevalence of GR2 and GR6 plasmids and traU virulence gene. Genome-based single nucleotide polymorphism phylogenetic analysis of the isolates with two novel ST types indicated that the two isolates belonged to the international clone II (IC2) within the same cluster. In conclusion, our data showed the dissemination of XDR-AB isolates harbored virulence genes and antibiotic resistance genes among four hospitals in Thailand. The results highlighted the difficulty posed for the empirical treatment of the patients with the A. baumannii infection.

Comparative genomic analysis and multi-drug resistance differences of Acinetobacter baumannii in Chongqing, China

Introduction

Multidrug-resistance in Acinetobacter baumannii has emerged as a serious problem to public health. There is still a significant gap in the understanding of the multidrug-resistance and the genome diversity evolutionary process of A. baumannii in China, especially in the central and western regions.

Methods

Ten A. baumannii strains were collected from three hospitals in Chongqing, China. Whole-genome re-sequencing was used to obtain differences in genomic levels among strains. The diversity were determined by multi-locus sequence typing method, and investigate the genetic relationship between the ten strains and others by phylogenetic analysis. Comparative analysis focused on resistance genes related to insertions and deletions (InDels) and single-nucleotide polymorphisms (SNPs) was performed.

Results

The overall G+C% content was 39.05%~39.43%, the average sequencing depth was 273.95~428.99, and the alignment ratio of the sequencing data was 92.93%~99.27%. A total of 42 InDels and 11,387 SNPs were detected in the coding sequence region of the isolates. Phylogenetic tree shows that the 10 A. baumannii isolates were divided into four relative groups, and there exist the possibility of cross-regional spread pattern. A total number of 19 drug resistance genes had been found in each strain, and efflux pump-related genes accounted for the most. Only AacA4 underwent a change in InDel. Six types of drug resistance genes were found in the SNPs resistance gene-related loci, among which gene ANT(3’’)-II and QacE mutations were found in each strain.

Conclusion

In this study, the main mechanism of A. baumannii multi-drug resistance is due to the multi-drug efflux pump related genes. The point mutations at the SNPs sites of the six types of resistance genes are the main differences in A. baumannii between Chongqing and the eastern coastal areas of China.

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.

Whole-Genome Sequences of Five Acinetobacter baumannii Strains From a Child With Leukemia M2

Acinetobacter baumannii is an opportunistic pathogen and is one of the primary etiological agents of healthcare-associated infections (HAIs). A. baumannii infections are difficult to treat due to the intrinsic and acquired antibiotic resistance of strains of this bacterium, which frequently limits therapeutic options. In this study, five A. baumannii strains (810CP, 433H, 434H, 483H, and A-2), all of which were isolated from a child with leukemia M2, were characterized through antibiotic susceptibility profiling, the detection of genes encoding carbapenem hydrolyzing oxacillinases, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), adherence and invasion assays toward the A549 cell line, and the whole-genome sequence (WGS). The five strains showed Multidrug resistant (MDR) profiles and amplification of the bla_OXA-23 gene, belonging to ST758 and grouped into two PFGE clusters. WGS of 810CP revealed the presence of a circular chromosome and two small plasmids, pAba810CPa and pAba810CPb. Both plasmids carried genes encoding the Sp1TA system, although resistance genes were not identified. A gene-by-gene comparison analysis was performed among the A. baumannii strains isolated in this study and others A. baumannii ST758 strains (HIMFG and INCan), showing that 86% of genes were present in all analyzed strains. Interestingly, the 433H, 434H, and 483H strains varied by 8–10 single-nucleotide variants (SNVs), while the A2 and 810CP strains varied by 46 SNVs. Subsequently, an analysis using BacWGSTdb showed that all of our strains had the same resistance genes and were ST758. However, some variations were observed in relation to virulence genes, mainly in the 810CP strain. The genes involved in the synthesis of hepta-acylated lipooligosaccharides, the pgaABCD locus encoding poly-β-1-6-N-acetylglucosamine, the ompA gene, Csu pili, bap, the two-component system bfms/bfmR, a member of the phospholipase D family, and two iron-uptake systems were identified in our A. baumannii strains genome. The five A. baumannii strains isolated from the child were genetically different and showed important characteristics that promote survival in a hospital environment. The elucidation of their genomic sequences provides important information for understanding their epidemiology, antibiotic resistance, and putative virulence factors.

Antibiotic-resistant clones in Gram-negative pathogens: presence of global clones in Korea

Antibiotic resistance is a global concern in public health. Antibiotic-resistant clones can spread nationally, internationally, and globally. This review considers representative antibiotic-resistant Gram-negative bacterial clones-CTX-M- 15-producing ST131 in Escherichia coli, extended-spectrum ß-lactamase-producing ST11 and KPC-producing ST258 in Klebsiella pneumoniae, IMP-6-producing, carbapenem-resistant ST235 in Pseudomonas aeruginosa, and OXA-23-producing global clone 2 in Acinetobacter baumannii-that have disseminated worldwide, including in Korea. The findings highlight the urgency for systematic monitoring and international cooperation to suppress the emergence and propagation of antibiotic resistance.

Isolation and Whole-genome Sequence Analysis of the Imipenem Heteroresistant Acinetobacter baumannii Clinical Isolate HRAB-85

OBJECTIVES

Heteroresistance is a phenomenon in which there are various responses to antibiotics from bacterial cells within the same population. Here, we isolated and characterised an imipenem heteroresistant Acinetobacter baumannii strain (HRAB-85).

METHODS

The genome of strain HRAB-85 was completely sequenced and analysed to understand its antibiotic resistance mechanisms. Population analysis and multilocus sequence typing were performed.

RESULTS

Subpopulations grew in the presence of imipenem at concentrations of up to 64μg/mL, and the strain was found to belong to ST208. The total length of strain HRAB-85 was 4,098,585bp with a GC content of 39.98%. The genome harboured at least four insertion sequences: the common ISAba1, ISAba22, ISAba24, and newly reported ISAba26. Additionally, 19 antibiotic-resistance genes against eight classes of antimicrobial agents were found, and 11 genomic islands (GIs) were identified. Among them, GI3, GI10, and GI11 contained many ISs and antibiotic-resistance determinants.

CONCLUSIONS

The existence of imipenem heteroresistant phenotypes in A. baumannii was substantiated in this hospital, and imipenem pressure, which could induce imipenem-heteroresistant subpopulations, may select for highly resistant strains. The complete genome sequencing and bioinformatics analysis of HRAB-85 could improve our understanding of the epidemiology and resistance mechanisms of carbapenem-heteroresistant A. baumannii.

Molecular epidemiology of bla OXA-23 -producing carbapenem-resistant Acinetobacter baumannii in a single institution over a 65-month period in north China

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii poses a significant threat to hospitalized patients, as few therapeutic options remain. Thus, we investigated the molecular epidemiology and mechanism of resistance of carbapenem-resistant A.baumannii isolates in Beijing, China.

METHODS

Carbapenem-resistant A.baumannii isolates (n = 101) obtained between June 2009 and November 2014 were used. Multilocus sequence typing (MLST) and PCR assays for class C and D β-lactamase were performed on all isolates. S1 nuclease pulsed-field gel electrophoresis (PFGE) and Southern blot hybridization were performed to identify the resistance gene location.

RESULTS

All 101 A.baumannii isolates were highly resistant to frequently used antimicrobials, and were considered multidrug resistant. A total of 12 sequence types (STs) were identified, including 10 reported STs and 2 novel STs. Eighty-seven isolates were classified to clonal complex 92 (CC92), among which ST191 and ST195 were the most common STs. The bla _OXA-23 gene was positive in most (n = 95) of the A.baumannii isolates. Using S1-nuclease digestion PFGE and Southern blot hybridization, 3 patterns of plasmids carrying bla _OXA-23 were confirmed. ST191 and ST195 (both harboring bla _OXA-23 ) caused outbreaks during the study period, and this is the first report of outbreaks caused by ST191 and ST195 in north China.

CONCLUSION

bla _OXA-23 -producing A.baumannii ST191 and ST 195 isolates can disseminate in a hospital and are potential nosocomial outbreak strains. Surveillance of imipenem-resistant A.baumannii and antimicrobial stewardship should be strengthened.

OXA-23 and ISAba1-OXA-66 class D β-lactamases in Acinetobacter baumannii isolates from companion animals

Acinetobacter baumannii is recognised as a major pathogen of nosocomial infections that frequently show resistance to last-resort antimicrobials. To investigate whether A. baumannii from companion animals harbour carbapenem resistance mechanisms, 223 clinical isolates obtained from veterinary clinics between 2000 and 2013 in Germany were screened for carbapenem-non-susceptibility employing meropenem-containing Mueller-Hinton agar plates. Minimum inhibitory concentration (MIC) data were obtained using the VITEK^®2 system. Assignment to international clones (ICs) was done by multiplex PCR or repetitive sequence-based PCR employing the DiversiLab system. Clonality was studied using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Genes encoding carbapenemases and aminoglycoside-modifying enzymes were detected by PCR. In three samples from dogs, carbapenem-resistant A. baumannii carrying the bla_OXA-23 gene on plasmids and located on transposon Tn2008 were identified. The isolates belonged to sequence type ST1^P (clonal complex CC1/IC1/pulsotype II) and ST10^P (CC10/IC8/pulsotype IV) according to the Pasteur MLST scheme, and to ST231^Ox (CC109) and ST585^Ox (CC447) following the Oxford scheme. Insertion sequence ISAba1 was identified upstream of bla_OXA-66 in 58 A. baumannii isolates. MLST referred them to ST2^P (CC2/IC2/pulsotypes I and III), ST208^Ox, ST350^Ox and ST556^Ox (all CC118), respectively. PFGE suggested nosocomial spread of these highly related strains, which frequently demonstrated a multidrug-resistant phenotype, in one veterinary clinic. These data show that A. baumannii from companion animals reveal resistance determinants and clonal lineages of strains globally emerging in humans. This suggests an interspecies transmission and warrants molecular surveillance of A. baumannii in veterinary clinics to mitigate its further spread.

Molecular Epidemiology of Multi-Drug Resistant Acinetobacter baumannii Isolated in Shandong, China

Acinetobacter baumannii is an emerging nosocomial pathogen prevalent in hospitals worldwide. In order to understand the molecular epidemiology of multi-drug resistant (MDR) A. baumannii, we investigated the genotypes of A. baumannii isolated from 10 hospitals in Shandong, China, from August 2013 to December 2013, by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Antimicrobial resistance genes were analyzed by PCR and DNA sequencing. By PFGE analysis, we discovered 11 PFGE types in these 10 hospitals. By MLST, we assigned these isolates to 12 sequence types (STs), 10 of which belong to the cloning complex CC92, including the prevalent ST369, ST208, ST195, and ST368. Two new STs, namely ST794 and ST809, were detected only in one hospital. All isolates of the MDR A. baumannii were resistant to carbapenem, except 2 isolates, which did not express the bla_OXA-23 carbapenemase gene, indicating bla_OXA-23 is the major player for carbapenem resistance. We also discovered armA is likely to be responsible for amikacin resistance, and may play a role in gentamicin and tobramycin resistance. aac(3)-I is another gene responsible for gentamicin and tobramycin resistance. In summary, we discovered that the majority of the isolates in Shandong, China, were the STs belonging to the CC92. Besides, two new STs were detected in one hospital. These new STs should be further investigated for prevention of outbreaks caused by A. baumannii.

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen.

The First Outbreak Caused by Acinetobacter baumannii ST208 and ST195 in China

This study aimed to analyze the clinical characteristics of patients and molecular mechanisms of the first outbreak mainly caused by sequence types (STs) 208 multidrug resistant (MDR) Acinetobacter baumannii in China. A total of 10 clinical samples were collected from 5 patients who were involved in the outbreak. Bacterial identification and antibiotic sensitivity tests were performed by the VITEK-2 COMPACT automated system. MICs of tigecycline for clinical isolates were determined using broth microdilution. The clonal relatedness of A. baumannii clinical isolates in our local settings was determinated by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). A total of 7 A. baumannii strains were isolated and all were MDR strains; two of them were carbapenem-nonsusceptible strains. bla OXA-23 was the only acquired carbapenemase gene in the isolates. The isolates belonged to a single clonal pulsotype determined by PFGE and two sequences types (STs) determined by MLST. The isolates belonged to the globally disseminated clonal complex 92, among which ST195 and ST208 were the most common sequence types (71.43% and 28.57%). The outbreak was successfully controlled by stringent infection control measures, especially improving the hand hygiene compliance and enhancing antimicrobial stewardship. In conclusion, this is the first description of an outbreak caused mainly by A. baumannii of ST208 in China. Infection control measures should be strengthened when infection outbreaks in hospital.

Complete genome sequence of Acinetobacter baumannii XH386 (ST208), a multi-drug resistant bacteria isolated from pediatric hospital in China

Acinetobacter baumannii is an important bacterium that emerged as a significant nosocomial pathogen worldwide. The rise of A. baumannii was due to its multi-drug resistance (MDR), while it was difficult to treat multi-drug resistant A. baumannii with antibiotics, especially in pediatric patients for the therapeutic options with antibiotics were quite limited in pediatric patients. A. baumannii ST208 was identified as predominant sequence type of carbapenem resistant A. baumannii in the United States and China. As we knew, there was no complete genome sequence reproted for A. baumannii ST208, although several whole genome shotgun sequences had been reported. Here, we sequenced the 4087-kilobase (kb) chromosome and 112-kb plasmid of A. baumannii XH386 (ST208), which was isolated from a pediatric hospital in China. The genome of A. baumannii XH386 contained 3968 protein-coding genes and 94 RNA-only encoding genes. Genomic analysis and Minimum inhibitory concentration assay showed that A. baumannii XH386 was multi-drug resistant strain, which showed resistance to most of antibiotics, except for tigecycline. The data may be accessed via the GenBank accession number CP010779 and CP010780.

Transition of blaOXA-58-like to blaOXA-23-like in Acinetobacter baumannii Clinical Isolates in Southern China: An 8-Year Study

BACKGROUND

The prevalence of carbapenem-resistant Acinetobacter baumannii in hospitals has been increasing worldwide. This study aims to investigate the carbapenemase genes and the clonal relatedness among A. baumannii clinical isolates in a Chinese hospital.

METHODS

Carbapenemase genes and the upstream locations of insertion sequences were detected by polymerase chain reaction (PCR), and the clonal relatedness of isolates was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing.

RESULTS

A total of 231 nonduplicate carbapenemase gene-harboring A. baumannii clinical isolates recovered from Shenzhen People's Hospital, were investigated between 2002 and 2009. blaOXA-23-like, blaOXA-58-like, blaOXA-40-like, and ISAba1-blaOXA-51-like were identified in 119, 107, 1, and 4 isolates, respectively. IS1008-ΔISAba3, ISAba3, and ISAba1 were detected upstream of the blaOXA-58-like gene in 69, 35, and 3 isolates, respectively. All blaOXA-23-like genes but one had an upstream insertion of ISAba1. blaOXA-58-like was the most common carbapenemase gene in A.baumannii before 2008, thereafter blaOXA-23-like became rapidly prevalent and replaced blaOXA-58-like in 2009. The majority of blaOXA-58-like-carrying isolates showed lower level of resistance to imipenem and meropenem (minimum inhibitory concentrations (MICs), 1 μg/ml to 16 μg/ml), compared with the majority of blaOXA-23-like-carrying isolates (MICs, 16 μg/ml to 64 μg/ml for both imipenem and meropenem). All 231 blaOXA carbapenemase gene-harboring isolates belonged to 14 PFGE types (A-N), and three dominant clones A, J, and H accounted for 43.3%, 42.0%, and 8.2% of the tested isolates, respectively. Clone A (sequence type ST92/ST208) with blaOXA-58-like was the most prevalent before 2008. Clone H (ST229) with blaOXA-23-like became striking between 2007 and 2008. Clone J (ST381) with blaOXA-23-like rapidly spread and replaced clones A and H in 2009.

CONCLUSION

This study is the first to reveal that the distinct blaOXA-23-like-carrying A. baumannii ST381 displaced the previously prevalent blaOXA-58-like-carrying A. baumannii ST92/ST208, resulting in the rapidly increasing resistance to carbapenems in A. baumannii in Shenzhen People's Hospital in 2009.

Characterization of carbapenem-resistant Acinetobacter baumannii isolates in a Chinese teaching hospital

Carbapenem-resistant Acinetobacter baumannii (CRAB) presents a serious therapeutic and infection control challenge. In this study, we investigated the epidemiological and molecular differences of CRAB and the threatening factors for contributing to increased CRAB infections at a hospital in western China. A total of 110 clinical isolates of A. baumannii, collected in a recent 2-year period, were tested for carbapenem antibiotic susceptibility, followed by a molecular analysis of carbapenemase genes. Genetic relatedness of the isolates was characterized by multilocus sequence typing. Sixty-seven of the 110 isolates (60.9%) were resistant to carbapenems, 80.60% (54/67) of which carried the bla_OXA-23 gene. Most of these CRAB isolates (77.62%) were classified as clone complex 92 (CC92), and sequence type (ST) 92 was the most prevalent STs, followed by ST195, ST136, ST843, and ST75. One CRAB isolate of ST195 harbored plasmid pAB52 from a Chinese patient without travel history. This plasmid contains toxin–antitoxin elements related to adaptation for growth, which might have emerged as a common vehicle indirectly mediating the spread of OXA-23 in CRAB. Thus, CC92 A. baumannii carrying OXA-23 is a major drug-resistant strain spreading in China. Our findings indicate that rational application of antibiotics is indispensable for minimizing widespread of drug resistance.

Molecular Epidemiology and Characterization of Genotypes of Acinetobacter baumannii Isolates from Regions of South China

The aim of this study was to analyze the molecular epidemiologic characteristics of Acinetobacter baumannii. A total of 398 isolates were collected in 7 regions of South China from January to June of 2012. Drug sensitivity was tested toward 15 commonly used antibiotics; thus, 146 multi-drug-resistant strains (resistant to more than 7 drugs) were identified, representing 36.7% of all isolates. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for molecular subtyping. According to the PFGE results (with a cutoff of 70% similarity for the DNA electrophoretic bands), 146 strains were subdivided into 15 clusters, with cluster A being the largest (33.6%, distributed in all districts except Jiaxing). Cluster B was also widespread and included 14.4% of all strains. In addition, MLST results revealed 11 sequence types (ST), with ST208 being the most prevalent, followed by ST191 and ST729. Furthermore, 4 novel alleles and 6 novel STs were identified. Our results showed that multi-drug-resistant A. baumannii in South China shares the origin with other widespread strains in other countries. The nosocomial infections caused by A. baumannii have been severe in South China. Continuous monitoring and judicious antibiotic use are required.

In Vivo Selection of Pan-Drug Resistant Acinetobacter baumannii during Antibiotic Treatment

PURPOSE

Colistin resistance in Acinetobacter baumannii (A. baumannii) is mediated by a complete loss of lipopolysaccharide production via mutations in lpxA, lpxC, and lpxD gene or lipid A modifications via mutations in the pmrA and pmrB genes. However, the exact mechanism of therapy-induced colistin resistance in A. baumannii is not well understood.

MATERIALS AND METHODS

We investigated the genotypic and phenotypic changes that underlie pan-drug resistance mechanisms by determining differences between the alterations in extensively drug-resistant (XDR) A. baumannii (AB001 and AB002) isolates and a pan-drug resistant (PDR) counterpart (AB003) recovered from one patient before and after antibiotic treatment, respectively.

RESULTS

All three clinical isolates shared an identical sequence type (ST138), belonging to the global epidemic clone, clonal complex 92, and all produced OXA-23 carbapenemase. The PDR AB003 showed two genetic differences, acquisition of armA gene and an amino acid substitution (Glu229Asp) in pmrB gene, relative to XDR isolates. No mutations were detected in the pmrA, pmrC, lpxA, lpxC, or lpxD genes in all three isolates. In matrix-assisted laser desorption ionization-time of flight analysis, the three isolates commonly showed two major peaks at 1728 m/z and 1912 m/z, but peaks at 2034 m/z, 2157 m/z, 2261 m/z, and 2384 m/z were detected only in the PDR A. baumannii AB003 isolate.

CONCLUSION

Our results show that changes in lipid A structure via a mutation in the pmrB gene and acquisition of armA gene might confer resistance to colistin and aminoglycosides to XDR A. baumannii strains, resulting in appearance of a PDR A. baumannii strain of ST138.

Extensively drug-resistant Acinetobacter baumannii in a Thai hospital: a molecular epidemiologic analysis and identification of bactericidal Polymyxin B-based combinations

Background

Limited knowledge of the local molecular epidemiology and the paucity of new effective antibiotics has resulted in an immense challenge in the control and treatment of extensively drug-resistant (XDR) Acinetobacter baumannii infections in Thailand. Antimicrobial combination regimens may be the only feasible treatment option in such cases. We sought to characterize the local molecular epidemiology and assess the bactericidal activity of various antibiotics individually and in combination against XDR A. baumannii in a Thai hospital.

Methods

All XDR A. baumannii isolates from Thammasat University Hospital were collected between October 2010 and May 2011. Susceptibility testing was conducted according to reference broth dilution methods. Pulse-field gel electrophoresis was used to genotype the isolates. Carbapenemase genes were detected using polymerase chain reaction. In vitro testing of clinically-relevant concentrations of imipenem, meropenem, doripenem, rifampicin and tigecycline alone and in combination with polymyxin B was conducted using multiple combination bactericidal testing.

Results

Forty-nine polymyxin B-susceptible XDR A. baumannii isolates were identified. bla_OXA-23 and bla_OXA-51 genes were detected in all isolates. Eight clonally related clusters were identified, resulting in the initiation of several infection control measures. Imipenem, meropenem, doripenem, rifampicin, and tigecycline in combination with PB respectively, exhibited bactericidal killing in 100%, 100%, 98.0%, 100% and 87.8% isolates respectively at 24 hours.

Conclusion

Molecular epidemiologic analysis can aid the early detection of infection outbreak within the institution, resulting in the rapid containment of the outbreak. Imipenem/meropenem/rifampicin in combination with polymyxin B demonstrated consistent bactericidal effect against 49 bla_OXA-23-harbouring XDR A. baumannii clinical isolates, suggesting a role of combination therapy in the treatment of these infections.

Genetic Characterization of ST195 and ST365 Carbapenem-Resistant Acinetobacter baumannii Harboring blaOXA-23 in Guangzhou, China

We investigated the distribution of resistance genes and the clonal relationships among carbapenem-resistant Acinetobacter baumannii isolates from the intensive care unit wards of two hospitals in Guangzhou, China. From 2012 to 2013, 57 A. baumannii isolates were obtained from blood cultures from two hospitals in Guangzhou. The antibiotic resistance profiles were determined by using the Vitek2 system and Etest strips. PCR was used to detect the genes encoding OXA-type carbapenemases and metallo-β-lactamases and the presence of ISAba1 upstream of the bla(OXA-51-like) gene and the bla(OXA-23-like) gene. Multilocus sequence typing (MLST) and sequence-based typing of bla(OXA-51-like) genes (SBT-bla(OXA-51-like )genes) were performed to analyze the genetic relationship of the isolates. Among the 57 isolates, 46 were carbapenem-resistant A. baumannii (CRAB) isolates. The bla(OXA-51-like) gene was identified in all 57 isolates, while the bla(OXA-23-like) gene was present in all 46 CRAB isolates. The MLST analysis grouped the A. baumannii isolates into five existing sequence types (STs) and five new STs. Fifty-two isolates belonged to the worldwide spread of clonal complex 92 (CC92), among which ST195 and ST365 were the most common STs. The MLST data and SBT-bla(OXA-51-like) genes showed that all isolates harboring the major bla(OXA-51-like) alleles, such as bla(OXA-66), belonged to CC92.

Clonal diversity of Acinetobacter baumannii from diabetic patients in Saudi Arabian hospitals

Carbapenem-resistant Acinetobacter baumannii (CR-AB) represents a major health-care problem, causing high rates of morbidity and mortality. This study investigated the clonality of CR-AB isolated from diabetic patients from different regions in Saudi Arabia, as well as the relatedness of the β-lactamase genes. A total of 64 non-repetitive CR-AB clinical isolates were collected from 16 different regions in Saudi Arabia from intensive care patients. Isolates were identified phenotypically by the Vitek 2 compact system and genotypically by amplification of the bla OXA-51-like gene. The target sequences were amplified by PCR and the clonal diversity of the isolates was explored by PFGE. Resistance studies revealed that the prevalence of imipenem and meropenem resistance was 92 % and 96 %, respectively, while the vast majority of the isolates were susceptible to tigecycline and colistin. In addition, bla VIM and bla OXA-23 were the most prevalent genes in the isolates under investigation, while ISAba1 was the most dominant insertion sequence. PFGE results showed 13 clusters; clone H was dominant, comprising 20 isolates from four hospitals, followed by clones C and F, comprising 11 isolates each from three and six hospitals, respectively. Moreover, the current study signified the clonal diversity of CR-AB in Saudi Arabia and showed the ability of some clones to infect patients in many different cities.

Antibiotic resistance and phylogenetic characterization of Acinetobacter baumannii strains isolated from commercial raw meat in Switzerland

The spread of antibiotic-resistant bacteria through food has become a major public health concern because some important human pathogens may be transferred via the food chain. Acinetobacter baumannii is one of the most life-threatening gram-negative pathogens; multidrug-resistant (MDR) clones of A. baumannii are spreading worldwide, causing outbreaks in hospitals. However, the role of raw meat as a reservoir of A. baumannii remains unexplored. In this study, we describe for the first time the antibiotic susceptibility and fingerprint (repetitive extragenic palindromic PCR [rep-PCR] profile and sequence types [STs]) of A. baumannii strains found in raw meat retailed in Switzerland. Our results indicate that A. baumannii was present in 62 (25.0%) of 248 (CI 95%: 19.7 to 30.9%) meat samples analyzed between November 2012 and May 2013, with those derived from poultry being the most contaminated (48.0% [CI 95%: 37.8 to 58.3%]). Thirty-nine strains were further tested for antibiotic susceptibility and clonality. Strains were frequently not susceptible (intermediate and/or resistant) to third- and fourth-generation cephalosporins for human use (i.e., ceftriaxone [65%], cefotaxime [32%], ceftazidime [5%], and cefepime [2.5%]). Resistance to piperacillin-tazobactam, ciprofloxacin, colistin, and tetracycline was sporadically observed (2.5, 2.5, 5, and 5%, respectively), whereas resistance to carbapenems was not found. The strains were genetically very diverse from each other and belonged to 29 different STs, forming 12 singletons and 6 clonal complexes (CCs), of which 3 were new (CC277, CC360, and CC347). RepPCR analysis further distinguished some strains of the same ST. Moreover, some A. baumannii strains from meat belonged to the clonal complexes CC32 and CC79, similar to the MDR isolates responsible for human infections. In conclusion, our findings suggest that raw meat represents a reservoir of MDR A. baumannii and may serve as a vector for the spread of these pathogens into both community and hospital settings.

Multidrug-resistant Acinetobactor baumannii isolated from a traveler returned from Brunei

We report a case of multidrug-resistant (MDR) Acinetobactor baumannii isolates obtained from a traveler returned from Brunei. Whole-genome sequencing analysis revealed that the isolates harbored blaOxA-23 and armA. The minimum inhibitory concentrations of antibiotics against the strain were as follows: imipenem, 32 μg/ml; meropenem, 32 μg/ml; ciprofloxacin, 16 μg/ml; amikacin, ≧ 1024 μg/ml; arbekacin, ≧ 1024 μg/ml; aztreonam, 64 μg/ml; colistin, 4 μg/ml. A. baumannii harboring both blaOxA-23 and armA is rarely reported in Japan, and, to the best of our knowledge, this is the second report of A. baumannii harboring both resistant genes in Japan.

Population dynamics of an Acinetobacter baumannii clonal complex during colonization of patients

Acinetobacter baumannii has emerged as one of the leading pathogens causing hospital-acquired infection. The success of A. baumannii as a pathogen has to a large extent been attributed to its capacity to remodel its genome. Several major epidemic clonal complexes of A. baumannii spread across different health care facilities around the world, each of which contains a subset of diversified strains. However, little is known about the population dynamics during colonization of A. baumannii within hosts. Here, whole-genome sequencing was used to analyze population dynamics of A. baumannii strains isolated from a group of patients at different time points as well as from different sites of a particular patient. Seven out of nine of the sampled A. baumannii strains belonged to the international clone II (CC92 clonal complex). While the A. baumannii strains were found to be stable in three patients, there was a change of A. baumannii strains in one patient. Comparative genomic analysis revealed that the accessory genome of these strains contained a large set of virulence-encoding genes and these virulence factors might play a role in determining population dynamics. Microscale genome modification has been revealed by analysis of single nucleotide polymorphisms (SNPs) between A. baumannii strains isolated from the same patient. Parallel evolutionary traits have been observed during genome diversification when A. baumannii colonize in different patients. Our study suggested that both antibiotic usage and host environment might impose selective forces that drive the rapid adaptive evolution in colonizing A. baumannii.