New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital

Bacterial Resistance in Hospital-Acquired Infections Acquired in the Intensive Care Unit: A Systematic Review

PURPOSE

In this review we present the status of the prevalence of bacteria resistant to antibiotics and the main antibiotic resistance genes that are reported in infections acquired in intensive care units (ICU) around the world.

METHODS

A systematic review based on the PRISMA guide was carried out, from the Science Direct, Redalyc, Scopus, Hinari, Scielo, Dialnet, PLOS, ProQuest, Taylor, Lilacs and PubMed/Medline databases. Inclusion criteria of this review were original research study published in a scientific journal in a 10-year time span from 1 January 2017 and 30 April 2022.

RESULTS

A total of 1686 studies were identified, but only 114 studies were considered eligible for inclusion. Klebsiella pneumoniae and Escherichia coli resistant to carbapenems and producers of extended-spectrum β-lactamases (ESBL) are the most frequently isolated pathogens in ICUs in Asia, Africa and Latin America. The blaOXA and blaCTX were antibiotic resistance genes (ARG) most commonly reported in different geographic regions (in 30 and 28 studies, respectively). Moreover, multidrug-resistant (MDR) strains were reported in higher frequency in hospital-acquired infections. Reports of MDR strains vary between continents, with the majority of publications being in Asia and between countries, with Egypt and Iran being highlighted. There is a predominance of few bacterial clones with MDR phenotype, for example, clonal complex 5 Methicillin-Resistant Staphylococcus aureus (CC5-MRSA) circulates frequently in hospitals in the United States, clone ST23-K. pneumoniae is reported in India and Iran, and clone ST260 carbapenemase-producing P. aeruginosa in the United States and Estonia.

CONCLUSION

Our systematic review reveals that ESBL- and carbapenemase-producing K. pneumoniae and E. coli are the most problematic bacteria that are reported, mainly in tertiary hospitals in Asia, Africa, and Latin America. We have also found propagation of dominant clones with a high degree of MDR, becoming a problem due to its high capacity to cause morbidity, mortality and additional hospital costs.

Acinetobacter baumannii: Pathogenesis, virulence factors, novel therapeutic options and mechanisms of resistance to antimicrobial agents with emphasis on tigecycline

WHAT IS KNOWN AND OBJECTIVE

Acinetobacter baumannii is one of the most important nosocomial pathogens with the ability to cause infections such as meningitis, pneumonia, urinary tract, septicaemia and wound infections. A wide range of virulence factors are responsible for pathogenesis and high mortality of A. baumannii including outer membrane proteins, lipopolysaccharide, capsule, phospholipase, nutrient- acquisition systems, efflux pumps, protein secretion systems, quarom sensing and biofilm production. These virulence factors contribute in pathogen survival in stressful conditions and antimicrobial resistance.

COMMENT

According to the World Health Organization (WHO), A. baumannii is one of the most resistant pathogens of ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, A. baumannii, Pseudomonas aeruginosa and Enterobacter spp.). In recent years, resistance to a wide range of antibiotics in A. baumannii has significantly increased and the high emergence of extensively drug resistant (XDR) isolates is challenging. Among therapeutic antibiotics, resistance to tigecycline as a last resort antibiotic has become a global concern. Several mechanisms are involved in tigecycline resistance, the most important of which is RND (Resistance-Nodulation-Division) family efflux pumps overexpression. The development of new therapeutic strategies to confront A. baumannii infections has been very promising in recent years.

WHAT IS NEW AND CONCLUSION

In the present review we highlight microbiological and virulence traits in A. baumannii and peruse the tigecycline resistance mechanisms and novel therapeutic options. Among the novel therapeutic strategies we focus on combination therapy, drug repurposing, novel antibiotics, bacteriophage therapy, antimicrobial peptides (AMPs), human monoclonal antibodies (Hu-mAbs), nanoparticles and gene editing.

Genome Sequence of Acinetobacter baumannii Strain SHOU-Ab01, Isolated from Chinese Giant Salamander (Andrias davidianus) Liver

This report describes the complete genome sequence of Acinetobacter baumannii strain SHOU-Ab01, which was isolated from the liver of a Chinese giant salamander (Andrias davidianus). SHOU-Ab01 belonged to sequence type 40 (ST40), and its genome contained a circular chromosome (size, 3,891,862 bp) and two circular plasmids (sizes, 8,571 bp and 5,870 bp).

Characterization of Sequence Types and Mechanisms of Resistance to Tigecycline Among Acinetobacter baumannii Isolated from Children

The present study aimed to investigate the mechanisms of resistance to tigecycline and to determine sequence types of Acinetobacter baumannii isolates recovered from children, using the Multilocus Sequence Typing (MLST). A total of 74 A. baumannii isolates were recovered from patients at one of the children's hospital in Tehran, Iran. Antimicrobial susceptibility testing of the isolates was performed for different classes of antibiotics and minimum inhibitory concentrations of colistin and tigecycline were determined using broth microdilution method and E-test strips, respectively. The presence of ISAba1, AbaR, tet(39), and tetX and the expressions of adeB, adeG, and adeJ efflux pump genes were measured using Polymerase Chain Reaction (PCR) and quantitative real-time PCR (RT-PCR), respectively. The diversity of mutations across the regulatory genes of RND efflux pumps (adeRS, adeL, and adeN) and trm gene were determined using their PCR amplification and DNA sequencing in tigecycline-resistant isolates. In addition, STs of tigecycline-resistant isolates were determined using MLST method. Three A. baumannii isolates were resistant to tigecycline. Several amino acid substitutions were identified in AdeRS, AdeN, and Trm but no alteration was found in AdeL. Nevertheless, adeB, adeG, and adeJ overexpression were observed in 1, 2, and 1 isolates, respectively. The tigecycline-resistant isolates belonged to ST1720 and ST2285. This is the first study reporting on ST2285 in A. baumannii populations. Among 74 isolates, two tigecycline susceptible isolates carried tet(39) gene but no tetX gene was detected. We concluded that mutations in regulatory genes of RND efflux pumps and the trm gene may play some important role in A. baumannii resistance to tigecycline.

Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890

Acinetobacter baumannii is an opportunistic gram-negative bacteria typically attributed to hospital-associated infection. It could also become multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) during a short period. Although A. baumannii has been documented extensively, complete knowledge on the antibiotic-resistant mechanisms and virulence factors responsible for pathogenesis has not been entirely elucidated. This study investigated the drug resistance pattern and characterized the genomic sequence by de novo assembly of PDR A. baumannii strain VJR422, which was isolated from a catheter-sputum specimen. The results showed that the VJR422 strain was resistant to any existing antibiotics. Based on de novo assembly, whole-genome sequences showed a total genome size of 3,924,675-bp. In silico and conventional MLST analysis of sequence type (ST) of this strain was new ST by Oxford MLST scheme and designated as ST1890. Moreover, we found 10,915 genes that could be classified into 45 categories by Gene Ontology (GO) analysis. There were 1,687 genes mapped to 34 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The statistics from Clusters of Orthologous Genes (COG) annotation identified 3,189 genes of the VJR422 strain. Regarding the existence of virulence factors, a total of 59 virulence factors were identified in the genome of the VJR422 strain by virulence factors of pathogenic bacteria databases (VFDB). The drug-resistant genes were investigated by searching in the Comprehensive Antibiotic Resistance Database (CARD). The strain harbored antibiotic-resistant genes responsible for aminoglycoside, β-lactam-ring-containing drugs, erythromycin, and streptogramin resistance. We also identified resistance-nodulation-cell division (RND) and the major facilitator superfamily (MFS) associated with the antibiotic efflux pump. Overall, this study focused on A. baumannii strain VJR422 at the genomic level data, i.e., GO, COG, and KEGG. The antibiotic-resistant genotype and phenotype as well as the presence of potential virulence associated factors were investigated.

Epidemiological and genomic characteristics of Acinetobacter baumannii from different infection sites using comparative genomics

Background

Acinetobacter baumannii is a common nosocomial pathogen that poses a huge threat to global health. Owing to the severity of A. baumannii infections, it became necessary to investigate the epidemiological characteristics of A. baumannii in Chinese hospitals and find the reasons for the high antibiotic resistance rate and mortality. This study aimed to investigate the epidemiologic and genetic characteristics of A. baumannii isolated from patients with hospital acquired pneumonia (HAP), bloodstream infection (BSI) and urinary tract infection (UTI) in China and uncover potential mechanisms for multi-drug resistance and virulence characteristics of A. baumannii isolates.

Results

All isolates were classified into two primary clades in core gene-based phylogenetic relationship. Clonal complex 208 (CC208) mainly consisted of ST195 (32 %) and ST208 (24.6 %). CC208 and non-CC208 isolates had carbapenem resistance rates of 96.2 and 9.1 %, respectively. Core genes were enriched in ‘Amino acid transport and metabolism’, ‘Translation’, ‘Energy production and conversion’, ‘Transcription’, ‘Inorganic ion transport and metabolism’ and ‘Cell wall/membrane/envelope synthesis’. Most isolates possessed virulence factors related to polysaccharide biosynthesis, capsular polysaccharide synthesis and motility. Eleven isolates belong to ST369 or ST191 (oxford scheme) all had the virulence factor cap8E and it had a higher positive rate in UTI (35.3 %) than in BSI (18.9 %) and HAP (12.9 %). ABGRI1 antibiotic resistance islands were responsible for streptomycin, tetracycline and sulfonate resistance. The bla_OXA−23 gene was the most probable cause for carbapenem resistance, although the bla_OXA−66 gene with nonsynonymous SNPs (F82L, I129L) was not.

Conclusions

A. baumannii is a genomically variable pathogen that has the potential to cause a range of infectious diseases. There is high proportion of carbapenem resistance in isolates from all three infection sites (HAP, BSI and UTI), which can be attributed to the bla_OXA−23 gene. CC208 is the predominant clone in bla_OXA−23-carrying A. baumannii that should be monitored. Virulence factors involving bacteria motility and polysaccharide biosynthesis which are widespread in clinical A. baumannii strains deserve our attention.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07842-5.

WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia

Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and to identify multilocus sequence types (MLST). Eleven strains isolated from humans in Vietnam were sequenced, and their AMR genes and MLST were compared to published genomes of strains originating from Southeast Asia, i.e., Thailand (n = 49), Myanmar (n = 38), Malaysia (n = 11), Singapore (n = 4) and Taiwan (n = 1). Ten out of eleven Vietnamese strains were CRAb and were susceptible only to colistin. All strains harbored ant(3")-IIa, armA, aph(6)-Id and aph(3") genes conferring resistance to aminoglycosides, and blaOXA-51 variants and blaADC-25 conferring resistance to ß-lactams. More than half of the strains harbored genes that confer resistance to tetracyclines, sulfonamides and macrolides. The strains showed high diversity, where six were assigned to sequence type (ST)/2, and two were allocated to two new STs (ST/1411-1412). MLST analyses of 108 strains from Southeast Asia identified 19 sequence types (ST), and ST/2 was the most prevalent found in 62 strains. A broad range of AMR genes was identified mediating resistance to ß-lactams, including cephalosporins and carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides (e.g., ant(3")-IIa, aph(3")-Ib, aph(6)-Id, armA and aph(3')-Ia), phenicoles (e.g., catB8), tetracyclines (e.g., tet.B and tet.39), sulfonamides (e.g., sul.1 and sul.2), macrolides and lincosamide (e.g., mph.E, msr.E and abaF). MLST and core genome MLST (cgMLST) showed an extreme diversity among the strains. Several strains isolated from different countries clustered together by cgMLST; however, different clusters shared the same ST. Developing an action plan on AMR, increasing awareness and prohibiting the selling of antibiotics without prescription must be mandatory for this region. Such efforts are critical for enforcing targeted policies on the rational use of carbapenem compounds and controlling AMR dissemination and emergence in general.

Genomic features, whole-genome phylogenetic and comparative genomic analysis of extreme-drug-resistant ventilator-associated-pneumonia Acinetobacter baumannii strain in a Vietnam hospital

OBJECTIVES

Acinetobacter baumannii is a major cause of ventilator-associated-pneumonia (VAP) worldwide due to its impressive propensity to rapidly acquire resistance elements to a wide range of antibacterial agents. We sought to explore the genomic features of this pathogen from a sputum specimen of a VAP male patient.

METHODS

Whole genome analysis of A. baumannii DMS06670 included de novo assembly; functional annotation, whole-genome-phylogenetic analysis, antibiotics genes identification, prophage regions, virulent factor and pan-genome analysis.

RESULTS

Assembly of whole-genome shotgun sequences of strain DMS06670 yielded an estimated genome size of 3.8 Mb with Sequence Type 447. Functional annotation and orthologous protein cluster analysis identified several potential antibiotic resistance genes was conducted (with 1 novel gene), prophage regions, virulent factors. The clusters of orthologous groups (COGs) analysis in protein sequence of the A. baumannii strain was compared with the other five genomes showed that the orthologous protein clusters responsible for multi-drug exist inside highly antimicrobial resistant strains. Whole-genome phylogenetic and in silico MLST analysis revealed that this A. baumannii strain is in the same clade as strains LAC-4 and BJAB0715. Comparative analysis of 23 available genomes of A. baumannii revealed a pan-genome consisting of 15,883 genes.

CONCLUSION

Our findings provide insight into the virulence-associated genes and then compared with the genomes of other A. baumannii strains by calculation of ANI values and pan-genome analysis. Functional studies of these pathogens are required to validate these findings.

Carbapenemase Genes and Multidrug Resistance of Acinetobacter Baumannii: A Cross Sectional Study of Patients with Pneumonia in Southern Vietnam

Background: Acinetobacter baumannii (Ab) is an opportunistic bacterial pathogen found in hospital-acquired infections including nosocomial pneumonia, especially multidrug-resistant Ab. This study aims to survey the drug resistance profiles of Ab isolated from patients in Thong Nhat Dong Nai General Hospital and assess the relationship between genotypes and antibiotic resistance; Methods: Ninety-seven Ab strains isolated from 340 lower respiratory tract specimens among pneumonia patients were used to screen the most common local carbapenemase genes. Antimicrobial susceptibility testing results and demographic data were collected and minimum inhibitory concentrations (MIC) of colistin were also determined; Results: Over 80% and 90% of Ab strains were determined as carbapenem-resistant and multidrug-resistant (MDR), respectively. Most of the strains carried carbapenemase genes, including blaOXA-51, blaOXA-23-like, blaOXA-58-like, and blaNDM-1, with proportions of 97 (100%), 76 (78.4%), 10 (10.3%), 6 (6.2%), respectively. Amongst these genes, blaOXA-23-like was the only gene which significantly influenced the resistance (p < 0.0001); and Conclusions: The severity of Ab antibiotic resistance is urgent and specifically related to carbapenemase encoding genes. Therefore, screening of MDR Ab and carbapenemase for better treatment options is necessary.

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.