Molecular Methods for Identification of Acinetobacter Species by Partial Sequencing of the rpoB and 16S rRNA Genes

Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii group in Taiwan

Acinetobacter, particularly the Acinetobacter baumannii group, is a major cause of nosocomial infections, and carbapenem-resistant Acinetobacter spp. are important human pathogens. We collected 492 Acinetobacter spp. strains from two hospitals in Taiwan and classified them using MALDI-TOF MS and blaOXA-51-like PCR; 94.5% were A. baumannii, and 5.5% were non-A. baumannii (NAB). We confirmed their identity by rpoB gene sequencing of 239 randomly selected A. baumannii strains and all 27 NAB strains. Our analysis revealed that the rpoB alleles of OXA51-like-negative strains matched those of two NAB species, A. seifertii and A. nosocomialis, while all OXA51-like-positive strains matched A. baumannii, as per the Pasteur MLST scheme database. Among the 492 strains, 240 exhibited carbapenem resistance, including 237 carbapenem-resistant A. baumannii (CRAB) strains and three CR-NAB strains. All CRAB strains were positive for blaOXA-51-like; 72.6% also carried blaOXA-23-like, 22.8% carried blaOXA-24-like, 3.4% co-carried blaOXA-23-like+blaOXA-24-like, and 1.27% carried blaOXA-51-like alone. Among the three CR-NAB strains, one carried blaNDM-1, and two co-carried blaOXA-58-like+blaIMP. We also established a new multiplex PCR method for rapid screening of common capsular types (KL), which showed a difference between CRAB and carbapenem-susceptible A. baumannii (CSAB). KL2, KL10, KL22, and KL52 accounted for 76.6% of CRAB strains, whereas about half of the CSAB strains were other KL types. Of the remaining CSAB strains, KL14 was the most predominant type at 10.3%. We further conducted MLST Pasteur typing for 262 isolates and found that the carbapenemase genes were correlated with either ST or KL types. Additionally, KL types showed correlations with ST types, carbapenem resistance, and certain clinical records. Whole-genome sequencing of a blaNDM-1-carrying A. seifertii strain revealed a plasmid transferable via in vitro conjugation, suggesting A. seifertii may be a reservoir for NDM-1 plasmids.IMPORTANCECarbapenem-resistant Acinetobacter spp. have been identified by the World Health Organization as a top priority for new antibiotic development. We established a rapid KL-typing method for efficient screening of Acinetobacter baumannii strains to enable epidemiological surveillance and provide a foundation for effective infection control. Our investigation of the molecular epidemiology of the A. baumannii group isolates revealed the prevalence of carbapenemase genes and major KL types among CR and CS strains of A. baumannii and NAB. We identified an A. seifertii strain carrying a Ti-type conjugative operon on a small plasmid that harbored genes encoding the NDM-1 carbapenemase alongside genes conferring resistance to aminoglycosides and bleomycin and closely resembled sequences detected in A. soli and A. pittii in Taiwan and China, respectively, suggesting its potential for transmitting multidrug resistance and contributing to the spread of antimicrobial resistance.

Molecular detection of Bartonella quintana, Acinetobacter baumannii and Acinetobacter haemolyticus in Pediculus humanus lice in Nigeria, West Africa

The human lice Pediculus humanus is distributed worldwide but, it thrives and flourishes under conflict situations where people are forced to live in crowded unhygienic conditions. Molecular methods were used to identify and screen human lice for the DNA of pathogens of public health importance in an area that has been under insurgency related to religious and political conflicts with tens of thousands of internally displaced people (IDP). DNA of Bartonella quintana, Acinetobacter baumannii and Acinetobacter haemolyticus was detected in 18.3%, 40.0% and 1.7%, respectively, of human lice collected from children in Maiduguri, Nigeria. More body lice than head lice were positive for pathogen's DNA (64.3% vs. 44.4%; χ2  = 1.3, p = 0.33), but the difference was not significant. Two lice samples were found to harbour mixed DNA of B. quintana and A. baumannii. Phylogenetic analysis of the cytochrome b (cytb) gene sequences of the positive lice specimens placed them into clades A and E. This is the first report on the molecular identification of human lice and the detection of the DNA of pathogens of public health importance in lice in Nigeria, West Africa. The findings of this study will assist policy makers and medical practitioners in formulating a holistic healthcare delivery to IDPs.

Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain

Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16 s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502 bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed that Acinetobacter sp. strain P1 exhibited the highest homology with the Acinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.

Screening and Molecular Identification of Bacteria from the Midgut of Amphimallon solstitiale Larvae Exhibiting Antagonistic Activity against Bacterial Symbionts of Entomopathogenic Nematodes

Entomopathogenic nematodes (Rhabditida: Steinernematidae and Heterorhabditidae) are a group of organisms capable of infecting larvae of insects living in soil, including representatives of the family Scarabaeidae. Their insecticidal activity is related to the presence of symbiotic bacteria Xenorhabdus spp. or Photorhabdus spp. in the alimentary tract, which are released into the insect body, leading to its death caused by bacterial toxins and septicemia. Although the antibacterial activities of symbionts of entomopathogenic nematodes have been well described, there is insufficient knowledge of the interactions between these bacteria and microorganisms that naturally inhabit the alimentary tract of insects infested by nematodes. In this study, 900 bacterial strains isolated from midgut samples of Amphimallon solstitiale larvae were tested for their antagonistic activity against the selected five Xenorhabdus and Photorhabdus species. Cross-streak tests showed significant antibacterial activity of 20 isolates. These bacteria were identified as Bacillus [Brevibacterium] frigoritolerans, Bacillus toyonensis, Bacillus wiedmannii, Chryseobacterium lathyri, Chryseobacterium sp., Citrobacter murliniae, Enterococcus malodoratus, Paenibacillus sp., Serratia marcescens and Serratia sp. Since some representatives of the intestinal microbiota of A. solstitiale are able to inhibit the growth of Xenorhabdus and Photorhrhabdus bacteria in vitro, it can be assumed that this type of bacterial interaction may occur at certain stages of insect infection by Steinernema or Heterorhabditis nematodes.

In vitro and in vivo toxicity and antibacterial efficacy of melittin against clinical extensively drug-resistant bacteria

BACKGROUND

Melittin is one of the most studied antimicrobial peptides, and several in vitro experiments have demonstrated its antibacterial efficacy. However, there is evidence showing melittin has non-promising effects such as cytotoxicity and hemolysis. Therefore, concerns about unwanted collateral toxicity of melittin lie ahead in the path toward its clinical development. With these considerations, the present study aimed to fill the gap between in vitro and in vivo studies.

METHODS

In the first step, in vitro toxicity profile of melittin was assessed using cytotoxicity and hemolysis tests. Next, a maximum intraperitoneal (i.p.) sub-lethal dose was determined using BALB/c mice. Besides toxicity, antimicrobial efficacy of melittin against extensively drug-resistant (XDR) Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus (MRSA), and KPC-producing Klebsiella pneumonia (KPC-KP) pathogens were tested using both in vitro and in vivo methods.

RESULTS

Melittin showed extensive hemolysis (HD50 = 0.44 µg/mL), and cytotoxicity (IC50 = 6.45 µg/mL) activities with i.p. LD50 value of 4.98 mg/kg in BALB/c mice. In vitro antimicrobial evaluation showed melittin MIC range from 8 to 32 µg/mL for the studied pathogens. Treatment of infected mice with repeated sub-lethal doses of melittin (2.4 mg/kg) displayed no beneficial effect on their survival and peritoneal bacterial loads.

CONCLUSIONS

These results indicate that melittin at its safe dose could not exhibit antimicrobial activity, which hinders its application in clinical practice.

Bacteria from the Midgut of Common Cockchafer (Melolontha melolontha L.) Larvae Exhibiting Antagonistic Activity Against Bacterial Symbionts of Entomopathogenic Nematodes: Isolation and Molecular Identification

The mechanisms of action of the complex including entomopathogenic nematodes of the genera Steinernema and Heterorhabditis and their mutualistic partners, i.e., bacteria Xenorhabdus and Photorhabdus, have been well explained, and the nematodes have been commercialized as biological control agents against many soil insect pests. However, little is known regarding the nature of the relationships between these bacteria and the gut microbiota of infected insects. In the present study, 900 bacterial isolates that were obtained from the midgut samples of Melolontha melolontha larvae were screened for their antagonistic activity against the selected species of the genera Xenorhabdus and Photorhabdus. Twelve strains exhibited significant antibacterial activity in the applied tests. They were identified based on 16S rRNA and rpoB, rpoD, or recA gene sequences as Pseudomonas chlororaphis, Citrobacter murliniae, Acinetobacter calcoaceticus, Chryseobacterium lathyri, Chryseobacterium sp., Serratia liquefaciens, and Serratia sp. The culture filtrate of the isolate P. chlororaphis MMC3 L3 04 exerted the strongest inhibitory effect on the tested bacteria. The results of the preliminary study that are presented here, which focused on interactions between the insect gut microbiota and mutualistic bacteria of entomopathogenic nematodes, show that bacteria inhabiting the gut of insects might play a key role in insect resistance to entomopathogenic nematode pressure.

Accurate identification of clinically important Acinetobacter spp.: an update

Acinetobacter species have emerged as one of the most clinically important pathogens. The phenotypic techniques which are currently available are insufficient in accurately identifying and differentiating the closely related and clinically important Acinetobacter species. Here, we discuss the advantages and limitations of the conventional phenotypic methods, automated identification systems, molecular methods and MALDI-TOF in the precise identification and differentiation of Acinetobacter species. More specifically, several species of this genus are increasingly reported to be of high clinical importance. Molecular characterization such as of bla_OXA-51-like PCR together with rpoB sequencing has high discriminatory power over the conventional methods for Acinetobacter species identification, especially within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex.

Acinetobacter species are considered to be one of the most important pathogens and associated with increased mortality. The species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex have emerged as high priority pathogens, especially in intensive care units, thereby posing a challenge to infection management practices. However, identification of Acinetobacter to the species level is difficult. Clear differentiation among various Acinetobacter species with available standard biochemical methods and automated systems is challenging. Although various molecular methods are available, they are not regularly used in diagnostic laboratories. The advantages and disadvantages of different methods useful in the accurate identification of Acinetobacter species are discussed in this review.

Characteristics of invasive Acinetobacter species isolates recovered in a pediatric academic center

BACKGROUND

Acinetobacter species are associated with increasing mortality due to emerging drug-resistance. Pediatric Acinetobacter infections are largely undefined in developed countries and clinical laboratory identification methods do not reliably differentiate between members of the Acinetobacter calcoaceticus-baumannii complex, leading to improper identification. Therefore we aimed to determine risk factors for invasive Acinetobacter infections within an academic, pediatric setting as well as defining microbiologic characteristics of predominant strains.

METHODS

Twenty-four invasive Acinetobacter isolates were collected from 2009-2013. Comparative sequence analysis of the rpoB gene was performed coupled with phenotypic characterization of antibiotic resistance, motility, biofilm production and clinical correlation.

RESULTS

Affected patients had a median age of 3.5 years, and 71 % had a central catheter infection source. rpoB gene sequencing revealed a predominance of A. pittii (45.8 %) and A. baumannii (33.3 %) strains. There was increasing incidence of A. pittii over the study. Two fatalities occurred in the A. pittii group. Seventeen percent of isolates were multi-drug resistant. A pittii and A. baumannii strains were similar in motility, but A pittii strains had significantly more biofilm production (P value = 0.018).

CONCLUSIONS

A. pittii was the most isolated species highlighting the need for proper species identification. The isolated strains had limited acute mortality in children, but the occurrence of more multi-drug resistant strains in the future is a distinct possibility, justifying continued research and accurate species identification.