The natural environment as a reservoir of pathogenic and non-pathogenic Acinetobacter species

Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter

The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.

Recovery and genetic characterization of clinically-relevant ST2 carbapenem-resistant Acinetobacter baumannii isolates from untreated hospital sewage in Zhejiang Province, China

The global transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant and grave threat to human health. To investigate the potential relationship between hospital sewage and the transmission of CRAB within healthcare facilities, isolates of Acinetobacter spp. obtained from untreated hospital sewage samples were subjected to antimicrobial susceptibility tests, genome sequencing, and bioinformatic and phylogenetic tree analysis, and that data were matched with those of the clinical isolates. Among the 70 Acinetobacter spp. sewage isolates tested, A. baumannii was the most prevalent and detectable in 5 hospitals, followed by A. nosocomialis and A. gerneri. Worryingly, 57.14 % (40/70) of the isolates were MDR, with 25.71 % (18/70) being resistant to carbapenem. When utilizing the Pasteur scheme, ST2 was the predominant type among these CRAB isolates, with Tn2006 (ΔISAba1-blaOXA-23-ATPase-yeeB-yeeA-ΔISAba1) and Tn2009 (ΔISAba1-blaOXA-23-ATPase-hp-parA-yeeC-hp-yeeB-ΔISAba1) being the key mobile genetic elements that encode carbapenem resistance. Seven A. gerneri isolates which harbored Tn2008 (ISAba1-blaOXA-23 -ATPase) and the blaPER-1 gene were also identified. Besides, an A. soil isolate was found to exhibit high-level of meropenem resistance (MIC ≥128 mg/L) and harbor a blaNDM-1 gene located in a core genetic structure of ISAba125-blaNDM-1-ble-trpF-dsbC-cutA. To investigate the genetic relatedness between isolates recovered from hospital sewage and those collected from ICUs, a phylogenetic tree was constructed for 242 clinical isolates and 9 sewage isolates. The results revealed the presence of two evolutionary clades, each containing isolates from both ICU and sewage water, suggesting that CRAB isolates in untreated sewage water were also the transmission clones or closely related evolutionary isolates recoverable in hospital settings. Findings in this work confirm that hospital sewage is a potential reservoir of CRAB.

Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains

Acinetobacter baumannii, an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates. Consequently, data on environmental A. baumannii and other Acinetobacter species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 Acinetobacter isolates representing 6 different species sourced from aquatic environments in South Australia. All 10 isolates were phylogenetically distinct compared to clinical and other non-clinical Acinetobacter strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified pdif modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than A. baumannii, including carbapenemase oxa58, tetracycline resistance gene tet(39), and macrolide resistance genes msr(E)-mph(E). These pdif modules were located on plasmids with high sequence identity to those circulating in globally distributed A. baumannii ST1 and ST2 clones. The environmental A. baumannii isolate characterized here (SAAb472; ST350) did not possess any native plasmids; however, it could capture two clinically important plasmids (pRAY and pACICU2) with high transfer frequencies. Furthermore, A. baumannii SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental Acinetobacter species to acquire and disseminate clinically important antimicrobial resistance genes, underscoring the need for further research into the ecology and evolution of this important genus.IMPORTANCEAntimicrobial resistance (AMR) is a global threat to human, animal, and environmental health. Studying AMR in environmental bacteria is crucial to understand the emergence and dissemination of resistance genes and pathogens, and to identify potential reservoirs and transmission routes. This study provides novel insights into the genomic diversity and AMR potential of environmental Acinetobacter species. By comparing the genomes of aquatic Acinetobacter isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry pdif modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental A. baumannii isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental Acinetobacter species may serve as reservoirs and vectors of clinically important genes. Consequently, further research is warranted to comprehensively understand the ecology and evolution of this genus.

Epidemiology and antimicrobial resistance trends of Acinetobacter species in the United Arab Emirates: a retrospective analysis of 12 years of national AMR surveillance data

Introduction

Acinetobacter spp., in particular A. baumannii, are opportunistic pathogens linked to nosocomial pneumonia (particularly ventilator-associated pneumonia), central-line catheter-associated blood stream infections, meningitis, urinary tract infections, surgical-site infections, and other types of wound infections. A. baumannii is able to acquire or upregulate various resistance determinants, making it frequently multidrug-resistant, and contributing to increased mortality and morbidity. Data on the epidemiology, levels, and trends of antimicrobial resistance of Acinetobacter spp. in clinical settings is scarce in the Gulf Cooperation Council (GCC) and Middle East and North Africa (MENA) regions.

Methods

A retrospective 12-year analysis of 17,564 non-duplicate diagnostic Acinetobacter spp. isolates from the United Arab Emirates (UAE) was conducted. Data was generated at 317 surveillance sites by routine patient care during 2010-2021, collected by trained personnel and reported by participating surveillance sites to the UAE National AMR Surveillance program. Data analysis was conducted with WHONET.

Results

Species belonging to the A. calcoaceticus-baumannii complex were mostly reported (86.7%). They were most commonly isolated from urine (32.9%), sputum (29.0%), and soft tissue (25.1%). Resistance trends to antibiotics from different classes during the surveillance period showed a decreasing trend. Specifically, there was a significant decrease in resistance to imipenem, meropenem, and amikacin. Resistance was lowest among Acinetobacter species to both colistin and tigecycline. The percentages of multidrug-resistant (MDR) and possibly extensively drug-resistant (XDR) isolates was reduced by almost half between the beginning of the study in 2010 and its culmination in 2021. Carbapenem-resistant Acinetobacter spp. (CRAB) was associated with a higher mortality (RR: 5.7), a higher admission to ICU (RR 3.3), and an increased length of stay (LOS; 13 excess inpatient days per CRAB case), as compared to Carbapenem-susceptible Acinetobacter spp.

Conclusion

Carbapenem-resistant Acinetobacter spp. are associated with poorer clinical outcomes, and higher associated costs, as compared to carbapenem-susceptible Acinetobacter spp. A decreasing trend of MDR Acinetobacter spp., as well as resistance to all antibiotic classes under surveillance was observed during 2010 to 2021. Further studies are needed to explore the reasons and underlying factors leading to this remarkable decrease of resistance over time.

Draft genome sequence of Acinetobacter sp. AYS6, a potential plant growth-promoting endophyte

Here, we report the draft genome sequence of Acinetobacter sp. AYS6, an endophyte isolated from the roots of maize plant in Mafikeng, South Africa. The genome was 7,072,605 bp and exhibited a GC content of 45.6% and 3,654 genes with 3,539 coding sequences, 64 rRNA, 60 tRNAs, and 2 CRISPR.

Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin

Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.

The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate

Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus Acinetobacter beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.

Swine farm groundwater is a hidden hotspot for antibiotic-resistant pathogenic Acinetobacter

Acinetobacter is present in the livestock environment, but little is known about their antibiotic resistance and pathogenic species in the farm groundwater. Here we investigated antibiotic resistance of Acinetobacter in the swine farm groundwater (JZPG) and residential groundwater (JZG) of a swine farming village, in comparison to a nearby (3.5 km) non-farming village (WTG) using metagenomic and culture-based approaches. Results showed that the abundance of antibiotic resistome in some JZG and all JZPG (~3.4 copies/16S rRNA gene) was higher than that in WTG (~0.7 copies/16S rRNA gene), indicating the influence of farming activities on both groundwater types. Acinetobacter accounted for ~95.7% of the bacteria in JZG and JZPG, but only ~8.0% in WTG. They were potential hosts of ~95.6% of the resistome in farm affected groundwater, which includes 99 ARG subtypes against 23 antibiotic classes. These ARGs were associated with diverse intrinsic and acquired resistance mechanisms, and the predominant ARGs were tetracyclines and fluoroquinolones resistance genes. Metagenomic binning analysis elucidated that non-baumannii Acinetobacter including A. oleivorans, A. beijerinckii, A. seifertii, A. bereziniae and A. modestus might pose environmental risks because of multidrug resistance, pathogenicity and massive existence in the groundwater. Antibiotic susceptibility tests showed that the isolated strains were resistant to multiple antibiotics including sulfamethoxazole (resistance ratio: 96.2%), levofloxacin (42.5%), gatifloxacin (39.0%), ciprofloxacin (32.6%), tetracycline (32.0%), doxycycline (29.0%) and ampicillin (12.0%) as well as last-resort polymyxin B (31.7%), colistin (24.1%) and tigecycline (4.1%). The findings highlight potential prevalence of groundwater-borne antibiotic-resistant pathogenic Acinetobacter in the livestock environment.

A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water

PURPOSE OF REVIEW

Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies.

RECENT FINDINGS

Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20 years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.

Whole-Genome Sequencing Snapshot of Clinically Relevant Carbapenem-Resistant Gram-Negative Bacteria from Wastewater in Serbia

Wastewater (WW) is considered a source of antibiotic-resistant bacteria with clinical relevance and may, thus, be important for their dissemination into the environment, especially in countries with poor WW treatment. To obtain an overview of the occurrence and characteristics of carbapenem-resistant Gram-negative bacteria (CR-GNB) in WW of Belgrade, we investigated samples from the four main sewer outlets prior to effluent into international rivers, the Sava and the Danube. Thirty-four CR-GNB isolates were selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS). AST revealed that all isolates were multidrug-resistant. WGS showed that they belonged to eight different species and 25 different sequence types (STs), seven of which were new. ST101 K. pneumoniae (bla_CTX-M-15/bla_OXA-48) with novel plasmid p101_srb was the most frequent isolate, detected at nearly all the sampling sites. The most frequent resistance genes to aminoglycosides, quinolones, trimethroprim-sulfamethoxazole, tetracycline and fosfomycin were aac(6')-Ib-cr (55.9%), oqxA (32.3%), dfrA14 (47.1%), sul1 (52.9%), tet(A) (23.5%) and fosA (50%), respectively. Acquired resistance to colistin via chromosomal-mediated mechanisms was detected in K. pneumoniae (mutations in mgrB and basRS) and P. aeruginosa (mutation in basRS), while a plasmid-mediated mechanism was confirmed in the E. cloacae complex (mcr-9.1 gene). The highest number of virulence genes (>300) was recorded in P. aeruginosa isolates. Further research is needed to systematically track the occurrence and distribution of these bacteria so as to mitigate their threat.

Biodegradation of Oil by a Newly Isolated Strain Acinetobacter junii WCO-9 and Its Comparative Pan-Genome Analysis

Waste oil pollution and the treatment of oily waste present a challenge, and the exploitation of microbial resources is a safe and efficient method to resolve these problems. Lipase-producing microorganisms can directly degrade waste oil and promote the degradation of oily waste and, therefore, have very significant research and application value. The isolation of efficient oil-degrading strains is of great practical significance in research into microbial remediation in oil-contaminated environments and for the enrichment of the microbial lipase resource library. In this study, Acinetobacter junii WCO-9, an efficient oil-degrading bacterium, was isolated from an oil-contaminated soil using olive oil as the sole carbon source, and its enzyme activity of ρ-nitrophenyl decanoate (ρ-NPD) decomposition was 3000 U/L. The WCO-9 strain could degrade a variety of edible oils, and its degradation capability was significantly better than that of the control strain, A junii ATCC 17908. Comparative pan-genome and lipid degradation pathway analyses indicated that A. junii isolated from the same environment shared a similar set of core genes and that the species accumulated more specific genes that facilitated resistance to environmental stresses under different environmental conditions. WCO-9 has accumulated a complete set of oil metabolism genes under a long-term oil-contamination environment, and the compact arrangement of abundant lipase and lipase chaperones has further strengthened the ability of the strain to survive in such environments. This is the main reason why WCO-9 is able to degrade oil significantly more effectively than ATCC 17908. In addition, WCO-9 possesses a specific lipase that is not found in homologous strains. In summary, A. junii WCO-9, with a complete triglyceride degradation pathway and the specific lipase gene, has great potential in environmental remediation and lipase for industry.

Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta

Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes bla_CTX-M, bla_IMP, and bla_TEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in bla_CTX-M and bla_TEM copy numbers and a mean increase in bla_IMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.

Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water

In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.

A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains

Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.

Specific Enriched Acinetobacter in Camellia Weevil Gut Facilitate the Degradation of Tea Saponin: Inferred from Bacterial Genomic and Transcriptomic Analyses

Beneficial gut bacteria can enhance herbivorous arthropod adaptation to plant secondary compounds (PSMs), and specialist herbivores provide excellent examples of this. Tea saponin (TS) of Camellia oleifera is triterpenoids toxic to seed-feeding weevil pest, Curculio chinensis (CW). Previous studies disclosed that Acinetobacter, which was specific enriched in the CW's gut, was involved in helping CW evade TS toxicity of C. oleifera. However, it is still not clear whether Acinetobacter is associated with other anti-insect compounds, and the molecular mechanism of Acinetobacter degradation of TS has not been clarified. To address these questions, we explored the relationship between host plant toxin content and Acinetobacter of CW gut bacteria. Results demonstrated that TS content significantly affected the CW gut microbiome structure and enriched bacteria functional for TS degradation. We further isolated Acinetobacter strain and conducted its genome and transcriptome analyses for bacterial characterization and investigation on its role in TS degradation. Biological tests were carried out to verify the ability of the functional bacterium within CW larvae to detoxify TS. Our results showed that TS-degrading bacteria strain (Acinetobacter sp. AS23) genome contains 47 genes relating to triterpenoids degradation. The AS23 strain improved the survival rate of CW larvae, and the steroid degradation pathway could be the key one for AS23 to degrade TS. This study provides the direct evidence that gut bacteria mediate adaptation of herbivorous insects to phytochemical resistance. IMPORTANCE Microorganism is directly exposed to the plant toxin environment and play a crucial third party in herbivores gut. Although previous studies have proved the existence of gut bacteria that help CWs degrade TS, the specific core flora and its function have not been explored. In this study, we investigated the correlation between the larva gut microbiome and plant secondary metabolites. Acinetobacter genus was the target flora related to TS degradation. There were many terpenoids genes in Acinetobacter sp. AS23 genome. Results of transcriptome analysis and biological tests suggested that steroid degradation pathway be the key pathway of AS23 to degrade TS. This study not only provides direct evidence that gut microbes mediate the rapid adaptation of herbivorous insects to phytochemical resistance, but also provides a theoretical basis for further research on the molecular mechanism of intestinal bacteria cooperating with pests to adapt to plant toxins.

Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station

BACKGROUND

Monitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS.

RESULTS

Here, we report how ISS-associated A. pittii (n = 20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n = 291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host-associated ISS metagenomes, we observed that viable A. pittii is increasing in relative abundance and therefore potentially exhibiting succession, being identified in >2X more metagenomic samples in back-to-back missions. ISS strains additionally contain functions that enable them to survive in harsh environments, including the transcriptional regulator LexA. Via a genome-wide association study, we identified a high level of mutational burden in methionine sulfoxide reductase genes relative to the most closely related Earth strains.

CONCLUSIONS

Overall, these results indicated a step forward in understanding how microorganisms might evolve and alter their antibiotic resistance phenotype in extreme, resource-limited, human-built environments. Video Abstract.

Deciphering the core seed endo-bacteriome of the highland barley in Tibet plateau

Highland barley (Hordeum vulgare var. nudum (L.) Hook.f., qingke) has unique physical and chemical properties and good potential for industrial applications. As the only crop that can be grown at high altitudes of 4200-4500 m, qingke is well adapted to extreme habitats at high altitudes. In this study, we analysed the seed bacterial community of 58 genotypes of qingke grown in different regions of Tibet, including qingke landraces, modern cultivars, and winter barley varieties, and characterised endophytic bacterial communities in seeds from different sources and the core endo-bacteriome of qingke. This study aim to provide a reference for the application of seed endophytes as biological inoculants for sustainable agricultural production and for considering microbe-plant interactions in breeding strategies. A total of 174 qingke seed samples from five main agricultural regions in Tibet were collected and subjected to investigation of endophytic endo-bacteriome using high-throughput sequencing and bioinformatics approaches. The phyla of endophytic bacteria in qingke seeds from different sources were similar; however, the relative proportions of each phylum were different. Different environmental conditions, growth strategies, and modern breeding processes have significantly changed the community structure of endophytic bacteria in seeds, among which the growth strategy has a greater impact on the diversity of endophytic bacteria in seeds. Seeds from different sources have conserved beneficial core endo-bacteriome. The core endo-bacteriome of qingke seeds dominated by Enterobacteriaceae may maintain qingke growth by promoting plant growth and assisting plants in resisting pests and diseases. This study reveals the core endo-bacteriome of qingke seeds and provides a basis for exploiting the endophytic endo-bacteriome of qingke seeds.

Antibiotic resistance and carriage class I integron in clinical isolates of Acinetobacter baumannii from Al Muthanna, Iraq

The goal of this work was to systematically characterize and detect class 1, 2, and 3 integrons with many antibiotic resistance A. baumannii strains collected from a clinical environment in Iraq's Al-Muthanna hospitals. In this investigation, 24 non-replicated clinical strains of A. baumannii were evaluated using Chrome agar as a selective medium and PCR of the rplB gene. The clonal relatedness of the isolates to class 1 integron was evaluated using a PCR technique. The prevalence of class 1 integron was detected by PCR in only 12 clones of A. baumannii followed by HinfI digestion analysis showing three identical bands at 160 bp, 1350 bp, and 870 bp. In addition, PCR sequencing confirmed the presence of gene cassette arrays consisting of aacA4-catB8-aadA1 (100%) in class 1 integron. The sequence analysis of the integron shows 97.87 identity with A. baumannii isolates from Australia (GenBank accession number CP054302) among A. baumannii isolates. The blast analysis of this class I integron showed that the presence of the intI1, aacA4-catB8-aadA1 genes can considerably boost the acquisition of MDR phenotypes in A. baumannii isolates. We concluded that antibiotics of many types are widely used. The presence of integrons in A. baumannii is concerning for public health. In the clinical setting, it appears that the class 1 integron can be used as a predictive biomarker for the presence of MDR phenotypes. In these bacteria, however, the integron does not possess carbapenemases genes.

What on earth? The impact of digestates and composts from farm effluent management on fluxes of foodborne pathogens in agricultural lands

The recycling of biomass is the cornerstone of sustainable development in the bioeconomy. In this context, digestates and composts from processed agricultural residues and biomasses are returned to the soil. Whether or not the presence of pathogenic microorganisms in these processed biomasses is a threat to the sustainability of the current on-farm practices is still the subject of debate. In this review, we describe the microbial pathogens that may be present in digestates and composts. We then provide an overview of the current European regulation designed to mitigate health hazards linked to the use of organic fertilisers and soil improvers produced from farm biomasses and residues. Finally, we discuss the many factors that underlie the fate of microbial pathogens in the field. We argue that incorporating land characteristics in the management of safety issues connected with the spreading of organic fertilisers and soil improvers can improve the sustainability of biomass recycling.

Prevalence, genetic diversity, antibiotic resistance and biofilm formation of Acinetobacter baumannii isolated from urban environments

AIM

Acinetobacter baumannii is a well-known nosocomial pathogen that has been isolated from different clinical sources. This pathogen also causes community-acquired infections, with mortality rates as high as 64%. The exact natural habitat of this bacterium is still unknown. In this study, we investigated the prevalence of A. baumannii in diverse soil and high-touch surface samples collected from a university campus, malls, parks, hypermarkets and produce markets, roundabout playground slides, and bank ATMs.

METHODS AND RESULTS

All obtained isolates were characterized for their antibiotic susceptibility, biofilm formation capacities, and were typed by multi-locus sequence analysis. A total of 63 A. baumannii isolates were recovered, along with 46 A. pittii and 8 A. nosocomialis isolates. Sequence typing revealed that 25 A. baumannii isolates are novel strains. Toilets and sink washing basins were the most contaminated surfaces, accounting for almost 50% of the recovered isolates. A number of A. baumannii (n=10), A. pittii (n=19) and A. nosocomialis (n=5) isolates were recovered from handles of shopping carts and baskets. The majority of isolates were strong biofilm formers and 4 exhibited a multi-drug resistant (MDR) phenotype.

CONCLUSIONS

Our study is the first to highlight community restrooms and shopping carts as potential reservoirs for pathogenic Acinetobacter species. Further studies are required to identify the reasons associated with the occurrence of A. baumannii inside restrooms. Proper disinfection of community environmental surfaces and spreading awareness about the importance of hand hygiene may prevent the dissemination of pathogenic bacteria within the community.

SIGNIFICANCE AND IMPACT OF STUDY

Serious gaps remain in our knowledge of how A. baumannii spreads to cause disease. This study will advance our understanding of how this pathogen spreads between healthcare and community environments. In addition, our findings will help healthcare decision makers implement better measures to control and limit further transmission of A. baumannii.

Characterization of carbapenem resistance in environmental samples and Acinetobacter spp. isolates from wastewater and river water in Poland

The aim of this study was to analyze the prevalence of carbapenem resistance genes in Acinetobacter spp. isolated from wastewater in a municipal WWTP and to determine their spread from treated wastewater to river water with the use of conventional and molecular microbiology methods (qualitative and quantitative PCR and metagenomic analysis). Samples of untreated and treated wastewater and samples of river water obtained upstream and downstream from the wastewater discharge point were collected in 3 seasons (February, June, and September) of 2019. Acinetobacter spp. isolates were obtained by the culture method on the CHROMagar™ Acinetobacter medium. Additionally, environmental DNA was extracted from the samples for metagenomic and qPCR analyses. The presence of beta-lactam resistance genes (Ambler class B and D), insertion sequence ISAba1, and class I, II, and III integron-integrase genes was determined, and the bacterial taxonomic structure and wastewater and river samples was analyzed. Out of the 301 isolates obtained on the CHROMagar™ Acinetobacter medium, 258 belonged to the genus Acinetobacter, including 21 isolates that were identified as Acinetobacter baumannii. The highest number of Acinetobacter spp. and A. baumannii isolates were obtained from wastewater and river water samples collected in June and September. The ISAba1/bla_OXA-51 complex was identified in 13 isolates, which confirms the occurrence of carbapenem-resistance isolates in the analyzed samples. The number of Acinetobacter isolates carrying antibiotic resistance genes (ARGs) increased in river water samples collected downstream from the wastewater discharge point (48 out of 258 isolates - 18.6%) compared to river water samples collected upstream from the wastewater discharge point (34 out of 258 isolates - 13.2%), which suggests that WWTP is a source of pollution in the natural environment. The conducted research provides evidence that bacteria of the genus Acinetobacter may spread alarming beta-lactam resistance in the environment and, therefore, pose a serious epidemiological threat.

Bioactivity and Chemical Profile of Rubus idaeus L. Leaves Steam-Distillation Extract

The leaves of Rubus idaeus L., a by-product of the fruit food industry, are a known source of bioactive molecules, although the chemical composition has only been partially investigated. The main objective of this study was to examine the biological activities and the chemical composition of the extract of leaves of R. idaeus (RH), obtained by steam distillation (SD). The antioxidant capacity; the total phenolic content (TPC); the cytotoxic activity against tumor cell lines; and the antibacterial activity, in addition to the study of the chemical fingerprinting, carried out by Gas/Chromatography-Mass-Spectrometry (GC/MS) and Headspace (HS)-GC/MS, were established. The extract showed a strong antioxidant capacity and a modest antibacterial activity against two bacterial strains, as well as significant cytotoxic activity against tumor cell lines (Caco-2 and HL60) and being proliferative on healthy cells. Many of the GC-identified volatile molecules (1,8-cineol, β-linalool, geraniol, caryophyllene, τ-muurolol, citral, α-terpineol, 3- carene, α-terpinen-7-al, etc.) can explain most of the biological properties exhibited by the extract of R. idaeus L. The high biological activity of the RH and the high compatibility with the various matrices suggest good prospects for this extract, both in the food and cosmetic fields or in dietary supplements for improving human health.

In vitro study to evaluate the antimicrobial activity of various multifunctional cosmetic ingredients and chlorphenesin on bacterial species at risk in the cosmetic industry

AIMS

We evaluated the activity of the preservative chlorphenesin and of four antimicrobial cosmetic multifunctional ingredients against various strains of gram-negative and gram-positive human opportunistic pathogens.

METHODS AND RESULTS

Growth kinetics, modelling growth parameters and statistical analyses enabled comparing bacterial behaviour in the presence and in the absence of the compound. Whatever compound tested (i.e. chlorphenesin, phenylpropanol, hexanediol, ethylhexylglycerin, hydroxyacetophenone) and strain origin (i.e. clinical versus industrial), the growth of 42 strains belonging to Acinetobacter spp., Burkholderia cepacia complex and Stenotrophomonas maltophilia, was totally inhibited. On the opposite all of the P. aeruginosa strains (n = 13) as well as 4 and 6 out of 10 strains of Pluralibacter gergoviae grew in the presence of chlorphenesin and ethylhexylglycerin, respectively. Some P. gergoviae and Staphylococcus hominis strains withstand hydroxyacetophenone. Within a species, the different strains show variable latency phase, growth rate (r) and carrying capacity (K). They can be similar, lower or higher than those measured in control conditions.

CONCLUSIONS

Data showed differences in the antimicrobial activity of compounds. Upon exposure, strains differed in their behaviour between and within species. Whatever species and strains, compound sensitivity could not be related to antibiotic resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

Most multifunctional ingredients showed significant antimicrobial properties against the wide panel of species and strains evaluated. This will help adjusting preservation strategies in the cosmetic industry.

Effect of Fe3+ on the sludge properties and microbial community structure in a lab-scale A2O process

During biological wastewater treatment, ferric salt (Fe³⁺) usually serves as an inorganic flocculant to improve the agglomeration and sedimentation of suspended solids, and thus the removal efficiency of pollutants to meet the increasing strictly regulated wastewater discharge standards. In this study, we investigated the effects of Fe³⁺ on the removal efficiencies of pollutants, sludge properties, dominant flora and metabolic pathways of bacterial community in a classical anaerobic-anoxic-oxic (A²O) process. The results showed that a Fe³⁺ concentration lower than 10 mg·L^-1 could improve the removal efficiencies of chemical oxygen demand (COD) and total nitrogen (TN), while an inhibition effect was exerted at concentration higher than 10 mg·L^-1. The maximum removal efficiencies of COD and TN were 97% and 89%, respectively, under the critical Fe³⁺ concentration of 10 mg·L^-1. Total phosphorous (TP) removal was constantly positively correlated with Fe³⁺ concentration, due to the enhanced adsorption of phosphorus on activated sludge with the increase of surface roughness. Thauera displayed the highest relative abundance, and certain bacteria in Proteobacteria, Dehloromonas and Candidatus-Competibacter exhibited good adaptability to high concentration of Fe³⁺. In the context of metabolic collaterals, the most abundant functional gene families were identified to be Carbohydrate Metabolism, Amino Acid Metabolism, Cell Motility, Membrane Transport, and Replication and Repair. This study provides an extensive mechanistic insight into the impact of Fe³⁺ on the A²O process, which is of fundamental significance to exploit the contributions of inorganic salts to biological wastewater treatment.

Draft Genome Sequence of Environmental Isolate Acinetobacter nosocomialis U20-HoPe-S34-3 from Germany

The draft genome sequence of Acinetobacter nosocomialis U20-HoPe-S34-3, isolated from soil sampled from the banks of the river Holtemme in Germany, is provided. The strain has an average nucleotide identity of 98.3% to the type strain of the species.

Antibiofilm and antivirulence potential of silver nanoparticles against multidrug-resistant Acinetobacter baumannii

We aimed to isolate Acinetobacter baumannii (A. baumannii) from wound infections, determine their resistance and virulence profile, and assess the impact of Silver nanoparticles (AgNPs) on the bacterial growth, virulence and biofilm-related gene expression. AgNPs were synthesized and characterized using TEM, XRD and FTIR spectroscopy. A. baumannii (n = 200) were isolated and identified. Resistance pattern was determined and virulence genes (afa/draBC, cnf1, cnf2, csgA, cvaC, fimH, fyuA, ibeA, iutA, kpsMT II, PAI, papC, PapG II, III, sfa/focDE and traT) were screened using PCR. Biofilm formation was evaluated using Microtiter plate method. Then, the antimicrobial activity of AgNPs was evaluated by the well-diffusion method, growth kinetics and MIC determination. Inhibition of biofilm formation and the ability to disperse biofilms in exposure to AgNPs were evaluated. The effect of AgNPs on the expression of virulence and biofilm-related genes (bap, OmpA, abaI, csuA/B, A1S_2091, A1S_1510, A1S_0690, A1S_0114) were estimated using QRT-PCR. In vitro infection model for analyzing the antibacterial activity of AgNPs was done using a co-culture infection model of A. baumannii with human fibroblast skin cell line HFF-1 or Vero cell lines. A. baumannii had high level of resistance to antibiotics. Most of the isolates harbored the fimH, afa/draBC, cnf1, csgA and cnf2, and the majority of A. baumannii produced strong biofilms. AgNPs inhibited the growth of A. baumannii efficiently with MIC ranging from 4 to 25 µg/ml. A. baumannii showed a reduced growth rate in the presence of AgNPs. The inhibitory activity and the anti-biofilm activity of AgNPs were more pronounced against the weak biofilm producers. Moreover, AgNPs decreased the expression of kpsMII , afa/draBC,bap, OmpA, and csuA/B genes. The in vitro infection model revealed a significant antibacterial activity of AgNPs against extracellular and intracellular A. baumannii. AgNPs highly interrupted bacterial multiplication and biofilm formation. AgNPs downregulated the transcription level of important virulence and biofilm-related genes. Our findings provide an additional step towards understanding the mechanisms by which sliver nanoparticles interfere with the microbial spread and persistence.

Comparative phylo-pangenomics reveals generalist lifestyles in representative Acinetobacter species and proposes candidate gene markers for species identification

Acinetobacter species have the potential to invade and colonize immunocompromised patients, therefore being well-known as opportunistic pathogens. Among these bacteria, the species of the Acinetobacter calcoaceticus-Acinetobacter baumannii "complex" (Acb members) emerge as the main often isolated bacteria in clinical specimens. The unequivocal taxonomy is crucial to correctly identify these species and associated with comparative genomic analyses aids to understand their life-styles as well. In this study, all publicly available Acinetobacter species at the date of this study preparation were analyzed. The results revealed that the Acb members are in fact a complex when phenotypic methods are confronted, while for comparative and phylogenomics analyses this term is misleading, since they composed a monophyletic group instead. Nine best gene markers (response regulator, recJ, recG, phosphomannomutase, pepSY, monovalent cation/H + antiporter subunit D, mnmE, glnE, and bamA) were selected for identification of Acinetobacter species. Moreover, representative strains of each species were split according their isolation sources in the categories: environmental, human, insect and non-human vertebrate. Neither niche-specific genome signature nor niche-associated functional and pathogenic potential were associated with their isolation source, meaning it is not the main force acting on Acinetobacter adaptation in a given niche and corroborating that their ubiquitous distribution is a reflex of their generalist life-styles.

Effect of indoor environmental exposure on seminal microbiota and its application in body fluid identification

Semen is a common body fluid type in forensic sexual assault cases. It is of great significance to effectively identify semen for restoring the crime scene and determining the nature of the case. Nowadays, microbiome-based method shows as a promising tool for forensic body fluid identification. To explore the environmental impact on microbial community of semen and its traceability, 16S rDNA high-throughput sequencing was conducted to ten paired semen samples. Affected by exposure, the diversity of microbial community decreased generally as the genus Staphylococcus exhibited a relatively significant increase. However, the genus Staphylococcus, Corynebacterium, Corynebacterium_1 were observed in almost all 20 samples. Community barplot analysis and heatmap analysis showed composition of the predominant microbe in semen at the phyla and genus level maintained basically, so that it could distinguish from vaginal fluid and saliva regardless of environmental exposure. Based on these results, we believe the application of single microbial marker may limit in semen identification, but the method depending on microbial community might be useful for distinguishing semen even under indoor exposure.