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Applied and Environmental Microbiology Feb 2024an important pathogen known for its widespread antibiotic resistance, has been the focus of extensive research within its genus, primarily involving clinical isolates....
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 and other species remain limited. Here, we utilized Illumina and Nanopore sequencing to analyze the genomes of 10 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 strains, often tens of thousands of single-nucleotide polymorphisms from their nearest neighbors. Despite the genetic divergence, we identified p modules (sections of mobilized DNA) carrying clinically important antimicrobial resistance genes in species other than , including carbapenemase tetracycline resistance gene ), and macrolide resistance genes ). These p modules were located on plasmids with high sequence identity to those circulating in globally distributed ST1 and ST2 clones. The environmental 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, SAAb472 possessed virulence genes and a capsular polysaccharide type analogous to clinical strains. Our findings highlight the potential for environmental 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 species. By comparing the genomes of aquatic isolates with clinical and non-clinical strains, we revealed that they are highly divergent yet carry p modules that encode resistance to antibiotics commonly used in clinical settings. We also demonstrated that an environmental isolate can acquire clinically relevant plasmids and carries virulence factors similar to those of hospital-associated strains. These findings suggest that environmental 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.
Topics: Animals; Humans; Anti-Bacterial Agents; Drug Resistance, Bacterial; Acinetobacter Infections; Macrolides; Plasmids; Acinetobacter baumannii; Anti-Infective Agents; Genomics; Microbial Sensitivity Tests; Drug Resistance, Multiple, Bacterial
PubMed: 38206028
DOI: 10.1128/aem.01654-23 -
Scientific Reports Aug 2023Water supply suspension-restoration can occur frequently due to the overhauling of civil infrastructure in developing countries and the shutdown of commercial buildings...
Water supply suspension-restoration can occur frequently due to the overhauling of civil infrastructure in developing countries and the shutdown of commercial buildings during the pandemic. For comprehensive insights into the effects of water supply suspension-restoration, this study characterized the variations of the pathogen community composition of the tap water and their infection risk under different water supply scenarios. Metagenomic sequencing revealed a significant change of the human pathogen profiles, among which the most dominant pathogen changed from Pseudomonas aeruginosa (4.91%) to Acinetobacter johnsonii (0.59%). Furthermore, absolute quantification of pathogens by propidium-monoazide-qPCR revealed that the abundance of the three typical pathogens (Pseudomonas aeruginosa, Mycobacterium avium and Salmonella sp.) showed an increase of 2.44 log to 3.60 log immediately after water supply suspension-restoration and did not return to the normal level even after 2-h supply restoration, except for Pseudomonas aeruginosa. Quantitative microbial risk assessment suggested the infection risks of the three pathogens arising from direct utilization of tap water under stable water supply, including dermal exposure and oral intake, were all above the threshold of 10, and evidently increased after water supply suspension-restoration. This study warns us against the risk induced by the pathogens in tap water, especially after water supply suspension-restoration.
Topics: Humans; Water Supply; Water; Mycobacterium avium; Pseudomonas aeruginosa; Water Microbiology
PubMed: 37528119
DOI: 10.1038/s41598-023-39225-z -
Frontiers in Public Health 2024Given the dense population on university campuses, indoor and outdoor airborne bacterial contamination may lead to the rapid spread of diseases in a university...
Given the dense population on university campuses, indoor and outdoor airborne bacterial contamination may lead to the rapid spread of diseases in a university environment. However, there are few studies of the characteristics of airborne and pathogenic bacterial communities in different sites on a university campus. In this study, we collected particulate matter samples from indoor and outdoor locations at a university in Bengbu City, Anhui Province, China, and analyzed the community characteristics of airborne and pathogenic bacteria using a high-throughput sequencing technique. The results showed that the composition of the dominant airborne and pathogenic bacterial communities was consistent among sites at the phylum and genus levels, with differences in their relative abundance. There were significant differences in the structure of the airborne and pathogenic bacterial communities between indoor and outdoor sites ( < 0.05). An analysis of similarities (ANOSIM) indicated that the structure of airborne bacterial communities in indoor sites was influenced by the room occupancy rate, ventilation conditions, and the extent of indoor furnishing ( < 0.05), while the structure of pathogenic bacterial communities was influenced by the number of individuals and spatial dimensions ( < 0.05). The impact of particle size on the structure of airborne and pathogenic bacterial communities was relatively minor. A total of 194 suspected pathogenic bacterial species were identified, accounting for 0.0001-1.3923% of the total airborne bacteria, all of which were conditional pathogens. Among them, , , and exhibited relatively high relative abundance, accounting for 24.40, 16.22, and 8.66% of the total pathogenic bacteria, respectively. Moreover, 18 emerging or re-emerging pathogenic bacterial species with significant implications for human health were identified, although their relative abundance was relatively low (0.5098%). The relative abundance of pathogenic bacteria in indoor environments was significantly higher than outdoors, with the laboratory and dormitory having the highest levels. The findings of this study provide valuable guidance for the prevention and control of airborne bacterial contamination and the associated health risks in both a campus environment and other public spaces with high occupancy rates.
Topics: Universities; Air Microbiology; China; Bacteria; Humans; Particle Size; Air Pollution, Indoor; Particulate Matter; Environmental Monitoring
PubMed: 38651126
DOI: 10.3389/fpubh.2024.1371656 -
Bioresource Technology Nov 2023The heterotrophic nitrification-aerobic denitrification (HNAD) process can remove nitrogen and organic carbon under aerobic conditions. To get the in-depth mechanism of...
Exploring influence mechanism of small-molecule carbon source on heterotrophic nitrification-aerobic denitrification process from carbon metabolism, nitrogen metabolism and electron transport process.
The heterotrophic nitrification-aerobic denitrification (HNAD) process can remove nitrogen and organic carbon under aerobic conditions. To get the in-depth mechanism of the HAND process, a strain named Acinetobacter johnsonii ZHL01 was isolated, and enzyme activity, electron transport, energy production, and gene expression of the strain were studied with small-molecule carbon sources, including sodium citrate, sodium acetate, sodium fumarate, and sodium succinate. The HNAD pathway of ZHL01 was NH→NHOH → NO, and nitrogen balance analysis shows that ZHL01 could assimilate and denitrify 58.29 ± 1.05 % and 16.58 ± 1.07 % of nitrogen, respectively. The assimilation, the nitrification/denitrification, and the respiration processes were regulated by the concentration of reduced nicotinamide adenine dinucleotide (NADH) produced from the different metabolic pathways of small-molecule carbon sources. The HNAD process occurs to reduce intracellular redox levels related to NADH concentrations. This discovery provides a theoretical basis for the practical application of HAND bacteria.
Topics: Nitrification; Denitrification; Electron Transport; Carbon; NAD; Aerobiosis; Heterotrophic Processes; Nitrogen; Nitrites
PubMed: 37586428
DOI: 10.1016/j.biortech.2023.129681 -
Fish & Shellfish Immunology Jun 2024The scavenger receptors (SRs) gene family is considered as the membrane-associated pattern recognition receptors that plays important roles in the immune responses of...
The scavenger receptors (SRs) gene family is considered as the membrane-associated pattern recognition receptors that plays important roles in the immune responses of organisms. However, there is currently limited research on the systematic identification of the SRs gene family in teleost and their role in the innate immunity of S. schegelii. In this study, we identified and annotated 15 SRs genes in S. schegelii. Through phylogenetic analysis, analysis of conserved domains, gene structure, and motif composition, we found that SRs gene family within different classes were relatively conserved. Additionally, we used qRT-PCR to analyze the expression patterns of SRs genes in immune-related tissues from healthy and Acinetobacter johnsonii-infected S. schegelii. The results showed that SRs genes exhibited different tissue expression patterns and the expression of SRs genes significantly changed after A. johnsonii infection. These results provided a valuable basis for further understanding of the functions of SRs in the innate immune response of S. schegelii.
PubMed: 38852787
DOI: 10.1016/j.fsi.2024.109686 -
Environmental Science & Technology Dec 2023Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs)...
Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs) have received little attention. Herein, 48 metagenomic data were applied to study the prevalence of PM-borne ARGs in and around full-scale food waste treatment plants (FWTPs). Overall, FWTP PM (2.82 ± 1.47 copies/16S rRNA gene) harbored comparable total abundance of ARGs to that of municipal wastewater treatment plant PM (WWTP), but was significantly enriched with the multidrug type (e.g., AdeC/I/J; < 0.05), especially the abundant multidrug ARGs could serve as effective indicators to define resistome profiles of FWTPs (Random Forest accuracy >92%). FWTP PM exhibited a decreasing enrichment of total ARGs along the FWTP-downwind-boundary gradient, eventually reaching levels comparable to urban PM (1.46 ± 0.21 copies/16S rRNA gene, = 12). The combined analysis of source-tracking, metagenome-assembled genomes (MAGs), and culture-based testing provides strong evidence that -dominated pathogens contributed significantly to shaping and disseminating multidrug ARGs, while abiotic factors (i.e., SO) indirectly participated in these processes, which deserves more attention in developing strategies to mitigate airborne ARGs. In addition, the exposure level of FWTP PM-borne resistant pathogens was about 5-11 times higher than those in urban PM, and could be more severe than hospital PM in certain scenarios (<41.53%). This work highlights the importance of FWTP in disseminating airborne multidrug ARGs and the need for re-evaluating the air pollution induced by municipal FWTP in public health terms.
Topics: Humans; Genes, Bacterial; Food; RNA, Ribosomal, 16S; Refuse Disposal; Bacteria; Anti-Bacterial Agents; Particulate Matter
PubMed: 37972223
DOI: 10.1021/acs.est.3c04681 -
Parasites, Hosts and Diseases Feb 2024Ticks host different pathogens as endosymbiont and nonpathogenic microorganisms and play an important role in reproductive fitness and nutrient provision. However, the...
Ticks host different pathogens as endosymbiont and nonpathogenic microorganisms and play an important role in reproductive fitness and nutrient provision. However, the bacterial microbiomes of white-tailed deer ticks have received minimal attention. This study aimed to examine the bacterial microbiome of ticks collected from Odocoileus virginianus on the Mexico-United States border to assess differences in microbiome diversity in ticks of different species, sexes, and localities. Five different tick species were collected: Rhipicephalus microplus, Dermacentor nitens, Otobius megnini, Amblyomma cajennense, and A. maculatum. The tick microbiomes were analyzed using next-generation sequencing. Among all tick species, the most predominant phylum was Proteobacteria, followed by Actinobacteria and Firmicutes. The ticks from Tamaulipas and Nuevo León presented the highest bacterial species diversity. Acinetobacter johnsonii and A. lwoffii were the common bacterial species in the microbiome of all ticks, Coxiella were present in R. microplus, and Dermacentor nitens also exhibited a Francisella-like endosymbiont. The microbiome of most females in D. nitens was less diverse than that of males, whereas R. microplus occurs in females, suggesting that microbiome diversity is influenced by sex. In the bacterial communities of A. maculatum and O. megnini, Candidatus Midichloria massiliensis, and Candidatus Endoecteinascidia fumentensis were the most predominant endosymbionts. These results constitute the initial report on these bacteria, and this is also the first study to characterize the microbiome of O. megnini.
Topics: Animals; Female; Male; Deer; Mexico; Rhipicephalus; Microbiota
PubMed: 38443775
DOI: 10.3347/PHD.23006 -
Poultry Science Feb 2024Chickens in commercial production are hatched in hatcheries without any contact with their parents and colonization of their skin and respiratory tract is therefore...
Chickens in commercial production are hatched in hatcheries without any contact with their parents and colonization of their skin and respiratory tract is therefore dependent on environmental sources only. However, since chickens evolved to be hatched in nests, in this study we evaluated the importance of contact between hens and chicks for the development of chicken skin and tracheal microbiota. Sequencing of PCR amplified V3/V4 variable regions of the 16S rRNA gene showed that contact with adult hens decreased the abundance of E. coli, Proteus mirabilis and Clostridium perfringens both in skin and the trachea, and Acinetobacter johnsonii and Cutibacterium acnes in skin microbiota only. These species were replaced by Lactobacillus gallinarum, Lactobacillus aviarius, Limosilactobacillus reuteri, and Streptococcus pasterianus in the skin and tracheal microbiota of contact chicks. Lactobacilli can be therefore investigated for their probiotic effect in respiratory tract in the future. Skin and respiratory microbiota of contact chickens was also enriched for Phascolarctobacterium, Succinatimonas, Flavonifractor, Blautia, and [Ruminococcus] torque though, since these are strict anaerobes from the intestinal tract, it is likely that only DNA from nonviable cells was detected for these taxa.
Topics: Animals; Female; Chickens; RNA, Ribosomal, 16S; Escherichia coli; Microbiota; Respiratory System
PubMed: 38052128
DOI: 10.1016/j.psj.2023.103302 -
Water Research Oct 2023Since the onset of the COVID-19 Pandemic, large amounts of chlorine-containing disinfectants have been used to interrupt the spread of SARS-CoV-2 and residual chlorine...
Since the onset of the COVID-19 Pandemic, large amounts of chlorine-containing disinfectants have been used to interrupt the spread of SARS-CoV-2 and residual chlorine eventually entered the hospital or municipal sewage treatment facilities. However, little is known about the effect of chlorine influx on the biological sewage treatment process. Here we investigated the effect of chlorine on the microbiome and the mechanism of microbial chlorine resistance in the activated sludge of the aerobic treatment process, using metagenomic and metatranscriptomic sequencing. We found that chlorine could negatively impact the aerobic treatment performance regarding nitrogen/COD removal with a dose-dependent effect, and the dual effects of chlorine dose and interaction time differentiated the microbial community in activated sludge. The decline of nitrogen/COD removal was attributed to the compressed activity of functional microorganisms, such as the ammonia oxidation bacteria, under chlorinated conditions, and the damage cannot be recovered in a short term. In addition, some microorganisms could survive in chlorinated conditions by up-regulating the chlorine resistance genes (CRGs) expression (approximately 1.5 times) and stimulating new CRGs expression. In particular, species Acinetobacter johnsonii could resist high concentrations of chlorine through various mechanisms, especially the overexpression of efflux pump function encoded by qac genes play a key role. Based on these results, considering the persistence of the epidemic and extensive use of chlorine disinfectants, it cannot be ignored that large amounts of residual chlorine are entering the biological treatment facility, and strictly de-chlorination measures or microbial chlorine resistance regulations before entering should be implemented.
Topics: Humans; Disinfectants; Chlorine; Sewage; Pandemics; COVID-19; SARS-CoV-2; Nitrogen
PubMed: 37572464
DOI: 10.1016/j.watres.2023.120453 -
Foodborne Pathogens and Disease May 2024Both and cause an increasing number of diseases in fish, resulting in great economic losses in aquaculture. In addition, the disease infected with or exhibited the...
Both and cause an increasing number of diseases in fish, resulting in great economic losses in aquaculture. In addition, the disease infected with or exhibited the similar clinical symptoms in aquatic animals. However, there is no effective means for the simultaneous detection of co-infection and discrimination them for these two pathogens. Here, we developed a duplex polymerase chain reaction (PCR) method based on the outer membrane protein A () gene of and . The specificity and validity of the designed primers were confirmed experimentally using simplex PCR. The expected amplicons for and had a size of 663 and 1404 bp, respectively. The optimal condition for duplex PCR were determined to encompass a primer concentration of 0.5 μM and annealing temperature of 57°C. This method was analytical specific with no amplification being observed from the genomic DNA of , , , and . The limit of detection was estimated to be 20 fg of genomic DNA for and 200 fg for , or 100 colony-forming units (CFU) of bacterial cells in both cases. The duplex PCR was capable of simultaneously amplifying target fragments from genomic DNA extracted from the bacteria and fish liver. For practical validation of the method, 20 diseased fish were collected from farms, among which 4 samples were PCR-positive for and . The duplex PCR method developed here is time-saving, specific, convenient, and may prove to be an invaluable tool for molecular detection and epidemiological investigation of and in the field of aquaculture.
PubMed: 38708669
DOI: 10.1089/fpd.2023.0149