Multiple Antibiotic Resistance Genes Research Articles

Genomic Insights into the Pathogenicity and Drug-Resistance of a Bacillus cereus Isolated from Human Teeth.

Bacillus cereus is a common bacterium found in the environment. Some strains can cause food poisoning, and very few can cause clinically severe infections, leading to death. Here, we characterized the genome sequence of B. cereus LIN78 isolated from teeth with deep caries and compared it with those of 25 other related species. Third-generation sequencing technology, bacteriological analyses, biochemistry, and mass spectrometry were applied to characterize the drug-resistance genes and virulence factors of B. cereus LIN78. The complete genome sequence of B. cereus Lin78 consists of 5647 genes distributed on a circular chromosome, a 393 kbp plasmid, and 928 pseudogenes (37.4% of whole-genome DNA). The LIN78 genome contains 14 sets of 16s, 23s, and 5s ribosomal RNA operons; 106 tRNA genes, one tmRNA, 12 genomic islands, six prophases, 64 repeats; 37 antibiotic-resistant genes; and 1119 putative virulence genes, including enterotoxins and cytolysins. The B. cereus LIN78 genome carries multiple copies of non-ribosomal polypeptide synthetase (NRPS) and post-translationally modified peptides (RiPPs). Phylogenetic analysis of the 26 B. cereus strains showed that B. cereus LIN78 is evolutionarily closely related to B. thuringiensis ATCC 10792 and B. cereus ATCC 14579. The newly isolated B. cereus carries many virulence genes, including enterotoxins and hemolysins, similar to B. anthracis, and multiple antibiotic resistance genes. These findings suggest that the strain has a potential risk of causing disease. Our studies are vital for further exploration of the evolution of B. cereus, its pathogenic mechanisms, and the control and treatment of bacterial infections.

Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors

The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included <i>APH3-Ib, tetW/N/W, mphA,</i> and <i>Haemophilus influenzae PBP3</i>, and multiple ARG <i>Escherichia coli soxS</i> that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially <i>Enterococcus, Staphylococcus, Acinetobacter, Streptococcus</i>, and <i>Escherichia</i> were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.

Genomic Characteristics of a Carbapenem-Resistant Klebsiella pneumoniae Co-Carrying bla NDM-5 and bla KPC-2 Capsular Type KL25 Recovered from a County Level Hospital in China.

Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China. Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server. The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including bla NDM-5, bla KPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA. The coexistence of bla KPC and bla NDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference. This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.

Distribution characteristics of antibiotic resistance genes and microbial diversity in the inshore aquaculture area of Wenchang, Hainan, China

The rapid development of marine aquaculture has led to the increased use and release of antibiotics into the marine environment, consequently contributing to the emergence of antibiotic resistance. Information on antibiotic resistance in nearshore marine aquaculture areas remains limited, and research on the microbial composition and potential hosts of antibiotic resistance genes (ARGs) in marine aquaculture areas is scarce. This study used SmartChip real-time fluorescent quantitative PCR and qPCR to quantitatively analyze 44 ARGs and 10 mobile genetic elements (MGEs) genes in 12 sampling points in the nearshore aquaculture area of Wenchang. High-throughput sequencing of 16S rRNA was used to study microbial diversity in the study area, to clarify the correlation between ARGs, MGEs, and microbial diversity, and to determine the possible sources and potential hosts of ARGs. The results showed that a total of 37 ARGs and 8 MGEs were detected in the study area. The detection rate of 9 ARGs (aac(6′)-Ib(aka aacA4)-02, catA1, cmlA, cfr, sul1, sul2, sulA/folP-01, tetC, tetX) was 100 %. The absolute abundance of ARGs in the 12 sampling points ranged from 2.75 × 107 to 3.79 × 1010 copies·L−1, and the absolute abundance of MGEs was 1.30 × 105 to 2.54 × 107 copies·L−1, which was relatively high compared to other research areas. ARGs and MGEs were significantly correlated, indicating that MGEs play an important role as a mediator in the spread of ARGs. At the phylum level, Proteobacteria and Cyanobacteria were the dominant bacteria in the study area, with HIMB11 and unidentifiedChloroplast being the dominant levels, respectively. Network analysis of ARGs and microorganisms (genus level) revealed that Cognatishimia, Thalassobius, Aestuariicoccus, Thalassotalea, and Vibrio were significantly correlated with multiple ARGs and were the main potential hosts of ARGs in the nearshore waters of Wenchang.

The microbiome, resistome, and their co-evolution in sewage at a hospital for infectious diseases in Shanghai, China.

The emergence of antibiotic-resistant bacteria (ARB) caused by the overuse of antibiotics severely threatens human health. Hospital sewage may be a key transmission hub for ARB. However, the complex link between the microbiome and resistomeresistance in hospital sewage remains unclear. In this study, metagenomic assembly and binning methods were used to investigate the microbial community, resistome, and association of antibiotic resistance genes (ARGs) with ARB in sewage from 10 representative sites (outpatient building, surgery building, internal medicine buildings [IMB1-4], staff dormitory, laboratory animal building, tuberculosis building [TBB], and hospital wastewater treatment plant) of a hospital in Shanghai from June 2021 to February 2022. A total of 252 ARG subtypes, belonging to 17 antibiotic classes, were identified. The relative abundance of KPC-2 was higher at IMBs and TBB than at other sites. Of the ARG-carrying contigs, 47.3%-62.6% were associated with mobile genetic elements, and the proportion of plasmid-associated ARGs was significantly higher than that of chromosome-associated ARGs. Although a similar microbiome composition was shared, certain bacteria were enriched at different sites. Potential pathogens Enterococcus B faecium and Klebsiella pneumoniae were primarily enriched in IMB2 and IMB4, respectively. The same ARGs were identified in diverse bacterial hosts (especially pathogenic bacteria), and accordingly, the latter possessed multiple ARGs. Furthermore, gene flow was frequently observed in the sewage of different buildings. The results provide crucial information on the characterization profiles of resistomes in hospital sewage in Shanghai.IMPORTANCEEnvironmental antibiotic resistance genes (ARGs) play a critical role in the emergence and spread of antimicrobial resistance, which poses a global health threat. Wastewater from healthcare facilities serves as a significant reservoir for ARGs. Here, we characterized the microbial community along with the resistome (comprising all antibiotic resistance genes) in wastewater from a specialized hospital for infectious diseases in Shanghai. Potential pathogenic bacteria (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus B faecium) were frequently detected in hospital wastewater and carried multiple ARGs. A complex link between microbiome and resistome was observed in the wastewater of this hospital. The monitoring of ARGs and antibiotic-resistant bacteria (ARB) in hospital wastewater might be of great significance for preventing the spread of ARB.

Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia

BackgroundStenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. MethodsThese bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. ResultsResults showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. ConclusionOur study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.

The prevalence of Staphylococcus aureus and the emergence of livestock-associated MRSA CC398 in pig production in eastern China.

Livestock-associated Staphylococcus aureus (LA-MRSA) has been of increasing concern due to its potential risk to humans. This study investigated the prevalence of MRSA in pig production in Eastern China and determined the genomic characteristics of pig-associated MRSA isolates by whole-genome sequencing (WGS). A total of 1,318 samples were collected from pig farms and pig slaughterhouses, and 150 S. aureus were identified, including 63 MRSA isolates and 87 MSSA isolates. MRSA was detected in all pig farms and pig slaughterhouses. The antimicrobial susceptibility test revealed that all MRSA isolates were multidrug-resistant. The WGS and MLST analysis demonstrated that 56 MRSA isolates belonged to clonal complex (CC) 398, and seven MRSA isolates belonged to CC9. All LA-MRSA isolates were absent of phiSa3 phage containing immune evasion cluster (IEC) and possessed an intact hlb gene. In addition, genes associated with Panton-Valentine leukocidin, typically indicative of human adaptation, were not detected. The analysis of antibiotic resistance genes (ARGs) demonstrated that all MRSA isolates contained multiple ARGs. All MRSA isolates had Plthe mecA gene and at least one tetracycline resistance gene. Both tetM and tetK were detected in all MRSA CC398 isolates, while tetL was detected in all MRSA CC9 isolates. The phenicol resistance gene fexA was detected in 51 MRSA isolates, while the linezolid resistance gene cfr was detected in 60 MRSA isolates. The emergence of LA-MRSA CC398 in four pig farms and one slaughterhouse in this study indicates the spread of this clonal complex in the pig production sector in Eastern China. Further investigations are required to understand the potential transmission routes of LA-MRSA CC398 within the pork production chain in China and to assess the potential risks to humans.

Mobility, bacterial hosts, and risks of antibiotic resistome in submicron bioaerosols from a full-scale wastewater treatment plant

Antibiotic resistome could be loaded by bioaerosols and escape from wastewater or sludge to atmosphere environments. However, until recently, their profile, mobility, bacterial hosts, and risks in submicron bioaerosols (PM1.0) remain unclear. Here, metagenomic sequencing and assembly were employed to conduct an investigation of antibiotic resistome associated with PM1.0 within and around a full-scale wastewater treatment plant (WWTP). More subtypes of antibiotic resistant genes (ARGs) with higher total abundance were found along the upwind-downwind-WWTP transect. ARGs in WWTP-PM1.0 were mainly mediated by plasmids and transposases were the most prevalent mobile genetic elements (MGEs) co-occurring with ARGs. A contig-based analysis indicated that very small proportions (15.32%–19.74%) of ARGs in WWTP-PM1.0 were flanked by MGEs. Proteobacteria was the most dominant host of ARGs. A total of 28 kinds of potential pathogens, such as Pseudomonas aeruginosa and Escherichia coli, carried multiple ARG types. Compared to upwind, WWTP and corresponding downwind were characterized by higher PM1.0 resistome risk. This study emphasizes the vital role of WWTPs in discharging PM1.0-loaded ARGs and antibiotic resistant pathogens to air, and indicates the need for active safeguard procedures, such as that employees wear masks and work clothes, covering the main emission sites, and collecting and destroying of bioaerosols.

Molecular characteristics of carbapenem-resistant Raoultella ornithinolytica

AbstractAim of this study was to explore molecular characteristics and resistance mechanisms of carbapenem-resistant Raoultella ornithinolytica (CR-ROR) isolated from patients in a hospital in China. Three CR-ROR strains were collected and bacterial identification was done by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) Vitek-MS and by digital DDH analysis. VITEK 2 compact system and Kirby-Bauer (K–B) disk diffusion were used for antimicrobial susceptibility testing. Whole genome sequencing was carried out using the Illumina platform NovaSeq sequencer. Abricate software was used for the prediction of antibiotic resistance genes of three CR-ROR strains. The phylogenetic tree was constructed through genome SNPs to investigate the genetic relationship of three CR-ROR strains. Three CR-ROR (WF1357, WF2441, and WF3367) strains were collected in this study. Two strains were isolated from neurosurgery (WF1357 and WF2441), and one was isolated from pulmonology department (WF3367). All strains harboured multiple antibiotic resistance genes. Two strains (WF1357, WF2441) carried the blaNDM-1 gene, one of the strains (WF3367) carried the blaKPC-2 gene. Three CR-RORs were resistant to different antimicrobial agents including carbapenems. The three CR-ROR strains collected in this study and 51 CR-ROR strain genomes downloaded from NCBI, were divided into six evolutionary groups (A-F). In this study, three CR-ROR strains were found to have a higher level of resistance to antibacterial agents and carried multiple antibiotic resistance genes. The CR-ROR strains carrying multiple antibacterial resistant genes require the stringent monitoring to avoid the spread of multidrug-resistant bacterial strains.

Global distribution and genomic characteristics of carbapenemase-producing Escherichia coli among humans, 2005–2023

Carbapenem-resistant Escherichia coli (CREC) has become a major public health problem worldwide. To date, there is a limited understanding of the global distribution of CREC. In this study, we performed a comprehensive genomic analysis of 7, 731 CRECs of human origin collected from different countries worldwide between 2005 and 2023. Our results showed that these CRECs were distributed in 75 countries, mainly from the United States (17.49%), China (14.88%), and the United Kingdom (14.73%). Eight carbapenemases were identified among the CRECs analyzed, including KPC, IMP, NDM, VIM, OXA, FRI, GES, and IMI. NDM was the most predominant carbapenemase (52.15%), followed by OXA (30.09%) and KPC (14.72%). Notably, all CRECs carried multiple antibiotic resistance genes (ARGs), with 178 isolates carrying mcr-1 and 9 isolates carrying tet(X). The CREC isolates were classified into 465 known sequence types (STs), with ST167 being the most common (11.5%). Correlation analysis demonstrated the significant role of mobile genetic elements in facilitating the transfer of carbapenem resistance genes. Furthermore, some CRECs from different countries showed high genetic similarity, suggesting clonal transmission exists. According to the GWAS results, the genetic difference of blaNDM-positive CRECs from China were mainly enriched in bacterial Type IV secretion system pathways compared with those from the United Kingdom and the United States. Therefore, continuous global surveillance of CRECs is imperative in the future.

Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing.

Cronobacter sakazakii is an opportunistic pathogen linked to outbreaks in powdered infant formula (PIF), primarily causing meningitis and necrotizing enterocolitis. Whole-genome sequencing (WGS) was used to characterize 18 C. sakazakii strains isolated from PIF (powdered infant formula) manufacturing plants (2011-2015). Sequence Type (ST) 1 was identified as the dominant sequence type, and all isolates carried virulence genes for chemotaxis, flagellar motion, and heat shock proteins. Multiple antibiotic resistance genes were detected, with all isolates exhibiting resistance to Cephalosporins and Tetracycline. A significant correlation existed between genotypic and phenotypic antibiotic resistance. The plasmid Col(pHAD28) was identified in the isolates recovered from the same PIF environment. All isolates harbored at least one intact phage. All the study isolates were compared with a collection of 96 publicly available C. sakazakii genomes to place these isolates within a global context. This comprehensive study, integrating phylogenetic, genomic, and epidemiological data, contributes to a deeper understanding of Cronobacter outbreaks. It provides valuable insights to enhance surveillance, prevention, and control strategies in food processing and public health contexts.

Antibiotics and antibiotic resistance genes in the water sources of the Wuhan stretch of the Yangtze River: Occurrence, distribution, and ecological risks

Given the ubiquitous detection of antibiotics and antibiotic resistance genes (ARGs) in waterbodies worldwide and increasing public attention to water resource safety, this study investigated the presence of antibiotics and ARGs in the water sources of the Wuhan stretch of the Yangtze River (YR) as well as potential ecological risks. In this study, 15 antibiotics and 10 ARGs in a source of drinking water were analyzed using solid-phase extraction-ultra performance liquid chromatography-mass spectrometry technology (SPE–UPLC–MS/MS) and real-time fluorescence quantitative polymerase chain reaction (qPCR). Fourteen antibiotics were detected in the samples from 18 water sources, with the highest concentration detected for tetracycline, reaching up to 1708.33 ng/L. The detection rates of norfloxacin, enrofloxacin, ofloxacin, tetracycline, and roxithromycin were 100%. The concentrations of antibiotics were highest in She Shui, followed by the Wuhan stretch of the lower reaches of the YR, whereas the lowest concentrations were found in the Wuhan stretch of the upper reaches of the YR which were approximately equal to those in the Han River (HR). Ofloxacin and roxithromycin presented a substantial threat to aquatic organisms with high sensitivity at the majority of the sampling sites. The overall abundance of ARGs was notably greater in the lower reaches of the YR compared with the upper reaches and the HR. The highest absolute abundance was observed for sulfa ARGs. Integron intl1 strongly correlated with sul1, sul2, ermB, and qnrS, and antibiotics, strongly correlated with multiple ARGs, suggesting that antibiotics and ARGs are present in water sources in Wuhan and may present a plausible hazard to both human and ecological well-being. Hence, regulating the spread and dissemination of antibiotics and ARGs in the environment is imperative. The findings of this research offer significant insights into the stewardship and safeguarding of aquatic reserves in the Wuhan stretch of the YR.

The origin and evolution of IncF33 plasmids based on large-scale data sets.

To comprehensively understand the formation and evolution of IncF33 plasmids, a global collection of whole-genome sequences of 863 strains positive for IncF33 plasmid replicons was analyzed. The results showed that the IncF33 plasmids were mainly identified in Enterobacterales, of which Escherichia coli (86.44%) was the dominant host, followed by Salmonella (8.57%) and Klebsiella pneumoniae (3.48%). Salmonella ST11 and K. pneumoniae ST11 were common and mostly from humans. IncF33 plasmids were found worldwide but prevalent in Chinese farm animals, predominantly carrying antibiotic resistance genes such as blaCTX-M-55, fosA3, blaTEM-1B, rmtB, and floR. Comparative genomics analysis of 103 complete IncF33 plasmid sequences showed highly similar backbones except for 16 lacking partial backbone fragments. Variable regions were diverse, containing various antibiotic resistance genes, insertion sequences, or other plasmid fragments. They can be roughly divided into two sublines based on the production of different CTX-M enzymes. Similar IncF33 plasmids from different countries were identified. Some early IncF33 plasmids lacked part of their leader regions, which showed over 99% homology with early F2:A-:B- plasmids, indicating that leader regions of IncF33 likely came from F2:A-:B- plasmids. In addition, IncF33 plasmids cointegrating with other types of plasmids to form new cointegrate plasmids are increasing, making them more efficient in their dissemination and persistence in Enterobacterales, which could pose a significant threat to global public health. IMPORTANCE Plasmids that capture multiple antibiotic resistance genes are spreading widely, leading to the emergence and prevalence of multidrug-resistant bacteria. IncF33 plasmids are a newly emerged plasmid type highly prevalent in animal-source Enterobacterales in China, and they are important vectors for transmitting several clinically important antibiotic resistance genes. The study revealed that the IncF33 plasmid is mainly prevalent in China animal-derived Escherichia coli and has the potential for cointegration and intercontinental dissemination. Therefore, it is crucial to enhance surveillance and control measures to limit the spread of IncF33 plasmids and their associated antibiotic resistance genes.

Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation

Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%–54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.

Microbial contamination risk of landfilled waste with different ages

Landfills are reservoirs of antibiotic resistance genes (ARGs) and pathogens, and humans are exposed to these pollutants during extensive excavation of old landfills. However, the microbial contamination risk of landfilled waste with different ages has not been assessed. In this study, human bacterial pathogens (HBPs), ARGs, and virulence factors (VFs) were systematically determined using metagenomic analysis. Results showed that the abundance of HBPs, ARGs, and VFs increased with landfill age, the percentage of HBPs in refuse with deposit age of 10–12 years (Y10) was 23.75 ± 0.49%, which was higher than that in fresh refuse (Y0, 17.99 ± 0.14%) and refuse with deposit age of 5–6 years (Y5, 19.14 ± 0.15%), indicating that old refuse had higher microbial contamination risk than fresh refuse. Multidrug, macrolide, lincosamide, streptogramine, and tetracycline resistance genes were the primary ARGs, whereas lipooligosaccharides, type IV pili, and polar flagella were the dominant VFs in refuse. The HBPs showed a significant positive correlation with ARGs and VFs. Listeria monocytogenes, Salmonella enterica, Streptococcus pneumoniae, Acinetobacter baumannii, and Escherichia coli possibly possess both multiple ARGs and VFs and could be listed as high-risk HBPs in refuse. Mobile genetic elements, especially transposons, showed positive correlations with most ARGs and VFs, and they were identified as the primary factors accounting for the variations in ARGs and VFs. These findings will help understand the spread of ARGs and VFs in landfills and evaluate the potential risk of microbiological contamination in refuse of different landfill ages, thus providing guidance for preventing disease infection during landfill excavations.

Complete genome sequences of bacteria isolated from cockroaches collected in a Bangladeshi hospital.

We report the complete genome sequences of four bacterial strains that were isolated from Blattella germanica (German cockroaches) that were found in three wards of the Rajshahi Medical College Hospital. Multiple antibiotic resistance genes were identified in each genome, with one genome containing multiple plasmid-encoded resistance genes.

Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment

Wastewater treatment plants (WWTPs) are considered as hotspots for the spread of antibiotic resistome into the environment. However, the differential contributions of WWTPs to the antibiotic resistome in the receiving river water and sediment are poorly understood. Here, based on metagenomic analysis, we found that the WWTP effluents significantly elevated the diversities and abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the receiving river water from the Qinghai-Tibet Plateau, but showed less interference with the antibiotic resistome in sediment. Estimated by SourceTracker, WWTPs contributed 60.691.8% of ARGs in downstream river water, much higher than those for sediment (7.7568.0%). A holistic comparison of ARG risks based on analysis of ARG combination, mobility risk, ARG hosts and ARG-carrying pathogens further revealed the great impacts of WWTP effluents on downstream river water rather than sediment. Among various MGEs, tnpA exhibited the greatest potential for the dissemination of ARGs, and displayed highest co-occurrence frequency with multiple ARGs. P. aeruginosa, E. cloacae, and E. coli were identified as the critical-priority pathogens of ARG hosts. This study demonstrated the much greater impacts of WWTP effluents on the downstream water compared with sediment, which is significant for developing effective strategies to mitigate ARG risks.

Emergence of carbapenem-resistant enterobacterales co-harboring blaOXA−78 and blaOXA−58 from India

BackgroundCarbapenem-Resistant Enterobacterales (CRE) has been categorized as pathogens of critical priority by World Health organization (WHO) as they pose significant threat to global public health. Carbapenemase production considered as the principal resistance mechanism against carbapenems and with the recent surge and expansion of carbapenemases and its variants among clinically significant bacteria in India, the present study reports expansion blaOXA−78 and blaOXA−58 of in CRE of clinical origin.MethodsBacterial isolates were collected from a tertiary referral hospital and identified through VITEK® 2 Compact automated System (Biomerieux, France). Rapidec® Carba NP (Biomerieux, France) was used to investigate carbapenemase production followed by antibiotic susceptibility testing through Kirby-Bauer Disc Diffusion method and agar dilution method. Class D carbapenemase genes were targeted through PCR assay followed by investigation of horizontal transmission of blaOXA−58 and blaOXA−78. Whole genome sequencing was carried out using Illumina platform to investigate the genetic context of blaOXA−58 and blaOXA−78 genes and further characterization of the CRE isolates.ResultsThe carbapenem-resistant Escherichia coli (BJD_EC456) and Serratia marcescens (BJD_SM81) received during the study from the tertiary referral hospital were isolated from sputum and blood samples respectively. PCR assay followed by whole genome sequencing revealed that the isolates co-harbor blaOXA−58 and blaOXA−78, a variant of blaOXA−51. Horizontal transfer of blaOXA−58 and blaOXA−78 genes were unsuccessful as these genes were located on the chromosome of the study isolates. Transposon Tn6080 was linked to blaOXA−78 in the upstream region while the insertion sequences ISAba26 and ISCfr1 were identified in the upstream and downstream region of blaOXA−58 gene respectively. In addition, both the isolates were co-harboring multiple antibiotic resistance genes conferring clinical resistance towards beta-lactams, aminoglycosides, fluroquinolones, sulphonamides, tetracyclines. BJD_EC180 belonged to ST2437 while BJD_SM81 was of an unknown sequence type. The nucleotide sequences of blaOXA−78 (OQ533021) and blaOXA−58 (OQ533022) have been deposited in GenBank.ConclusionsThe study provides a local epidemiological information regarding carbapenem resistance aided by transposon and insertion sequences associated blaOXA−78 and blaOXA−58 genes associated and warrants continuous monitoring to prevent their further dissemination into carbapenem non-susceptible strains thereby contributing to carbapenem resistance burden which is currently a global concern.

Characterisation of a Novel Tigecycline Resistance Gene tet(X22) and its Coexistence with blaNDM-1 in a Pseudomonas caeni Isolate

ObjectivesThe emergence of pathogens that are resistant to both tigecycline and carbapenem poses a threat to public health globally. Continuous emergence of novel tet(X) variants accelerates the tigecycline resistance crisis. This study aimed to characterise the novel tigecycline resistance gene tet(X22) and its coexistence with carbapenem resistance gene blaNDM-1 in Pseudomonas caeni. MethodsThis P. caeni isolate co-harbouring tet(X22) and blaNDM-1 was systematically investigated using antimicrobial susceptibility testing, conjugation assays, genome sequencing, bioinformatic analyses, cloning of tet(X22) and functional analysis, and protein structure prediction. ResultsThe carbapenem-resistant and tigecycline-resistant P. caeni isolate CE14 was obtained from chicken faeces in 2022. CE14 carried multiple antibiotic resistance genes, including the novel tet(X22) and blaNDM-1. Tet(X22) exhibited 64.72–90.48% amino acid identity with other variants [Tet(X) to Tet(X21)]. Cloning of the gene tet(X22) and protein structure prediction revealed that Tet(X22) confers resistance to tetracyclines, including tigecycline. tet(X22) and blaNDM-1 were located in two multidrug-resistant regions of the chromosome. ConclusionsThe occurrence of the novel ISCR2-flanked tet(X22) in P. caeni suggests that the tet(X) variant has adapted to new hosts and may widely spread to further expand the host range. The future global spread of such pathogens co-harbouring tet(X) and blaNDM variants needs to be continuously monitored according to the One Health approach.

Identification of antibiotic resistant bacteria communities and a GeoChip based study of resistome in Fusarium wilt diseased and healthy soil

Soil plays a crucial role as a significant reservoir for antibiotic resistance genes (ARGs). Despite the extensive research conducted in this area, there remains a need for further investigation, particularly concerning diverse types of agricultural soil. This comprehensive study examined Fusarium wilt diseased and healthy soil samples to investigate the spectrum of ARGs and identify bacteria potentially harboring these genes. The level of antibiotic resistance (AR) in the two soil types was detected by using culture plate counts (PC). We quantified and identified antibiotic resistant bacteria (ARB) against nine antibiotics. From the PC results, the relative number of ARB (number of ARB/total number culturable bacteria) resistant to erythromycin, lincomycin, sulfonamides, streptomycin sulfate, kanamycin, and enrofloxacin in the diseased soil was significantly higher than that in the healthy soil (One-way ANOVA, p < 0.01). The GeoChip (version 5.0) was employed to identify ARGs and antibiotic biosynthetic genes (ABGs). Interestingly, despite the presence of similar ARGs in both soil types, the Fusarium wilt diseased soil demonstrated a significantly elevated abundance of the tetracycline (tetX) resistance gene compared to the healthy soil. A robust correlation (r ≥ 0.8) between multidrug efflux pumps and ARGs indicates that natural antibiotics as selective pressures for transportation mechanisms. Our analysis identified diverse ARB phylotypes and multiple ARGs in both soil types. Incorporating these soil types into ARGs risk assessments and relevant monitoring is essential for a comprehensive understanding of AR dynamics in various environments.