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180900.9964Deciphering antibiotic resistance genes and plasmids in pathogenic bacteria from 166 hospital effluents in Shanghai, China. Although previous studies using phenotypic or metagenomic approaches have revealed the patterns of antibiotic resistance genes (ARGs) in hospital effluents in local regions, limited information is available regarding the antibiotic resistome and plasmidome in human pathogenic bacteria in hospital effluents of megacity in China. To address this knowledge gap, we analyzed effluent samples from 166 hospitals across 13 geographical districts in Shanghai, China, using both cultivation-based approaches and metagenomics. A total of 357 strains were isolated from these samples, with the predominant species being Escherichia coli (n = 61), Aeromonas hydrophila (n = 57), Klebsiella pneumoniae (n = 48), and Aeromonas caviae (n = 42). Those identified indicator bacteria were classified into biosafety level 1 (BSL-1, 60 %) and BSL-2 (40 %). We identified 1237 ARG subtypes across 22 types, predominantly including beta-lactam, tetracycline, multidrug, polymyxin, and aminoglycoside resistance genes, using culture-enriched phenotypic metagenomics. Mobile genetic elements such as plasmids, transposons (tnpA), integrons (intI1), and insertion sequences (IS91) were abundant. We recovered 135 plasmids classified into mobilizable (n = 94) and non-mobilizable (n = 41) types. Additionally, 80 metagenome-assembled genomes (MAGs) were reconstructed from the hospital effluents for the assessment of ARG transmission risks, including genes for last-line antibiotics such as bla(NDM), bla(KPC), bla(imiH), and mcr. This study is the first to comprehensively characterize and assess the risk of antimicrobial resistance levels and plasmidome in the hospital effluents of China's megacity, providing city-wide surveillance data and evidence to inform public health interventions.202539612873
94210.9962Occurrence of multidrug resistant Gram-negative bacteria and resistance genes in semi-aquatic wildlife - Trachemys scripta, Neovison vison and Lutra lutra - as sentinels of environmental health. Emergence of antimicrobial resistance (AMR) in bacterial pathogens has been recognized as a major public health concern worldwide. In the present study, antimicrobial resistant Gram-negative bacteria (AMRGNB) and AMR genes were assessed in semi-aquatic wild animals from a highly populated and intensive farming region of Spain, Catalonia. Cloacal/rectal swab samples were collected from 241 animals coming from invasive species Trachemys scripta (n = 91) and Neovison vison (n = 131), and endangered-protected species Lutra lutra (n = 19). Accordingly, 133 (55.2%) isolates were identified as AMRGNB. Escherichia coli and Pseudomonas fluorescens were among the bacteria most frequently isolated in all animal species, but other nosocomial agents such as Klebsiella pneumoniae, Salmonella spp. or Citrobacter freundii, were also prevalent. The phenotypic susceptibility testing showed the highest resistance to β-lactams (91%). Molecular analysis showed 25.3% of turtles (15.4% ESBL/Ampc genes), 21% of Eurasian otters (10.5% ESBL/Ampc genes) and 14.5% of American minks (8.4% ESBL/Ampc genes) were positive to AMR genes. The genotyping frequency was tetM (20.6%), blaCMY-2 (13%), ermB (6.1%), blaCMY-1 (4.6%), blaCTX-M-15 (3.1%) and mcr-4 (0.8%). Turtles had a larger prevalence of AMRGNB and AMR genes than mustelids, but American mink carried mcr-4 colistin-resistance gene. Moreover, cluster analysis of AMR gene distribution revealed that an ESBL/AmpC cluster in a highly populated area comprising big metropolitan regions, and another tetM/emrB cluster in an expended area with highly intensive livestock production. Although the mcr-4 positive case was not included in those clusters, that case was found in a county with a high pig farm density. In conclusion, semi-aquatic wild animals are a good sentinel for environmental contamination with AMRGNB and AMR genes. Therefore, One Health Approach is urgently needed in highly populated regions, and with intensive livestock production like Catalonia.202235341839
272020.9962Phenotypic and genotypic characterization of antimicrobial resistance in Enterococcus spp. Isolated from the skin microbiota of channel catfish (Ictalurus punctatus) in Southeastern United States. BACKGROUND: Aquaculture systems may contribute to the emergence and persistence of antimicrobial-resistant (AMR) bacteria, posing risks to animal, environmental, and human health. This study characterized the phenotypic and genotypic antimicrobial resistance profiles of Enterococcus spp. isolated from the skin microbiota of 125 channel catfish (Ictalurus punctatus) harvested from two earthen ponds in Alabama, USA. METHODS: Skin swabs from the body of channel catfish were enriched in Enterococcosel broth and cultured on Enterococcosel agar at 28 °C for 24 h. Isolates were confirmed using Biolog Gen III and VITEK(®)2, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Thirty-five randomly sampled isolates underwent whole-genome sequencing for genotypic characterization. RESULTS: 36% of isolates exhibited multidrug resistance (resistance to ≥ 3 antimicrobial classes), with the highest resistance rates observed for ampicillin (44.8%), rifampicin (42.4%), and tetracycline (38.4%). The most prevalent resistance genes were aac(6')-Iid (65.7%), aac(6')-Ii (22.9%), efmA, and msr(C) (20.0% each). Plasmid replicons rep1 and repUS15 frequently co-occurred with resistance genes. Biofilm-associated genes, including efaA, fsrA, fsrB, sprE, ebpABC, ace, and scm, were commonly detected. Multivariate analyses (PERMANOVA, PCA) revealed no significant species-level differences in resistance burden or biofilm gene carriage, indicating similar resistance and virulence gene carriage across species in this dataset. CONCLUSIONS: The skin microbiota of pond-raised catfish harbors antimicrobial-resistant Enterococcus spp. with mobile resistance elements and biofilm-associated virulence factors, suggesting a potential role in AMR persistence within aquaculture settings. These findings support the need for targeted AMR surveillance in fish-associated microbiota as part of integrated One Health strategies.202540760424
226730.9962MOLECULAR CHARACTERIZATION AND DETECTION OF MULTIDRUGRESISTANT GENE IN BACTERIAL ISOLATES CAUSING LOWER RESPIRATORY TRACT INFECTIONS (LRTI) AMONG HIV/AIDS PATIENTS ON HIGHLY ACTIVE ANTIRETROVIRAL THERAPY (HAART) IN UYO, SOUTH-SOUTH NIGERIA. BACKGROUND: Antibiotic-resistant genes (ARGs) pose a significant challenge in modern medicine, rendering infections increasingly difficult to treat as bacteria acquire mechanisms to resist antibiotics. Addressing ARGs necessitates a multifaceted approach, encompassing surveillance efforts to monitor their presence and the development of strategies aimed at managing and curbing the spread of antibiotic resistance. Hence, this study characterized the genetic determinants of antibiotic resistance among isolates responsible for Lower Respiratory Tract Infections (LRTIs) in People Living with HIV/AIDS (PLWHA) in Uyo. METHODS: Sputum samples were collected from 61 LRTI suspects, with bacterial isolates identified using VITEK-2 technology. Polymerase chain reaction assays were employed to detect resistance genes within the isolates. RESULTS: Results revealed a bacterial etiology in 39.3% of the samples, with a majority (79.2%) originating from St. Luke Hospital, Anua (SLHA), and the remainder (20.8%) from the University of Uyo Teaching Hospital (UUTH). Staphylococcus aureus emerged as the predominant isolate (46.6%), while resistance was notably high against Gentamicin and Sulphamethazole/Trimethoprim. Conversely, Azithromycin, imipenem, clindamycin, erythromycin, and ceftriaxone displayed relatively lower resistance levels across all isolates. Notably, four resistance genes CTX-M, Aac, KPC, and MecA were identified, with CTX-M detected in all multidrug-resistant isolates. This underscores the predominantly community-acquired nature of resistance as conferred by CTX-M. CONCLUSION: In conclusion, this study underscores the critical importance of continued vigilance and proactive measures in combating antibiotic resistance, particularly within vulnerable populations such as PLWHA. By elucidating the genetic mechanisms underlying antibiotic resistance, informed targeted interventions can be mitigated to curb threats posed by multidrug-resistant bacteria in clinical settings.202440385712
94940.9961Molecular and clinical insights into extended-spectrum β-lactamase genes of Klebsiella pneumoniae isolated from neonatal sepsis in Ethiopia. BACKGROUND: Klebsiella bacterial strains harboring Extended-Spectrum Beta-Lactamase (ESBL) enzymes are the primary culprits behind neonatal sepsis globally. These strains significantly impact clinical outcomes due to their multi-drug resistance patterns in local healthcare settings. In response to this spiraling threat, we studied the prevalence and clinical implications of ESBL-encoding genes in neonates hospitalized with confirmed sepsis. METHODS: A correlational study was conducted on 51 neonates diagnosed with sepsis caused by ESBL-positive Klebsiella pneumoniae at Jimma Medical Center spanning from May 2022 to July 2023. Antimicrobial resistance profiles of the bacterial isolates were determined using the Kirby-Bauer diffusion test, while multiplex polymerase chain reaction (mPCR) techniques were employed to identify resistance genes. The correlation between resistance genes and treatment outcomes was analyzed using the phi coefficient (φ) with a significance level below 0.05. The data management was executed through the utilization of WHONET and STATA software platforms. RESULTS: The sample consisted of 26 (50.9%) male and the remaining 25 (49.1%) female neonates, with diverse clinical characteristics. All 51 Klebsiella pneumoniae isolates were 100% resistant to trimethoprim/sulfamethoxazole and ceftriaxone, but showed varying resistance profiles ranging from 30.8% to meropenem to 94.2% to ceftazidime. Notably, all isolates demonstrated multidrug resistance, with 23% of cases showing resistance to seven different antimicrobial classes. The most prevalent resistance genes identified were bla(CTX-M) (96.1%), bla(TEM) (94.1%), and bla(SHV) (88.2%). The majority of isolates (94.1%) carried at least two resistance genes, such as bla(TEM) and bla(CTX) (94.1%), bla(TEM) and bla(SHV) (86.2%), and bla(CTX) and bla(SHV) (86.2%). Notably, 84.3% of the bacteria harbored the trio of bla(TEM), bla(CTX), and bla(SHV) resistance genes, and only the presence of bla(SHV) in monogenic (φ = 0.4, P = 0.01) or the trio of bla(TEM), bla(CTX), and bla(SHV) genes (φ = 0.3, P = 0.02) showed positive correlation with neonatal mortality. CONCLUSION: We observed a significant prevalence of multidrug-resistant Klebsiella pneumoniae strains among neonates. Moreover, ESBL-resistance genes were widespread, with the blaSHV gene showing a correlation with increased neonatal mortality. These findings emphasize the urgent need for enhanced infection prevention measures, robust antimicrobial resistance surveillance, innovative treatment strategies, antibiotic stewardship initiatives, further research into resistance transfer mechanisms as well as hierarchical predictors of neonatal mortality. CLINICAL TRIAL NUMBER: Not applicable.202439695444
263250.9961Environmental Spread of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli and ESBL Genes among Children and Domestic Animals in Ecuador. BACKGROUND: There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human-animal interfaces exist. OBJECTIVES: This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS). METHODS: We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs. RESULTS: A total of 264 3GCR-EC isolates from children (n = 21), dogs (n = 20), and chickens (n = 18) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes (n = 14) at relatively large distances. Isolates from children and domestic animals shared the same blaCTX-M allelic variants, and the most prevalent were blaCTX-M-55 and blaCTX-M-65, which were found in isolates from children, dogs, and chickens. DISCUSSION: This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum β-lactamase) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child-animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729.202133617318
185460.9961Whole genome analysis reveals the distribution and diversity of plasmid reservoirs of NDM and MCR in commercial chicken farms in China. The increase in multidrug-resistant (MDR) Enterobacteriaceae presents a significant challenge to clinical treatment, particularly in infections where carbapenems and colistin serve as the last-resort antimicrobial agents. In this study, we isolated 119 non-repetitive gram-negative bacteria from MacConkey medium supplemented with imipenem and colistin. The isolates were dominated by Klebsiella pneumoniae (58.0%, n = 69) and Escherichia coli (31.1%, n = 37). The predominant sequence types (STs) of E. coli were ST226, ST1286, and ST11738, whereas K. pneumoniae displayed ST152, ST395, and ST709 as major types. Genomic analysis identified mcr-1/3/8/9 in 44 strains and bla(NDM) in 63 strains across various species. IncX3 (n = 57) and IncFII (n = 5) were the most common bla(NDM-5)-carrying plasmid types. Several plasmid replicons were associated with mcr genes, including IncI2, IncX4, and novel plasmids. Remarkably, we discovered four combinations of bla(NDM) and mcr co-occurrence in 28 isolates, including bla(NDM-5)/mcr-1, bla(NDM-5)/mcr-3, bla(NDM-5)/mcr-8, and bla(NDM-5)/mcr-9. Our findings reveal that chicken farms are significant reservoirs for both bla(NDM) and mcr genes, with frequent co-occurrence of these resistance determinants. The presence of these genes alongside other resistance factors, such as blaESBL, highlights a critical public health risk. This study underscores the need for enhanced surveillance and intervention strategies to mitigate the spread of MDR pathogens from agricultural environments to clinical settings.IMPORTANCEThis study reveals that commercial poultry farms in China serve as critical reservoirs for MDR gram-negative bacteria harboring carbapenemase (bla(NDM)) and mobilized colistin resistance (mcr) genes. By analyzing 119 isolates, we uncovered extensive genetic diversity and plasmid-mediated co-occurrence of these resistance determinants, enabling bacteria to evade nearly all available treatments. Alarmingly, the horizontal transfer of resistance genes via highly mobile plasmids facilitates their spread across microbial communities and potentially into clinical settings. These findings underscore the urgent need to address antibiotic overuse in agriculture and strengthen surveillance under the One Health framework. The persistence of MDR pathogens in poultry environments highlights a significant risk for zoonotic transmission, emphasizing the necessity of coordinated interventions to curb the global antimicrobial resistance crisis.202540488461
185270.9961Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective. Antibiotic resistance (AR) remains a major threat to public and animal health globally. However, AR ramifications in developing countries are worsened by limited molecular diagnostics, expensive therapeutics, inadequate numbers of skilled clinicians and scientists, and unsanitary environments. The epidemiology of Gram-negative bacteria, their AR genes, and geographical distribution in Africa are described here. Data were extracted and analyzed from English-language articles published between 2015 and December 2019. The genomes and AR genes of the various species, obtained from the Pathosystems Resource Integration Center (PATRIC) and NCBI were analyzed phylogenetically using Randomized Axelerated Maximum Likelihood (RAxML) and annotated with Figtree. The geographic location of resistant clones/clades was mapped manually. Thirty species from 31 countries and 24 genera from 41 countries were analyzed from 146 articles and 3,028 genomes, respectively. Genes mediating resistance to β-lactams (including bla (TEM-1), bla (CTX-M), bla (NDM), bla (IMP), bla (VIM), and bla (OXA-48/181)), fluoroquinolones (oqxAB, qnrA/B/D/S, gyrA/B, and parCE mutations, etc.), aminoglycosides (including armA and rmtC/F), sulfonamides (sul1/2/3), trimethoprim (dfrA), tetracycline [tet(A/B/C/D/G/O/M/39)], colistin (mcr-1), phenicols (catA/B, cmlA), and fosfomycin (fosA) were mostly found in Enterobacter spp. and Klebsiella pneumoniae, and also in Serratia marcescens, Escherichia coli, Salmonella enterica, Pseudomonas, Acinetobacter baumannii, etc., on mostly IncF-type, IncX(3/4), ColRNAI, and IncR plasmids, within IntI1 gene cassettes, insertion sequences, and transposons. Clonal and multiclonal outbreaks and dissemination of resistance genes across species and countries and between humans, animals, plants, and the environment were observed; Escherichia coli ST103, K. pneumoniae ST101, S. enterica ST1/2, and Vibrio cholerae ST69/515 were common strains. Most pathogens were of human origin, and zoonotic transmissions were relatively limited.IMPORTANCE Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Here, we used different methods to map out the geographical hot spots, sources, and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., Neisseria meningitis/gonorrhoeae, Vibrio cholerae, Campylobacter jejuni, etc., were common pathogens shuttling AR genes in Africa. Transmission of the same clones/strains across countries and between animals, humans, plants, and the environment was observed. We recommend Enterobacter spp. or K. pneumoniae as better sentinel species for AR surveillance.202033234606
199280.9961Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), β-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were A/C (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudo-cassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARC5: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-VIa, sul1). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARC5 were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.201931057528
210490.9961A systematic review and meta-analysis on antibiotic resistance genes in Ghana. BACKGROUND: Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources. METHODS: A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis. RESULTS: Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was bla(CTX-M), with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by bla(TEM) (19.5% [95% CI: 9.7-29.3]), and bla(SHV) (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for bla(NDM) to 10.3% (95% CI: 1.9-18.7) for bla(OXA). Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources. CONCLUSION: This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.202540075357
1346100.9961High prevalence of multidrug resistant Escherichia coli isolated from fresh vegetables sold by selected formal and informal traders in the most densely populated Province of South Africa. Contaminated fresh produce has increasingly been implicated in foodborne disease outbreaks. As microbiological safety surveillance in South Africa is limited, a total of 545 vegetable samples (spinach, tomato, lettuce, cucumber, and green beans) were purchased from retailers, street traders, trolley vendors and farmers' markets. Escherichia coli, coliforms and Enterobacteriaceae were enumerated and the prevalence of Escherichia coli, Salmonella spp. and Listeria monocytogenes determined. E. coli isolates were characterized phenotypically (antibiotic resistance) and genotypically (diarrheagenic virulence genes). Coliforms, E. coli and Enterobacteriaceae counts were mostly not significantly different between formal and informal markets, with exceptions noted on occasion. When compared to international standards, 90% to 98% tomatoes, 70% to 94% spinach, 82% cucumbers, 93% lettuce, and 80% green bean samples, had satisfactory (≤ 100 CFU/g) E. coli counts. Of the 545 vegetable samples analyzed, 14.86% (n = 81) harbored E. coli, predominantly from leafy green vegetables. Virulence genes (lt, st, bfpA, eagg, eaeA, stx1, stx2, and ipaH) were not detected in the E. coli isolates (n = 67) characterized, however 40.30% were multidrug-resistant. Resistance to aminoglycosides (neomycin, 73.13%; gentamycin, < 10%), penicillins (ampicillin, 38.81%; amoxicillin, 41.79%; augmentin, < 10%), sulfonamides (cotrimoxazole, 22.39%), tetracycline (19.4%), chloramphenicol (11.94%), cephalosporins (cefepime, 34.33%), and carbapenemases (imipenem, < 10%) were observed. This study highlights the need for continued surveillance of multidrug resistant foodborne pathogens in fresh produce retailed formally and informally for potential consumer health risks. PRACTICAL APPLICATION: The results indicate that the microbiological quality of different vegetables were similar per product type, regardless of being purchased from formal retailers or informal street traders, trolley vendors or farmers' markets. Although no pathogenic bacteria (diarrheagenic E. coli, Salmonella spp. or L. monocytogenes) were isolated, high levels of multidrug-resistance was observed in the generic E. coli isolates. These findings highlight the importance of microbiological quality surveillance of fresh produce in formal and informal markets, as these products can be a reservoir of multidrug resistant bacteria harboring antibiotic resistance and virulence genes, potentially impacting human health.202133294974
850110.9960Flies as carriers of antimicrobial resistant (AMR) bacteria in Nigerian hospitals: A workflow for surveillance of AMR bacteria carried by arthropod pests in hospital settings. The dissemination of antimicrobial resistant (AMR) bacteria by flies in hospitals is concerning as nosocomial AMR infections pose a significant threat to public health. This threat is compounded in low- and middle-income countries (LMICs) by several factors, including limited resources for sufficient infection prevention and control (IPC) practices and high numbers of flies in tropical climates. In this pilot study, 1,396 flies were collected between August and September 2022 from eight tertiary care hospitals in six cities (Abuja, Enugu, Kaduna, Kano, Lagos and Sokoto) in Nigeria. Flies were screened via microbiological culture and bacterial isolates were phenotypically and genetically characterised to determine carriage of clinically important antibiotic resistance genes (ARGs). Several clinically relevant ARGs were found in bacteria isolated from flies across all hospitals. bla(NDM) was detected in 8% of flies and was predominantly carried by Providencia spp. alongside clinically relevant Enterobacter spp, Escherichia coli and Klebsiella pneumoniae isolates, which all exhibited a multidrug resistant phenotype. mecA was detected at a prevalence of 6.4%, mostly in coagulase-negative Staphylococci (CoNS) as well as some Staphylococcus aureus, of which 86.8% were multidrug resistant. 40% of flies carried bacteria with at least one of the two ESBL genes tested (bla(OXA)(-1) and bla(CTX-M-15)). This multi-site study emphasised that flies in hospital settings carry bacteria that are resistant to multiple classes of antibiotics, including both routinely used and reserve antibiotics. A greater understanding of the global clinical significance and burden of AMR attributable to insect pests is required.202539862724
842120.9960Molecular characterization of antimicrobial resistance genes and plasmid profiles in enterobacterales isolated from urinary tract infections in rural outpatient women in Otavalo, Ecuador. BACKGROUND: The rise of antibiotic-resistant bacteria poses a significant public health threat, particularly in the context of urinary tract infections (UTIs), which rank as the second most common ambulatory illness. UTIs are often caused by Enterobacterales species, such as Escherichia coli and Klebsiella pneumoniae, with increasing resistance to critical antibiotics complicating treatment. Indigenous rural populations, like those in Ecuador, face unique challenges due to cultural, social, and economic barriers that hinder access to healthcare, exacerbating the issue of antibiotic resistance. METHODS: This study analyzed 154 Enterobacterales strains isolated from ambulatory UTI cases in outpatiens from Otavalo, Ecuador, between October 2021 and February 2022. DNA was extracted, and the presence of antibiotic resistance genes (ARGs) was screened using PCR for extended-spectrum beta-lactamases and carbapenemases. Plasmid incompatibility groups were identified through replicon typing, and multi-locus sequence typing (MLST) was performed to characterize strains. RESULTS: The analysis revealed four prevalent ARGs, with bla(TEM) being the most common (87.01% of isolates), followed by bla(CTX-M-1) (44.16%), bla(SHV) (18.83%), and bla(CTX-M-9) (13.64%). No carbapenemases or mcr-1 genes were detected. Among the incompatibility groups, IncFIB, IncF, and IncY were the most prevalent. A diverse array of ARG combinations was observed, indicating significant plasmid-mediated genetic plasticity. MLST identified 33 distinct sequence types among E. coli isolates, with ST10 and ST3944 being the most frequent. For K. pneumoniae, ST15 and ST25 were predominant. CONCLUSIONS: This study reveals significant antibiotic resistance among Enterobacterales from urinary tract infections in rural outpatients in Ecuador. The bla(TEM) gene was found in 87.01% of isolates, with notable clones like E. coli ST10 and ST3944 linked to extraintestinal infections. K. pneumoniae ST15 and ST25 were prevalent, indicating multidrug resistance. The findings highlight the need for ongoing surveillance and targeted public health strategies to combat resistance in these vulnerable communities.202541131447
5612130.9960Epidemiological factors associated with the prevalence of mobile genetic elements, and antimicrobial resistance patterns in Klebsiella pneumoniae of farm environments in Bangladesh. Farm environments serve as reservoirs for antibiotic-resistant bacteria and mobile genetic elements (MGEs), spreading resistance genes. Klebsiella pneumoniae, a nosocomial opportunistic pathogen, often acquires resistance through MGEs. This study examined the prevalence, resistance patterns, and factors associated with MGEs in K. pneumoniae isolates, focusing on environmental and management practices. 48 pooled samples were collected from environmental niches in three major districts of Bangladesh including Dhaka, Barisal, and Sylhet and analyzed using standard microbiological techniques and PCR. Antibiotic susceptibility was assessed per CLSI (2020) guidelines, and multidrug-resistant (MDR) strains were identified. Genotypic resistance patterns and mobile genetic elements (MGEs), including class 1 integrons and plasmids, were detected via PCR. Fisher's exact test evaluated factors associated with MGEs. Overall, 66.66% tested positive for K. pneumoniae. Regarding resistance patterns, the highest resistance was observed to ertapenem (90.6%) and ampicillin (84%), while complete sensitivity was noted to several antibiotics, including amikacin and tigecycline. Among the tested isolates, 53.12% were identified as MDR. Genotypic analysis revealed that bla(CTX-M), bla(NDM-5,)bla(Oxa-1) and bla(Oxa-48) were the most prevalent. Additionally, the presence of MGEs including class 1 integron and IncQ type plasmid were significantly associated with factors such as poor sanitation, antibiotic misuse, and high cattle density, highlighting critical areas for intervention. This study revealed that MDR K. pneumoniae circulates in food animals' farm environments in Bangladesh, with environmental factors strongly linked to the presence of MGEs. Farm niches, particularly soil, act as key reservoirs of MGEs and resistance genes. Importantly, these also carry serious implications for human health, as resistance genes may transfer to clinical settings, exacerbating the burden of AMR. Strengthening environmental and agricultural policies through a One Health approach is essential to mitigate the public health threat posed by antimicrobial resistance.202540619416
856140.9960Oral colonisation by antimicrobial-resistant Gram-negative bacteria among long-term care facility residents: prevalence, risk factors, and molecular epidemiology. BACKGROUND: For residents of long-term care facilities (LTCFs), antimicrobial-resistant bacteria (ARB) are a risk factor, yet their oral colonisation, potentially leading to aspiration pneumonia, remains unclear. This study was undertaken to survey the prevalence, phenotypic characteristics, and molecular epidemiology of antimicrobial-resistant Gram-negative bacteria in the oral cavity of LTCF residents, and to analyse the risk factors for such carriers. METHODS: This study involved 98 residents of a LTCF in Hiroshima City, Japan, aged between 55 and 101 years. Oropharyngeal swabs were collected and plated on screening media for ESBL-producing and carbapenem-resistant bacteria; isolates were identified and tested for antibiotic susceptibility; biofilm formation was tested in vitro; identification of epidemic clones were pre-determined by PCR; resistance genes, sequence types, and whole-genome comparison of strains were conducted using draft genome sequences. Demographic data and clinical characterisations were collected and risk factors analysed. RESULTS: Fifty-four strains from 38% of the residents grew on screening media and comprised predominantly of Acinetobacter spp. (35%), Enterobacteriaceae spp. (22%), and Pseudomonas spp. (19%). All Escherichia coli isolates carried CTX-M-9 group and belonged to the phylogroup B2, O25:H4 ST131 fimH30 lineage. Six Acinetobacter baumannii isolates presented identical molecular characteristics and revealed more biofilm production than the others, strongly suggesting their clonal lineage. One Acinetobacter ursingii isolate displayed extensive resistance to various ß-lactams due to multiple acquired resistance genes. One Pseudomonas aeruginosa isolate showed exceptional resistance to all ß-lactams including carbapenems, aminoglycosides, and a new quinolone, showing a multidrug-resistant Pseudomonas aeruginosa (MDRP) phenotype and remarkable biofilm formation. Genome sequence analysis revealed this isolate was the bla(IMP-1)-positive clone ST235 in Japan. Strokes (cerebral infarction or cerebral haemorrhage) and percutaneous endoscopic gastrostomy tubes were recognised as risk factors for oral colonisation by ARB in the LTCF residents. CONCLUSIONS: ARB, as defined by growth on screening agar plates, which carried mobile resistance genes or elements or conferred high biofilm formation, were already prevalent in the oral cavity of LTCF residents. Health-care workers involved in oral care should be aware of antimicrobial resistance and pay special attention to transmission prevention and infection control measures to diminish ARB or mobile resistance elements dissemination in LTCFs.202032131899
2100150.9960Prevalence of Bacteria and Antimicrobial Resistance Genes in Hospital Water and Surfaces. Purpose Antimicrobial resistance (AMR) has become a worldwide environmental and public health problem, causing more than 250,000 deaths per year. Unregulated usage, unsafe hospital practices, and misuse in veterinary contribute to the development of multidrug resistance in various bacteria. Hospital water was hypothesized to be a hotspot for AMR transmission because of (1) increased exposure to antibiotic load, (2) poor drainage and sanitation system, (3) interaction between environmental and clinical microbes. The purpose of the research was to assess the biodiversity and AMR in hospital tap waters. Methodology In this study, the microflora of the hospital tap water and hospital surfaces was observed by obtaining water samples from the intensive care unit (ICU), surgical wards, and washrooms. These were processed through membrane filtration and spread on seven different media (Aeromonas Medium, Azide Dextrose Agar, MacConkey Agar, Mannitol Salt Agar, Pseudomonas Cetrimide Agar, Salmonella Shigella Agar, and Thiosulfate Citrate Bile Salts Sucrose Agar). Surface samples were collected from the faucet, basin, and drain and directly spread on the media plates. Isolates were identified using standard bacteriological and biochemical tests. Kirby-Bauer disk diffusion method was performed using 21 antibiotic disks from 10 different antibiotic classes. They included ampicillin (AMP), amoxicillin (AML), piperacillin-tazobactam (TZP), cefipime (FEP), cefoxitin (FOX), ceftazidime (CAZ), ceftriaxone (CRO), imipenem (IMP), meropenem (MEM), ciprofloxacin (CIP), moxifloxacin (MXF), levofloxacin (LEV), amikacin (AK), gentamicin (CN), tigecycline (TGC), aztreonam (ATM), erythromycin (E), clindamycin (DA), rifampicin (RD), colistin (CT), and chloramphenicol (C). The results were interpreted according to EUCAST guidelines for the antibiogram of the isolates; 38 isolates were selected out of 162 based on different parameters for genotyping and detection of six beta-lactamase genes (blaSHV, blaTEM, blaCTX-M, blaOXA, blaKPC, blaNDM). Results Among these 162 isolates, 82 were obtained from water sources and 80 were collected from surfaces (faucet, basin, drain). The isolates included a variety of bacteria including Aeromonas spp. (20%), Klebsiella spp. (13%), Staphylococcus aureus (13%), Pseudomonas spp.(10%), Escherichia coli (9%), Vibrio spp. (8%), Enterococcus spp. (6%), Shigella spp. (6%), Salmonella spp. (4%), Acinetobacter spp. (3%), Staphylococcus epidermitis (3%), Streptococci spp. (2%), Proteus spp. (1%), Citrobacter spp. (1%), and Serratia spp. (1%). A diverse range of microbes were identified including clinically relevant bacteria, which shows that the urban water cycle is already contaminated with multidrug-resistant microflora of the hospital settings. Macrolide and lincosamide showed the highest resistance followed by penicillin, monobactam, and cephalosporins. blaSHV and blaTEM were prevalent in samples. blaNDM was also found which manifests as a real threat since it causes resistance against carbapenems and colistin, antibiotics reserved as a last resort against infections. Conclusions This study presented the ground reality of antibiotic resistance in Pakistan and how its subsequent spread poses a great threat to the strides made in the field of medicine and public health. Strict regulations regarding antibiotic usage, hospital effluent, and urban water sanitation must be imposed to curb the devastating effects of this increasing phenomenon.202134790487
849160.9960Bacterial Genomics for National Antimicrobial Resistance Surveillance in Cambodia. BACKGROUND: Antimicrobial resistance (AMR) surveillance in low- and middle-income countries (LMICs) often relies on poorly resourced laboratory processes. Centralized sequencing was combined with cloud-based, open-source bioinformatics solutions for national AMR surveillance in Cambodia. METHODS: Blood cultures growing gram-negative bacteria were collected at 6 Cambodian hospitals (January 2021 to October 2022). Isolates were obtained from pure plate growth and shotgun DNA sequencing performed in country. Using public nucleotide and protein databases, reads were aligned for pathogen identification and AMR gene characterization. Multilocus sequence typing was performed on whole-genome assemblies and haplotype clusters compared against published genomes. RESULTS: Genes associated with acquired resistance to fluoroquinolones were identified in 59%, trimethoprim/sulfamethoxazole in 45%, and aminoglycosides in 52% of 715 isolates. Extended-spectrum β-lactamase encoding genes were identified in 34% isolates, most commonly blaCTX-M-15, blaCTX-M-27, and blaCTX-M-55 in Escherichia coli sequence types 131 and 1193. Carbapenemase genes were identified in 12% isolates, most commonly blaOXA-23, blaNDM-1, blaOXA-58, and blaOXA-66 in Acinetobacter species. Phylogenetic analysis revealed clonal strains of Acinetobacter baumannii, representing suspected nosocomial outbreaks, and genetic clusters of quinolone-resistant typhoidal Salmonella and extended-spectrum β-lactamase E. coli cases suggesting community transmission. CONCLUSIONS: With accessible sequencing platforms and bioinformatics solutions, bacterial genomics can supplement AMR surveillance in LMICs.202539163245
1811170.9959Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut. The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface. IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.202539945541
5267180.9959Diversity and antibiotic resistance of cultivable bacteria in bulk tank milk from dairy farms in Shandong Province, China. INTRODUCTION: This study systematically analyzed bacterial diversity and antimicrobial resistance (AMR) profiles in bulk tank milk from five dairy farms (n = 30) in Shandong Province, China, to assess public health risks associated with microbial contamination and provide critical data for regional quality control and AMR risk assessment in dairy production systems. METHODS: Total bacterial counts were quantified, revealing significant inter-farm variation (P < 0.05) with a range of 3.94-6.68 log CFU/mL. Among 129 bacterial isolates, genus-level dominance and species prevalence were identified. Antimicrobial susceptibility testing (AST) against 10 agents was performed using integrated resistance criteria combining Clinical and Laboratory Standards Institute (CLSI) standards and epidemiological cutoff values (ECOFFs). Nine resistance genes targeting seven antibiotic classes were detected via PCR. RESULTS: The highest resistance rate was observed for sulfadiazine (53.2%) and the lowest for levofloxacin (6.0%). Multidrug resistance was detected in 23% (20/87) of isolates, with 14 strains meeting ECOFFs-based resistance criteria. PCR analysis showed sul1 (70.5%) and ant(4')-Ia (54.3%) as the most prevalent resistance genes, while mcr-1, lnu (B), and bla (NDM-1) were absent in all isolates. Regional resistance variations correlated significantly with farm management practices. DISCUSSION: These findings underscore the impact of historical antibiotic use on AMR dissemination. Enhanced AMR surveillance in raw milk, improved antibiotic stewardship, and targeted interventions are crucial to mitigate public health risks from microbial contamination and horizontal gene transfer of resistance determinants.202540771950
3068190.9959Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes. Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.202540833454