blaOXA Genes Research Articles

Cross-transmission of Acinetobacter junii carrying blaOXA-58 in a neonatal ICU.

Nasal colonization of two preterm infants in our neonatal ICU by Acinetobacter junii carrying the blaOXA-58 carbapenem resistance gene was demonstrated. To study whether the two isolates were identical and to investigate the hypotheses of cross-transmission. Antibiotic susceptibility tests of the two isolates were performed by standard diffusion and the MICs of carbapenems determined by the MIC-gradient strip method. The blaOXA-58 gene was detected by PCR. Isolates were compared using SNP analysis performed after WGS. The timelines of the two cases were determined based on the investigations and the study of the patients' records. The two isolates corresponded to the same strain, with case 1 being the index case, demonstrating cross-transmission to case 2. Acquisition of the strain was likely due to the recent carbapenem treatment of case 1 and cross-transmission due to the high amount of care administered to the two preterm infants. This is the first description of cross-transmission of A. junii carrying the blaOXA-58 gene.

Genomic Insights into and In Vitro Evaluation of Antimicrobial Combination Therapies for Carbapenem-Resistant Acinetobacter baumannii.

Background and Objectives: Acinetobacter baumannii (A. baumannii), particularly carbapenem-resistant A. baumannii (CRAB), represents a grave concern in healthcare settings and is associated with high mortality. This study aimed to conduct molecular, mutational, and phylogenetic analyses of specific genes in CRAB and evaluate the synergistic effects of selected antimicrobial combinations. Materials and Methods: Phenotypic characterization was performed on six CRAB strains by using the Modified Hodge Test (MHT) and IMP-EDTA Double-Disc Synergy Test (IMP-EDTA DDST). Carbapenemase- and metallo-beta-lactamase-encoding genes were amplified by using Polymerase Chain Reaction. Phylogenetic analysis using the MEGA 11 tool was used to determine the evolutionary relatedness of these genes. Mutational analysis was performed by using I-Mutant, MUPro, and PHD-SNP bioinformatics tools to predict mutations in the carbapenemase-encoding genes. Microdilution checkerboard titration assessed the synergistic effects of antimicrobial combinations (azithromycin-meropenem, rifampicin-meropenem, meropenem-colistin, and azithromycin-colistin) on these CRAB isolates. Results: The phenotypic characterization of six CRAB isolates revealed positive results for MHT and IMP-EDTA DDST. The molecular characterization revealed that carbapenemase- and MBL-encoding genes were present in all isolates with varying frequencies, including blaOXA-51 (100%) and blaIMP (0%). The sequence analysis revealed high evolutionary relatedness to sequences in the NCBI database. The mutational analysis identified 16 mutations, of which 1 mutation (P116L) in the blaOXA-58 gene predicted a change in the protein product, potentially contributing to carbapenem resistance. The checkerboard titration method did not reveal any synergism among the tested antimicrobial combinations against CRAB. Conclusion: This study's findings underscore the significant challenges posed by CRAB isolates harboring multiple resistant genes in treatment. This highlights the urgent need for novel antimicrobial agents, a crucial step towards reducing mortality rates not only in Pakistan but also globally.

Identification of bla OXA-23 gene in resistant Pseudomonas aeruginosa strains isolated from cows and humans in Basra province, Iraq.

Pseudomonas aeruginosa is an infectious agent of great importance for animals and humans. It causes serious infections that show high resistance to antibiotics. This study investigated the molecular detection of blaOXA-23 gene in antibiotic-resistant P. aeruginosa strains isolated from cows and humans. In total, 120 samples, comprised 60 from cows (30 milk and 30 nasal discharge) and 60 from their owners (30 urine and 30 sputum), were individually collected, cultured, and tested for P. aeruginosa through molecular analysis targeting the blaOXA-23 gene. P. aeruginosa antibiotic-resistant isolates were identified by performing antibiotic susceptibility testing and detecting biofilm formation. In total, 74.17% positive P. aeruginosa isolates, including 66.67% and 81.67% for cows and humans, respectively. Subsequently, positive cow isolates were detected in 60% of milk samples and 73.33% of nasal discharge samples; while positive human isolates were detected in 76.67% of urine samples and 86.66% of sputum samples. Targeting blaOXA-23 gene, 58.43% of cultured isolates were positive for P. aeruginosa by polymerase chain reaction. Respectively, positive isolates were detected in 66.67% and 45.46% of cow milk and nasal discharges as well as in 60.87% and 61.54% of human urine and sputum. The antibiotic susceptibility test revealed that all isolates were resistant to all applied antibiotics, particularly imipenem. Results of biofilm formation revealed 67.31% total positives, including 51.43% strong, 34.285% moderate, and 14.285% weak reactions. In addition, although values of the total positive cows and humans differed insignificantly, total positives showed insignificant variation between values of milk and nasal discharges of cows as well as between urine and sputum of humans; however, significant differences were identified in the distribution of strong, moderate, and weak positivity of these samples. Antibiotic overuse contributes extensively to increasing the prevalence of resistant P. aeruginosa isolates carrying the blaOXA-23 gene in both cows and humans. Furthermore, studies in other Iraqi areas are necessary to support our findings. The main limitations include that the number of tested samples is relatively low, and there is a need to use a large number of samples from different sources. Also, the current methods for detection of resistant isolates are still culture-based approaches.

Distribution of extended-spectrum β-lactamase producing Escherichia coli genes in an integrated poultry-fish farming system in Bogor, Indonesia.

The excessive use of antimicrobials in livestock farming leads to the emergence and dissemination of antimicrobial-resistant organisms. This study aimed to detect extended-spectrum β-lactamase (ESBL)-producing Escherichia coli genes in integrated poultry-fish farms in Bogor, Indonesia. A total of 256 samples were collected from six poultry-fish farms. One hundred and seventy-five chicken cloaca swabs, 60 fish skin swabs, six pond water samples, and 15 farmer's hand swabs. ESBL-producing E. coli was confirmed through double-disk diffusion. The specific primers and probe genes for quantitative polymerase chain reaction detection of ESBL-producing E. coli targeted blaTEM, blaCTX-M, blaSHV, and blaOXA-48 genes. Among the 256 samples tested, 145 (56.6%) were positive for E. coli, and 67.6% (98/145) were identified as ESBL-producing E. coli. The most ESBL-producing E. coli isolates were obtained from chicken cloaca (78.3%, 72/92), followed by pond water (66.7%, 4/6), fish skin (47.6%, 20/42), and farmer's hand swabs (40%, 2/5). About 100% of the isolates carried the genes blaTEM and blaCTX-M, whereas 17.3% and 24.5% carried blaSHV and blaOXA-48, respectively. ESBL-producing E. coli genes were investigated in chicken cloaca, fish, pond water, and farmers' hands within an interconnected poultry-fish farming operation. The ESBL-producing E. coli in chickens can transfer resistant genes to aquatic environments. The transfer could harm other aquatic species and food chains, potentially threatening human health.

Distribution of Carbapenemase Genes among Carbapenem-Resistant Klebsiella pneumoniae Isolates from the Patients in Najaf, Iraq

Abstract Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global threat, causing serious community- and hospital-acquired infections with limited treatment options. Understanding the local epidemiology of CRKP is crucial for guiding antimicrobial stewardship and infection control measures. This study aimed to investigate the phenotypic characteristics, antimicrobial resistance profiles, and carbapenemase genes among CRKP isolates from the patients in Najaf, Iraq. Methods: This cross-sectional research was performed at diverse hospitals and centers in Najaf, Iraq, from September 2023 to March 2024. The study was approved by the Ethics Committee of Kufa University. CRKP isolates were collected from various health-care facilities and tested for hypermucoviscosity, antimicrobial susceptibility, and carbapenemase production using phenotypic methods. The presence of carbapenemase genes (blaNDM, blaVIM, blaKPC, blaOXA-48, blaOXA-23, and blaOXA-51) was examined by polymerase chain reaction. Results: Of the 27 CRKP isolates, 9 (33.3%) exhibited a hypermucoviscous phenotype. Regarding antimicrobial resistance, 12 (44.4%) were multidrug resistant, 14 (51.9%) were extensively drug resistant, and 1 (3.7%) was pandrug resistant. Phenotypic carbapenemase production was detected in 5 (18.5%) and 11 (40.7%) isolates by the modified Hodge test and E-test metallo-β-lactamase strips, respectively. Molecular analysis revealed that all CRKP harbored the blaOXA-51 gene, whereas blaNDM, blaOXA-23, and blaVIM were detected in 70.4%, 40.7%, and 11.1% of the isolates, respectively. Neither blaKPC nor blaOXA-48 genes were found. In addition, 22 (81.5%) isolates carried multiple carbapenemase genes. Conclusions: The high prevalence of blaOXA-51 and blaNDM carbapenemases, along with the high rates of multidrug resistance among CRKP isolates in Najaf, Iraq, are alarming. This necessitates the immediate implementation of effective antimicrobial stewardship and infection control measures to prevent the further spread of these difficult-to-treat pathogens.

Coexistence of β-lactamase genes and biofilm forming potential among carbapenem-resistant Acinetobacter baumannii in Lahore, Pakistan.

Our goal was to investigate the antimicrobial resistance due to beta-lactamase genes and virulent determinants (biofilm-forming ability) expressed by Acinetobacter collected from health settings in Pakistan. A cross-sectional study was conducted for the molecular characterization of carbapenemases and biofilm-producing strains of Acinetobacter spp. Two twenty-three imipenem-resistant Acinetobacter isolates were analyzed from 2020 to 2023.The combination disk test and modified hodge test were performed. Biofilm forming ability was determined by polystyrene tube assay. Multiplex polymerase chain reaction (PCR) for virulent and biofilm-forming genes, and 16S rRNA sequencing were performed. 118 (52.9%) carbapenem-resistant Acinetobacter (CR-AB) were isolated from wounds and pus, 121 (54.2%) from males, and 92 (41.2%) from 26-50-years-olds. More than 80% of strains produced β-lactamases and carbapenemases. Based on the PCR amplification of the ITS gene, 174 (78.0%) CR-AB strains were identified from CR-Acinetobacter non-baumannii (ANB). Most CR-AB were strong and moderate biofilm producers. Genetic analysis revealed the blaOXA-23, blaTEM, blaCTX-M blaNDM-1 and blaVIM were prevalent in CR-AB with frequencies 91 (94.8%), 68 (70.8%), 19 (19.7%), 53 (55.2%), 2 (2.0%) respectively. Among virulence genes, OmpA was dominant in CR-AB isolates from wound (83, 86.4%), csuE 63 (80.7%) from non-wound specimens and significantly correlated with blaNDM and blaOXA genes. Phylogenetic analysis revealed three different clades for strains based on specimens. CR-AB was highly prevalent in Pakistan and associated with wound infections. The genes, blaOXA-23, blaTEM, blaCTX-M, and blaNDM-1 were detected in CR-AB. Most CR-AB were strong biofilm producers with virulent genes OmpA and csuE.

Carbapenemase gene blaOXA-48 detected at six freshwater sites in Northern Ireland discharging onto identified bathing locations.

Faecal contamination of surface waters has the potential to spread not only pathogenic organisms but also antimicrobial resistant organisms. During the bathing season of 2021, weekly water samples, from six selected coastal bathing locations (n=93) and their freshwater tributaries (n=93), in Northern Ireland (UK), were examined for concentrations of faecal indicator bacteria Escherichia coli and intestinal enterococci. Microbial source tracking involved detection of genetic markers from the genus Bacteroides using PCR assays for the general AllBac marker, the human HF8 marker and the ruminant BacR marker for the detection of human, and ruminant sources of faecal contamination. The presence of beta-lactamase genes blaOXA-48, blaKPC, and blaNDM-1 was determined using PCR assays for the investigation of antimicrobial resistance genes that are responsible for lack of efficacy in major broad-spectrum antibiotics. The beta-lactamase gene blaOXA-48 was found in freshwater tributary samples at all six locations. blaOXA-48 was detected in 83% of samples that tested positive for the human marker and 69% of samples that tested positive for the ruminant marker over all six locations. This study suggests a risk of human exposure to antimicrobial resistant bacteria where bathing waters receive at least episodically substantial transfers from such tributaries.

Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates.

Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.

Detection of Klebsiella pneumoniae Carbapenem Resistance Genes by qPCR: Choosing the Right Method for Total DNA Extraction.

Rapid and accurate detection of Klebsiella pneumoniae carbapenem resistance is important for infection control and targeted antibiotic therapy. PCR-based assay performance heavily depends on the quality and quantity of template DNA. Challenges arise from the necessity to isolate chromosomal and large plasmid-encoded resistance genes simultaneously from a limited number of target cells and to remove PCR inhibitors. qPCRs for the detection of K. pneumoniae strains carrying blaOXA-48, blaNDM-1, blaKPC-2, and blaVIM-1 carbapenemase genes were developed. We compared the performance of template DNA extracted with silica column-based methods, reversed elution systems, and lysis-only methods either from diluted culture fluid or from a synthetic stool matrix which contained PCR inhibitors typically present in stool. The synthetic stool matrix was chosen to mimic K. pneumoniae containing rectal swabs or stool samples in a reproducible manner. For total DNA isolated from culture fluid, resistance gene detection by qPCR was always possible, independent of the extraction method. However, when total DNA was isolated from synthetic stool matrix spiked with K. pneumoniae, most methods were insufficient. The best performance of template DNA was obtained with reversed elution. This highlights the importance of choosing the right DNA extraction method for consistent carbapenem resistance detection by PCR.

Exploring the presence, genomic traits, and pathogenic potential of extended-spectrum β-lactamase Escherichia coli in freshwater, wastewater, and hospital effluents.

The purpose of this work was to study extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) in freshwaters, hospital effluents, and wastewaters during two sampling campaigns in 2021. Water sampling was performed at 24 stations in the Ourthe watershed in Belgium. A total of 644 ESBL (n=642) and AmpC (n=2) E. coli strains were isolated. Disk-diffusion assays were performed following the EUCAST's recommendations. All strains were tested for the presence of blaCTX-M-1, blaCTX-M-2, and blaCTX-M-9 gene groups by PCR. Genes belonging to blaCTX-M-1 and blaCTX-M-9 groups were detected, respectively, in 73.6% and 14.9% of the strains. No blaCTX-M-2 group's gene was found. A subset of strains (n=40) was selected for whole genome sequencing. Escherichia coli serotype O18: H7 ST 1463 was predominant (n=14) in the sequenced strains and showed pathogenicity in the Galleria mellonella larvae model. β-lactamase genes identified were blaCTX-M (n=21), with blaCTX-M-15 mostly represented (n=15), as well as blaTEM (n=11), blaOXA (n=7), blaSHV (n=9), and carbapenemase (CP) genes were observed in several strains-blaKPC-3 (n=19), blaNDM-1 (n=1), blaVIM-1 (n=2), and blaOXA-244 (n=2)-even from freshwaters. ESBL-EC are widely distributed in the aquatic environment in Belgium and contain a variety of ESBL and CP genes.

Unveiling the ecological landscape of bacterial β-lactam resistance in Delhi-national capital region, India: An emerging health concern

Inappropriate antibiotic use not only amplifies the threat of antimicrobial resistance (AMR), moreover exacerbates the spread of resistant bacterial strains and genes in the environment, underscoring the critical need for effective research and interventions. Our aim is to assess the prevalence and resistance characteristics of β-lactam resistant bacteria (BLRB) and β-lactamase resistant bacterial genes (BLRBGs) under various environmental conditions within Delhi NCR, India. Using a culture-dependent method, we isolated 130 BLRB from 75 different environmental samples, including lakes, ponds, the Yamuna River, agricultural soil, aquatic weeds, drains, dumping yards, STPs, and gaushalas. Tests for antibiotic susceptibility were conducted in addition to phenotypic and genotypic identification of BLs and integron genes. The water and sediment samples recorded an average bacterial abundance of 3.6 × 106 CFU/mL and an average ampicillin-resistant bacterial count of 2.2 × 106 CFU/mL, which can be considered a potent reservoir of BLRB and BLRBGs. The majority of the BLRB discovered are opportunistic pathogens from the Bacillus, Aeromonas, Pseudomonas, Enterobacter, Escherichia, and Klebsiella genera, with Multiple Antibiotic Resistance (MAR) index ≥0.2 against a wide variety of β-lactams and β-lactamase (BLs) inhibitor combinations. The antibiotic resistance pattern was similar in the case of bacteria isolated from STPs. Meanwhile, bacteria isolated from other sources were diverse in their antibiotic resistance profile. Interestingly, we discovered that 10 isolates of various origins produce both Extended Spectrum BLs and Metallo BLs, as well as found harboring blaTEM, blaCTX, blaOXA, blaSHV, int-1, and int-3 genes. Enterobacter cloacae (S50/A), a common nosocomial pathogen isolated from Yamuna River sediment samples at Nizamuddin point, possesses three BLRBGs (blaTEM, blaCTX, and blaOXA) and a MAR index of 1.0, which is a major cause for concern. Therefore, identifying the source, origin and dissemination of BLRB and BLRGs in the environment is of the utmost importance for designing effective mitigation approaches to reduce a load of antimicrobial resistance factors in the environmental settings.

Genetic profile and characterization of antimicrobial resistance in Acinetobacter baumannii post-COVID-19 pandemic: a study in a tertiary hospital in Recife, Brazil.

To investigate the genetic profile and characterize antimicrobial resistance, including the main β-lactam antibiotic resistance genes, in Acinetobacterbaumannii isolates from a tertiary hospital in Recife-PE, Brazil, in the post-COVID-19 pandemic period. Acinetobacter baumannii isolates were collected between 2023 and 2024 from diverse clinical samples. Antimicrobial resistance testing followed standardized protocols, with β-lactamase-encoding genes detected via PCR and sequencing. Investigation into ISAba1 upstream of blaOXA-carbapenemase and blaADC genes was also conducted. Genetic diversity was assessed through ERIC-PCR. Among the 78 A. baumannii, widespread resistance to multiple antimicrobials was evident. Various acquired β-lactamase-encoding genes (blaOXA-23,-24,-58,-143, blaVIM, and blaNDM) were detected. Furthermore, this is the first report of blaVIM-2 in A. baumannii isolates harboring either the blaOXA-23-like or the blaOXA-143 gene in Brazil. Molecular typing revealed a high genetic heterogeneity among the isolates, and multi-clonal dissemination. The accumulation of genetic resistance determinants underscores the necessity for stringent infection control measures and robust antimicrobial stewardship programs to curb multidrug-resistant strains.

β-lactamase expression induces collateral sensitivity in Escherichia coli

Major antibiotic groups are losing effectiveness due to the uncontrollable spread of antimicrobial resistance (AMR) genes. Among these, β-lactam resistance genes –encoding β-lactamases– stand as the most common resistance mechanism in Enterobacterales due to their frequent association with mobile genetic elements. In this context, novel approaches that counter mobile AMR are urgently needed. Collateral sensitivity (CS) occurs when the acquisition of resistance to one antibiotic increases susceptibility to another antibiotic and can be exploited to eliminate AMR selectively. However, most CS networks described so far emerge as a consequence of chromosomal mutations and cannot be leveraged to tackle mobile AMR. Here, we dissect the CS response elicited by the acquisition of a prevalent antibiotic resistance plasmid to reveal that the expression of the β-lactamase gene blaOXA-48 induces CS to colistin and azithromycin. We next show that other clinically relevant mobile β-lactamases produce similar CS responses in multiple, phylogenetically unrelated E. coli strains. Finally, by combining experiments with surveillance data comprising thousands of antibiotic susceptibility tests, we show that β-lactamase-induced CS is pervasive within Enterobacterales. These results highlight that the physiological side-effects of β-lactamases can be leveraged therapeutically, paving the way for the rational design of specific therapies to block mobile AMR or at least counteract their effects.

Characterization of Acinetobacter baumannii at a tertiary hospital in Guangzhou: a genomic and clinical study

Acinetobacter baumannii (AB) infections have become a global public health concern due to the continued increase in the incidence of infection and the rate of resistance to carbapenems. This study aimed to investigate the genomic features of AB strains recovered from a tertiary hospital and assess the clinical implications of the findings. A total of 217 AB strains were collected between 2016 and 2018 at a tertiary hospital in Guangzhou, with 183 (84.33%) being carbapenem-resistant AB (CRAB), with the main mechanism being the carriage of the blaOXA-23 gene. The overall mortality rate of patients caused by such strains was 15.21% (n = 33). Artificial lung ventilation and the use of meropenem were mortality risk factors in AB-infected patients, while KL2 AB infection was negatively associated. Core genome multilocus sequence typing and clustering analysis were performed on the integrated AB genome collection from the NCBI database and this study to illustrate the population structure among China. The results revealed diverse core genome profiles (n = 17) among AB strains from China, and strains from this single hospital exhibited most of the core genome profiles (n = 13), suggesting genetic variability within the hospital and transmission across the country. These findings show that the high transmission potential of the CRAB strains and meropenem usage that confers a selective advantage of CRAB clinically are two major factors that pose significant challenges to the effective clinical management of AB infections. Understanding the genetic features and transmission patterns of clinical AB strains is crucial for the effective control of infections caused by this pathogen.

Carbapenem-resistant Enterobacterales in wastewater resources and healthy carriers: A survey in Iran

ABSTRACT The carbapenem-resistant Enterobacterales (CRE) pose a pressing public health concern. Here, we investigated the frequency of CRE bacteria, carbapenemase-encoding genes, and the molecular epidemiology of carbapenemase-resistant Escherichia coli in wastewater resources and healthy carriers in Iran. Out of 617 Enterobacterales bacteria, 24% were carbapenem-resistant. The prevalence of CRE bacteria in livestock and poultry wastewater at 34% and hospital wastewater at 33% was significantly higher (P ≤ 0.05) than those in healthy carriers and municipal wastewater at 22 and 17%, respectively. The overall colonization rate of CRE in healthy individuals was 22%. Regarding individual Enterobacterales species, the following percentages of isolates were found to be CRE: E. coli (18%), Citrobacter spp. (24%), Klebsiella pneumoniae (28%), Proteus spp. (40%), Enterobacter spp. (25%), Yersinia spp. (17%), Hafnia spp. (31%), Providencia spp. (21%), and Serratia spp. (36%). The blaOXA-48 gene was detected in 97% of CRE isolates, while the blaNDM and blaVIM genes were detected in 24 and 3% of isolates, respectively. The B2 phylogroup was the most prominent group identified in carbapenem-resistant E. coli isolates, accounting for 80% of isolates. High prevalence of CRE with transmissible carbapenemase genes among healthy people and wastewater in Iran underscores the need for assertive measures to prevent further dissemination.

Phenotypic and genotypic analysis of antimicrobial resistance and population structure of gastroenteritis-related Aeromonas isolates

BackgroundThe population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with gastroenteritis are not well understood. The aims of the study were to: (1) investigate the antimicrobial susceptibility profiles of Aeromonas species isolated from patients with gastroenteritis; (2) explore the relationship between AMR genes and resistance phenotypes; and (3) describe the population structure of these isolates and provide evidence of transmission events among them.MethodsThis microbiological survey was performed at the Microbiology Laboratory of the Emek Medical Center in Afula, Israel. Cultivation of Aeromonas was attempted from stool samples that tested positive by PCR. Antimicrobial susceptibility testing (AST) was performed using the Sensititre GN3F microdilution panel. Whole genome sequencing (WGS) was done using the Illumina NextSeq500/550 system. Phylogenetic studies involved multi-locus sequence typing (MLST) and core genome (cg) MLST. Resistance mechanisms were identified using the Comprehensive Antibiotic Resistance Database and compared with the AST results.ResultsThe study included 67 patient-unique isolates. The species that were identified included A. caviae (n = 58), A. dhakensis (n = 3), A. media (n = 2), A. veronii (n = 2) and A. hydrophila (n = 2). Isolates were almost uniformly susceptible to amikacin, gentamicin, aztreonam, cefepime, ceftazidime, ciprofloxacin and meropenem. All isolates with the exception of 1–2 isolates were resistant to ampicillin, cefazolin and ampicillin-sulbactam which was compatible with the presence of the blaOXA genes. Variable resistance rates were observed to cefuroxime, cefoxitin, ceftriaxone, piperacillin-tazobactam that were not correlated with the presence of other β-lactamase genes. Resistance to tetracycline and trimethoprim-sulfamethoxazole correlated with the presence of tetA and sul1, respectively. The population structure of A. caviae was highly diverse with the minority of the isolates (16/57) clustering into six defined sequence types. A cgMLST-based distance of four genes was found in one pair of isolates, suggesting common source transmission.ConclusionsA. caviae is the dominant species related to gastroenteritis and is characterized by a diverse population structure, with almost no evidence for common-source transmission. Resistance rates to most antimicrobial agents were low and partially matched with the presence of resistance genes.

Genomic characterization of carbapenem and colistin-resistant Klebsiella pneumoniae isolates from humans and dogs.

Carbapenem and colistin-resistant Enterobacteriaceae, including Klebsiella pneumoniae, have become a growing global concern, posing a significant threat to public health. Currently, there is limited information about the genetic background of carbapenem and colistin-resistant K. pneumoniae isolates infecting humans and dogs in Thailand. This study aimed to characterize carbapenem and colistin-resistant genes in six resistant K. pneumoniae clinical isolates (three from humans and three from dogs) which differed in their pulse field gel electrophoresis profiles. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), antimicrobial susceptibility testing, and whole-genome sequencing were employed to identify and analyze the isolates. All six isolates were carbapenemase-producing K. pneumoniae isolates with chromosomally carried blaSHV, fosA, oqxA and oqxB genes, as well as nine to 21 virulence genes. The isolates belonged to five multilocus sequence types (STs): one isolate from a human and one from a dog belonged to ST16, with the other two human isolates being from ST340 and ST1269 and the other two dog isolates were ST147 and ST15. One human isolate and two dog isolates harbored the same blaOXA-232 gene on the ColKP3 plasmid, and one dog isolate carried the blaOXA-48 gene on the IncFII plasmid. Notably, one human isolate exhibited resistance to colistin mediated by the mcr-3.5 gene carried on the IncFII plasmid, which co-existed with resistance determinants to other antibiotics, including aminoglycosides and quinolones. In conclusion, this study provides a comprehensive characterization of both chromosome- and plasmid-mediated carbapenem and colistin resistance in a set of K. pneumoniae clinical isolates from unrelated humans and dogs in Thailand. The similarities and differences found contribute to our understanding of the potential widescale dissemination of these important resistance genes among clinical isolates from humans and animals, which in turn may contribute to outbreaks of emerging resistant clones in hospital settings.

Occurrence and characteristics of blaOXA-181-carrying Klebsiella aerogenes from swine in China

Klebsiella aerogenes is a largely understudied opportunistic pathogen that can cause sepsis and lead to high mortality rates. In this study, we reported the occurrence of carbapenem-resistant blaOXA-181-carrying Klebsiella aerogenes from swine in China and elucidate their genomic characteristics. A total of 126 samples, including 109 swine fecal swabs, 14 environmental samples, and three feed samples were collected from a pig farm in China. The samples were enriched with LB broth culture and then inoculated into MacConkey agar plates for bacterial isolation. After PCR detection of carbapenemases genes, the blaOXA-181-carrying isolates were subjected to antimicrobial susceptibility testing, and whole-genome sequence analysis. Four Klebsiella aerogenes isolates carrying the blaOXA-181 gene were obtained from swine faecal samples. All the 4 strains were belonged to ST438. The blaOXA-181 genes were located in IncX3-ColKP3 hybrid plasmids with the core genetic structure of IS26-ΔIS3000-ΔISEcp1-blaOXA-181-ΔlysR-ΔereA-ΔrepA-ISKpn19-tinR-qnrS1-ΔIS2-IS26, which suggests the potential for horizontal transfer and further dissemination of this resistance gene among Enterobacteriaceae and other sources. This study represents the first instance of OXA-181-producing K. aerogenes being identified from swine faeces in China. It is crucial to maintain continuous monitoring and ongoing attention to the detection of K. aerogenes carrying blaOXA-181 and other resistance genes in pigs.

Rumi and Pasteurized Kareish Cheeses Are a Source of β-Lactam-Resistant Salmonella in the Nile Delta Region of Egypt: Insights into Their Incidence, AMR Pattern, Genotypic Determinants of Virulence and β-Lactam Resistance.

The spread of superbugs in dairy products can jeopardize global public health. To date, information on the incidence rates of virulent and β-lactams-resistant (BLR) Salmonella in cheeses from rural areas of Egypt has been lacking. Biochemical, serological, antibiotic susceptibility, and multiplex PCR (M-PCR) tests were performed to identify and characterize Salmonella isolates. In this study, 44 (15.71%) Salmonella isolates of eight different serotypes were recovered from 280 samples of Rumi and pasteurized Kariesh cheeses across the Nile Delta region of Egypt. The most predominant serotypes were S. Typhimurium, S. Enteritidis, and S. Infantis. The virulence genes (invA, stn, and hilA) were identified in all isolates. However, spvC was only detected in S. Typhimurium. The highest resistance was developed against Erythromycin and Clindamycin (90.91%), followed by Ceftazidime and Cephalothin (84.09%). Meropenem and colistin were the most effective antibiotics. A high proportion (79.55%) of multi-drug resistance (MDR) isolates carried narrow spectrum (NS), extended-spectrum (ES), and AmpC-BLR genes. The blaOXA-1, blaOXA-2, blaTEM-1, blaCTX-M, blaCMY-1, and blaCMY-2 BLR genes were positive in 37.04%, 29.63%, 25.93%, 14.81%, 37.04%, and 3.70% of isolates, respectively. In conclusion, a high prevalence of virulence and BLR genes harboring Salmonella strains in Egyptian cheeses is considered a great threat to public health.

An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages

Plasmids carrying antibiotic resistance genes (ARG) are the main mechanism of resistance dissemination in Enterobacterales. However, the fitness-resistance trade-off may result in their elimination. Chromosomal integration of ARGs preserves resistance advantage while relieving the selective pressure for keeping costly plasmids. In some bacterial lineages, such as carbapenemase producing sequence type ST38 Escherichia coli, most ARGs are chromosomally integrated. Here we reproduce by experimental evolution the mobilisation of the carbapenemase blaOXA-48 gene from the pOXA-48 plasmid into the chromosome. We demonstrate that this integration depends on a plasmid-induced fitness cost, a mobile genetic structure embedding the ARG and a novel antiplasmid system ApsAB actively involved in pOXA-48 destabilization. We show that ApsAB targets high and low-copy number plasmids. ApsAB combines a nuclease/helicase protein and a novel type of Argonaute-like protein. It belongs to a family of defense systems broadly distributed among bacteria, which might have a strong ecological impact on plasmid diffusion.