Co-existence of NDM-, aminoglycoside- and fluoroquinolone-resistant genes in carbapenem-resistant Escherichia coli clinical isolates from Pakistan

Strict relationship between phenotypic and plasmid-associated genotypic of multidrug-resistant Escherichia coli isolated from Taihe Black-Boned Silky Fowl farms

Taihe Black-Boned Silky Fowl (TBSF) is a unique breed in China, characterized by a high concentration of melanin deposited throughout its body. Compared to broiler chickens, many antibiotics exhibit significantly longer withdrawal periods in TBSF. Given that antibiotic exposure is widely recognized as the primary selective pressure driving the persistence and dissemination of antibiotic resistance genes (ARGs) across diverse environments, it is crucial to investigate the occurrence and prevalence of ARGs within TBSF farming systems. In this study, 34 Escherichia coli strains isolated from 22 TBSF farms were subjected to phenotypic and genotypic analyses. The isolates were tested for susceptibility to 28 antimicrobial drugs representing nine antibiotic classes to determine their antimicrobial resistance phenotypes. Draft genome sequences of these E. coli strains were obtained, and the ARGs carried by mobile genetic elements, particularly plasmids, were analyzed for their association with susceptibility phenotype. The genetic context of key ARGs in these E. coli isolates was further characterized. Network analysis was employed to investigate the correlations between ARGs, phenotypes, and drug residues. The results demonstrated that high rates of antimicrobial resistance were observed, with 100 % and 29.4 % of isolates exhibiting resistance to four or more and eight or more antibiotic classes, respectively. According to whole-genome sequencing, a total of 143 ARGs were identified. The antimicrobial resistance phenotypes were consistently correlated with the presence of corresponding ARGs in the 34 E. coli genomes. 100 % of the β-lactams antibiotics resistant mechanism could be attributed to the presence of the resistance gene blaTEM and/or blaOXA-10. Similarly, resistance to tetracyclines, chloramphenicols, aminoglycosides, and fluoroquinolones was fully explained by the presence of tetR and/or tetA, floR and/or cmlA, ant(3'')-IIa, aph(3'')-Ib, aph(6)-Id, aac(3)-IId, and aadA, and qnrS and/or mutant gyrA/parC/mdtH. The majority of these key ARGs were found to be plasmid-associated. This study verified and highlighted the prevalent horizontal gene transfer of ARGs in TBSF farms. Factors such as hygiene status, biosecurity measures, and other environmental conditions might play a more significant role than antimicrobial usage in facilitating the horizontal gene transfer of ARGs in TBSF farms. Appropriate measures should be taken to control the transmission and dissemination of these mobile genetic elements associated ARGs and prevent their entry into the human clinical environment from TBSF breeding environment.

Food Safety Concerns in Pakistan: Monitoring of Antimicrobial-Resistant Bacteria and Residue Contamination in Commercially Available Fish and Poultry Meat Samples

Food safety is a critical issue in the 21st century due to antibiotic-resistant bacteria causing harmful foodborne diseases. This comprehensive study meticulously examined the presence of bacterial isolates, quinolone residue, and antimicrobial resistance genes in samples of broiler and fish meat. Forty samples were collected from various locations in the Faisalabad metropolis. The samples underwent culture on various types of agar, and the Vitek 2 compact system was used to confirm the isolates along with determining the minimum inhibitory concentration of antibiotics. Additionally, polymerase chain reaction was used to identify antimicrobial-resistant genes, and an enzyme-linked immunosorbent assay (ELISA) kit was employed to detect quinolone residue in each sample. Out of 40 fish samples, 66 polymicrobials were identified with Escherichia coli being the most prevalent (26.6%), followed by Klebsiella pneumoniae (16.6%) and Acinetobacter baumannii (15%). Furthermore, 70 polymicrobial were identified in the broiler samples, with 41.6% E. coli and 15% K. pneumoniae. In fish isolates, 14 (21%) qnr gene, 18 (27.2%) blaCTX-M, and 11 (16.6%) blaNDM-1, and in broiler samples, 19 (27.1%) qnr gene, 19 (27.1%) blaTEM and 22 (31.4%) blaCTX-M, and 5 (7.1%) blaNDM-1 were found. Eighteen (45%) broiler and 7 (17.5%) fish samples with more than 100 µg per kg (ppb) for quinolone residues. The study concluded that the increased prevalence of multidrug-resistant bacteria and quinolone residue poses a significant threat to consumer health.

Genomic analysis of blaNDM-1-carrying-Pseudomonas aeruginosa ST2407 in the chromosome from Brazil

Pseudomonas aeruginosa, an opportunistic pathogen often found in Healthcare-associated infections (HAI), has shown increased resistance to carbapenems (imipenem, meropenem, doripenem), the primary treatment options. We've seen a rise in carbapenemase-producing P. aeruginosa in Brazil, including NDM-producers. This study characterises an isolate carrying blaNDM-1 from a patient's skin fragment in a Brazilian hospital. The whole genomic sequence (WGS) of P. aeruginosa CCBH26428 was extracted and sequenced using Illumina and minION platforms. The assembly used MinION results mapped with Illumina reads, and annotation was performed by the RAST server. Resistance genes and clonality were identified using the CABGen platform. Additional information was carried out by manual annotation using Geneious software and BLAST tool. The genomic analysis revealed a genome of 6.995.008 bp and G+C 65.9 %. P. aeruginosa CCBH26428 belongs to ST2407. The blaNDM gene, associated with ISAba125, was found in a 63.862 pb genomic region flanked by IS26 insertion sequences. This region also contained the repA of the plasmid incompatibility group IncC2 and other resistance genes, suggesting it is a possible "translocation unit". Additionally, 17 resistance genes, mutations in OprD and GyrA, and several virulence genes were detected, potentially exacerbating the infection. This study is report a WGS analysis of P. aeruginosa carrying blaNDM-1 in Brazil, highlighting the role of IS26 in the acquisition and spread of resistance genes between plasmids and chromosomes.

The Rising Tide of Antibiotic Resistance: A Study on Extended-Spectrum Beta-Lactamase and Carbapenem-Resistant Escherichia coli and Klebsiella pneumoniae

BACKGROUND

The global spread of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Enterobacterales (CRE) poses a significant concern. Acquisition of antimicrobial resistance genes leads to resistance against several antibiotics, limiting treatment options. We aimed to study ESBL-producing and CRE transmission in clinical settings.

METHODS

From clinical samples, 227 ESBL-producing and CRE isolates were obtained. The isolates were cultured on bacterial media and confirmed by VITEK 2. Antibiograms were tested against several antibiotics using VITEK 2. The acquired resistance genes were identified by PCR.

RESULTS

Of the 227 clinical isolates, 145 (63.8%) were Klebsiella pneumoniae and 82 (36.1%) were Escherichia coli; 76 (33.4%) isolates were detected in urine, 57 (25.1%) in pus swabs, and 53 (23.3%) in blood samples. A total of 58 (70.7%) ESBL-producing E. coli were resistant to beta-lactams, except for carbapenems, and 17.2% were amikacin-resistant; 29.2% of E. coli isolates were resistant to carbapenems. A total of 106 (73.1%) ESBL-producing K. pneumoniae were resistant to all beta-lactams, except for carbapenems, and 66.9% to ciprofloxacin; 38 (26.2%) K. pneumoniae were resistant to carbapenems. Colistin emerged as the most effective antibiotic against both bacterial types. Twelve (20.6%) E. coli isolates were positive for blaCTX-M, 11 (18.9%) for blaTEM, and 8 (33.3%) for blaNDM. Forty-six (52.3%) K. pneumoniae isolates had blaCTX-M, 27 (18.6%) blaTEM, and 26 (68.4%) blaNDM.

CONCLUSION

This study found a high prevalence of drug-resistant ESBL-producing and CRE, highlighting the need for targeted antibiotic use to combat resistance.

Transcontinental Dissemination of Enterobacterales Harboring blaNDM-1 in Retail Frozen Shrimp

The global food trade provides a means of disseminating antimicrobial resistant (AMR) bacteria and genes. Using selective media, carbapenem-resistant species of Enterobacterales (Providencia sp. and Citrobacter sp.), were detected in a single package of imported frozen shrimp purchased from a grocery store in Ohio, USA. Polymerase chain reaction confirmed that both isolates harbored blaNDM-1 genes. Following PacBio long read sequencing, the sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline. The blaNDM-1 genes were found in IncC plasmids, each with different antimicrobial resistance island configuration. We found that the blaNDM-1 AMR islands had close relationships with previously reported environmental, food, and clinical isolates detected in Asia and the United States, highlighting the importance of the food chain in the global dissemination of antimicrobial resistance.