IS26 drives the dissemination of bla CTX-M genes in an Ecuadorian community

IMPORTANCE

The horizontal gene transfer events are the major contributors to the current spread of CTX-M-encoding genes, the most common extended-spectrum β-lactamase (ESBL), and many clinically crucial antimicrobial resistance (AMR) genes. This study presents evidence of the critical role of IS26 transposable element for the mobility of bla CTX-M gene among Escherichia coli isolates from children and domestic animals in the community. We suggest that the nucleotide sequences of IS26-bla CTX-M could be used to study bla CTX-M transmission between humans, domestic animals, and the environment, because understanding of the dissemination patterns of AMR genes is critical to implement effective measures to slow down the dissemination of these clinically important genes.

Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?

IMPORTANCE

Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.

Isolation of Pseudomonas aeruginosa from Persistent Bacterial Coinfection of a COVID-19 Patients with Molecular Detection of Antibiotics Resistance Genes

Pseudomonas aeruginosa (P. aeruginosa) have a considerable risk to public health in the world, due to its high ability to develop resistance to different classes of antibiotics. It has been discovered as a prevalent coinfection pathogen that causes sickness exacerbation in COVID-19 patients. This study aimed to determine the prevalence of P. aeruginosa from COVID-19 patients in Al Diwaniyah province, Iraq and to identify its genetic resistance pattern. 70 clinical samples were obtained from severe cases of patients (RT-PCR positive for SARS-COV-2 on a nasopharyngeal swab) who attended Al Diwaniyah Academic Hospital. 50 P. aeruginosa bacterial isolates were detected via microscopic examination, routine cultured and biochemical testing, then validated by the VITEK-2 compact system. VITEK reported 30 positive results, which later confirmed through molecular detection using 16s RNA specific for detection and a phylogenetic tree.20 isolates had positive PCR findings and 5 isolates submitted to GenBank with accession numbers OL314557.1, OL314556.1, OL314555.1, OL314554.1, OL314553.1.For antibiotic resistance genes, the number of the isolates containing blaOXA-1 and blaCTX-M 18 (90 percent) and 16 (80 percent) respectively. To study its adaptation in a SARS-CoV-2 infected environment, genomic sequencing investigations were undertaken with phenotypic validation. In conclusion, we demonstrate that multidrug resistant P. aeruginosa play an important role in in vivo colonization in COVID-19 patients and could be one of the causes of death of these patients which indicates the great challenge to clinicians in the facing of this serious disease.

Novel chromosomal insertions of ISEcp1-blaCTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli

Background

The epidemiology of extended-spectrum β-lactamases (ESBLs) has undergone dramatic changes, with CTX-M-type enzymes prevailing over other types. bla_CTX-M genes, encoding CTX-M-type ESBLs, are usually found on plasmids, but chromosomal location is becoming common. Given that bla_CTX-M-harboring strains often exhibit multidrug resistance (MDR), it is important to investigate the association between chromosomally integrated bla_CTX-M and the presence of additional antimicrobial resistance (AMR) genes, and to identify other relevant genetic elements.

Methods

A total of 46 clinical isolates of cefotaxime-resistant Enterobacteriaceae (1 Enterobacter cloacae, 9 Klebsiella pneumoniae, and 36 Escherichia coli) from Zambia were subjected to whole-genome sequencing (WGS) using MiSeq and MinION. By reconstructing nearly complete genomes, bla_CTX-M genes were categorized as either chromosomal or plasmid-borne.

Results

WGS-based genotyping identified 58 AMR genes, including four bla_CTX-M alleles (i.e., bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-27, and bla_CTX-M-55). Hierarchical clustering using selected phenotypic and genotypic characteristics suggested clonal dissemination of bla_CTX-M genes. Out of 45 bla_CTX-M gene-carrying strains, 7 harbored the gene in their chromosome. In one E. cloacae and three E. coli strains, chromosomal bla_CTX-M-15 was located on insertions longer than 10 kb. These insertions were bounded by ISEcp1 at one end, exhibited a high degree of nucleotide sequence homology with previously reported plasmids, and carried multiple AMR genes that corresponded with phenotypic AMR profiles.

Conclusion

Our study revealed the co-occurrence of ISEcp1-bla_CTX-M-15 and multiple AMR genes on chromosomal insertions in E. cloacae and E. coli, suggesting that ISEcp1 may be responsible for the transposition of diverse AMR genes from plasmids to chromosomes. Stable retention of such insertions in chromosomes may facilitate the successful propagation of MDR clones among these Enterobacteriaceae species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00941-8.

Prevalence and distribution of blaCTX-M, blaSHV, blaTEM genes in extended- spectrum β- lactamase- producing E. coli isolates from broiler farms in the Philippines

Background

Antimicrobial resistance is a worldwide problem causing serious health threats. Escherichia coli is one of the most important bacteria that causes resistance problem. These bacteria produce an enzyme called extended-spectrum β-lactamase (ESBL) that allows it to become resistant to a wide variety of penicillins and cephalosporins. Currently, no information or published studies on ESBL-producing E.coli in broilers are available in the Philippines.

This cross-sectional study was conducted to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)-encoding genes, bla_CTX-M, bla_SHV, and bla_TEM, among E. coli isolates from broiler farms in Luzon, Philippines.

Results

Results showed a farm prevalence of 66. 67%. A total of 69 (44.23%) ESBL-producing E. coli were isolated from boot swabs and cloacal swab samples from broiler farms. All major bla_CTX-M groups except bla_CTX-M-25 group were identified in the isolates. The most prevalent group was bla_CTX-M-1, 72.46% (CI: 60.38–82.54%), followed by bla_CTX-M-2, bla_CTX-M-9 group and bla_CTX-M-8. The bla_TEM and bla_SHV genes were identified in 57.97 and 27.54% of isolates, respectively. The bla_CTX-M and bla_TEM were the most common gene combinations (33.33%). Coexistence of bla_CTX-M types was observed in 50 (73.53%) isolates.

Conclusion

This study shows the high prevalence, diversity of patterns and coexistence of ESBL genes in the E. coli isolates from cloacal and boot swabs from broiler farms which pose risks of possible transmission to the environment, other animals and human.

Prevalence of TEM, SHV, and CTX-M genes of extended-spectrum β-lactamase-producing Escherichia coli strains isolated from urinary tract infections in adults

Urinary tract infections (UTIs) are one of the major sources of widespread infectious diseases in the community as well as in the hospitals which increase the cause of morbidity and mortality. Prevalence of extended-spectrum-β-lactamase (ESBL)-producing uropathogenic E. coli isolates has been found to be increased rapidly across the world. The present study was undertaken to find out the frequency of bla _TEM, bla _CTX-M, and bla _SHV genes among E. coli isolates from UTI and detect their sensitivity pattern. A total of 112 non-repeated E. coli isolates obtained from urine samples of UTI diagnosed patients were included in this study. Antibiotic susceptibility test was done by disc diffusion method. Seventy seven (68.75%) isolates were MDR and tested for ESBL. ESBL-positive isolates were screened for bla _TEM, bla _CTX-M, and bla _SHV genes by monoplex PCR (polymerase chain reaction). Among 46 ESBL-producing E. coli isolates, 8.69% harboured all the three bla genes. The bla _TEM was the predominant (93.47%) gene followed by bla _CTX-M (82.6%) and bla _SHV (4.34%). It can be concluded that the prevalence of MDR (multidrug resistance) ESBL-producing E. coli appears to be high and the highest identified gene was bla _TEM. The knowledge of resistance pattern can help physician's select suitable empirical antibiotic regimens, so that antibiotics showing high-resistance pattern can be avoided.