Genotypic and phenotypic profiles of antibiotic-resistant bacteria isolated from hospitalised patients in Bangladesh

Emerging multi-drug resistant and extended-spectrum β-lactamase (ESBL)-positive enterotoxigenic E. coli (ETEC) clones circulating in aquatic environments and in patients

Diarrheal disease pathogens often spread through water-borne routes. Enterotoxigenic Escherichia coli (ETEC) is a major bacterial agent causing diarrheal disease in children, adults, and travelers in endemic areas. In addition, ETEC is responsible for outbreaks of water and food-borne gasteroenteritis globally, ETEC isolates also show robust survival capacity in various environmental settings, including aquatic environments. During the last decade, studies of ETEC isolates have indicated a rapid increase in multi-drug resistant and extended-spectrum β-lactamase (ESBL)-positive human-specific ETEC strains. These have been found in both environmental water sources and human patients, warranting the urgent need for focused monitoring of antibiotic resistance development in ETEC. Whole genome sequencing (WGS) of isolates from environmental, animal, and human sources enables in silico surveillance of emerging pathogenic and multi-drug resistant strains. This method allows for re-analysis of genomic data, aiding in identification of new variants of pathogenic clones. By integrating data from diverse sources inclusing sequenced isolates, we found that certain ETEC clonal lineages e.g., those expressing certain toxin-colonization factor profiles including STp/CS6, LT STh/CS2 + CS3, and LT STh/CFA/I are more at risk to develop multi-drug resistance than other ETEC lineages. Comparizon of multi-locus sequence types from papers with WGS data indicated ST182, ST4, ST2332 and new ST types to be emerging multi-drug resistant ETEC. We conclude that further studies on sequenced ETEC/E. coli genomes are needed to enhance our understanding of the dynamics of ETEC evolution, and the relation of virulence and resistance profiles in both environmental and clinical isolates.

Single nucleotide polymorphisms and penicillin non-susceptibility among invasive Streptococcus pneumoniae from Vietnam and India: Insights from a comparative genomics study

OBJECTIVES

Streptococcus pneumoniae (S. pneumoniae) is a significant cause of global morbidity and mortality across all age groups. Antimicrobial resistance (AMR), particularly penicillin resistance, is a significant treatment challenge. The study investigates AMR patterns among S. pneumoniae isolates from Vietnam, a country with high penicillin non-susceptibility, and India which in comparison has lower penicillin non-susceptibility. The present study focuses on penicillin resistance-associated genes and single nucleotide polymorphisms (SNPs), that contribute to pathogenicity.

METHODS

Invasive S. pneumoniae belonging to serotypes 23F (n = 13) and 19F (n = 20) genome sequences from Vietnam (n = 13) and India (n = 20) were retrieved and annotated to identify core genes. These genes were screened for antimicrobial resistance using the database. The genome sequences were mapped to a reference genome to detect the gene variants and were analysed for identifying specific mutations that contribute to pathogenicity.

RESULTS

Annotations identified pbp1a, pbp2b, and pbp2x (pbpX) as relevant AMR genes. In Vietnam, pbpX was a core gene, with 41 SNPs detected, of which 7 were deleterious mutations contributing to penicillin resistance. In contrast, pbpX was completely absent in the Indian genomes analysed.

CONCLUSIONS

The current study highlights the genetic basis of penicillin non-susceptibility among invasive S. pneumoniae serotypes 23F and 19F and focuses on regional variations in resistance between India and Vietnam. The pbpX was identified as a core gene among penicillin-resistant pneumococci in Vietnam. In India, the absence of pbpX highlights genomic diversity, distinct from the uniformity observed in Vietnamese genomes. The study further predicts that deleterious SNPs are associated with pathogenicity.

Occurrence of Plasmid-Mediated Quinolone Resistance and Carbapenemase-Encoding Genes in Pseudomonas aeruginosa Isolates from Nosocomial Patients in Aguascalientes, Mexico

Pseudomonas aeruginosa is a leading cause of healthcare-associated infections, which are related to substantial morbidity and mortality. The incidence of Plasmid-Mediated Quinolone Resistance (PMQR) determinants has been previously reported in this bacterium. However, there is limited information regarding the presence of PMQR and carbapenemase-encoding genes simultaneously. This study aims to analyze the prevalence of these determinants on P. aeruginosa strain isolated from clinical patients in the State of Aguascalientes, Mexico. Fifty-two P. aeruginosa isolates from nosocomial patients were collected from Centenario Hospital Miguel Hidalgo. This is a retrospective observational study conducted at a single center. Antibiotic susceptibility was tested using the Vitek-2 system. Only carbapenem-resistant isolates were included in this study. Carbapenemase-encoding genes and PMQR determinants were screened by polymerase chain reaction (PCR). Resistance rates of 100% were found on tigecycline and ceftriaxone. Of the 52 isolates, 34.6% were positive for the qnr genes, 46.2% for the oqxA gene, and 25% for the aac-(6')-lb gene. The most frequent carbapenemase genes found in the samples were blaOXA-51 (42.3%), blaOXA-1 (15.4%), and blaVIM (15.4%). blaOXA-51 co-carrying oqxA was detected in 21.1% of the isolates, blaOXA-51 co-carrying aac-(6')-lb in 11.5%, blaVIM co-carrying aac-(6')-lb in 3.8%, and blaKPC co-carrying oqxA in 5.8%. Systematic surveillance to detect carbapenemase-encoding genes and PMQR determinants, and rational prescription using the last-line drugs could help in preventing the dissemination of multidrug-resistant determinants.

Epidemiological pattern and genomic insights into multidrug-resistant ST491 Acinetobacter baumannii BD20 isolated from an infected wound in Bangladesh: Concerning co-occurrence of three classes of beta lactamase genes

OBJECTIVE

Multidrug-resistant (MDR) Acinetobacter baumannii is a major issue within healthcare facilities in Bangladesh due to its frequent association with hospital-acquired infections. In this study we report on a carbapenem-resistant draft genome sequence of an A. baumannii BD20 sample isolated from an infected wound in Bangladesh.

METHODS

A. baumannii BD20 was isolated from an infected burn wound. Whole-genome sequencing was carried out and annotated using PGAP and Prokka. Sequence type, antimicrobial resistance genes, virulence factor genes, and metal resistance genes were investigated. Core genome multilocus sequence typing-based phylogenomic analysis between A. baumannii BD20 and 213 A. baumannii strains retrieved from the NCBI GenBank database was performed using the BacWGSTdb 2.0 server.

RESULTS

A. baumannii BD20 (MLST 491) was resistant to all the antibiotics tested, except for colistin and polymyxin B. Along with many other antibiotic resistance genes, the isolate harbored three classes of beta lactamase-producing genes: blaGES-11 (class A), blaOXA-69 (class D), blaADC-10 (class C), and blaADC-11 (class C). Additionally, the strain carried several virulence genes and metal resistance determinants, which may contribute to its increased virulence. Core genome MLST-based phylogenomic analysis revealed that A. baumannii BD20 was closely related to another ST491 strain isolated from Singapore.

CONCLUSIONS

The findings of this study underscore the growing challenge of MDR A. baumannii, emphasizing the need for vigilant surveillance and infection-control measures in healthcare settings in order to address these emerging threats effectively.

Extended-spectrum beta-lactamase in Escherichia coli isolated from humans, animals, and environments in Bangladesh: A One Health perspective systematic review and meta-analysis

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has been linked to both life-threatening hospital- and community-acquired infections across the globe. Here, we conducted a systematic review and meta-analysis to evaluate the prevalence of ESBL in E. coli isolated from humans, animals, and environments in Bangladesh. Following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, the current systematic review and meta-analysis was taken into account for studies published between 2010 and 2021 in peer-reviewed journals. The meta-analysis was performed on "R" version 4.2.2. A total of 36 studies were included in this systematic review and meta-analysis; among them, 22 were human, seven were animal, four were environmental, and three were multidisciplinary studies. The meta-analysis revealed that the pooled prevalence of ESBL-producing E. coli in Bangladesh was 21% (95% CI: 15%-27%). On the sample basis, the pooled prevalence of ESBL-producing E. coli in humans, animals, and environments was 17% (95% CI: 11%-23%), 22% (95% CI: 9%-34%), and 39% (95% CI: 16%-62%), respectively. All the pooled prevalence of ESBL-producing E. coli showed substantial heterogeneity (I2 > 75%; p < 0.05) among the selected studies. This systematic review reported 13 different types of resistance genes encoding ESBL, such as blaTEM-1 (37.5%), blaCMY (34.6%), blaCTX-M-1 (20.7%), blaCTX-M-15 (16.1%), blaTEM (12.3%), blaCTX-M and blaOXA (9.6%), blaOXA-1 (5.8%), blaampC (3.9%), blaSHV (3.8%), blaCMY-2 (2.3%), blaCTX-M-14 (1.3%), and blaCTX-M-9 (0.3%). Moreover, 39 types of epidemiologically important clones (including ST10 and ST131) were detected in ESBL-producing E. coli isolated from humans, animals, and environments in Bangladesh. To the best of our knowledge, this is the first systematic review and meta-analysis of integrated studies on ESBL-producing E. coli using the One Health approach in Bangladesh. The high prevalence of ESBL-producing E. coli, their resistance genes, and epidemiologically important clones in humans, animals, and environments highlights the importance of implementing comprehensive antimicrobial resistance (AMR) surveillance under a One Health perspective to mitigate the AMR consequences in Bangladesh.

Antimicrobial Activity of Apis mellifera Bee Venom Collected in Northern Peru

Due to the emergence of microorganisms resistant to antibiotics and the failure of antibiotic therapies, there is an urgent need to search for new therapeutic options, as well as new molecules with antimicrobial potential. The objective of the present study was to evaluate the in vitro antibacterial activity of Apis mellifera venom collected in the beekeeping areas of the city of Lambayeque in northern Peru against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Bee venom extraction was performed by electrical impulses and separated using the Amicon ultra centrifugal filter. Subsequently, the fractions were quantified by spectrometric 280 nm and evaluated under denaturant conditions in SDS-PAGE. The fractions were pitted against Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29213, and Pseudomonas aeruginosa ATCC 27853. A purified fraction (PF) of the venom of A. mellifera and three low molecular weight bands of 7 KDa, 6 KDa, and 5 KDa were identified that showed activity against E. coli with a MIC of 6.88 µg/mL, while for P. aeruginosa and S. aureus, it did not present a MIC. No hemolytic activity at a concentration lower than 15.6 µg/mL and no antioxidant activity. The venom of A. mellifera contains a potential presence of peptides and a predilection of antibacterial activity against E. coli.

Prevalence of silver resistance determinants and extended-spectrum β-lactamases in bacterial species causing wound infection: First report from Bangladesh

Background

The use of silver is rapidly rising in wound care and silver-containing dressings are widely used along with other antibiotics, particularly β-lactams. Consequently, concerns are being raised regarding the emergence of silver-resistance and cross-resistance to β-lactams. Therefore, this study aimed to determine the phenotypic and genotypic profiles of silver-resistance and extended-spectrum β-lactamases in isolates from chronic wounds.

Methods

317 wound swab specimens were collected from tertiary hospitals of Dhaka city and analysed for the microbial identification. The antibiotic resistance/susceptibility profiles were determined and phenotypes of silver resistant isolates were examined. The presence of silver-resistance (sil) genes (silE, silP, and silS) and extended-spectrum β-lactamases (ESBL) (CTX-M-1, NDM-1, KPC, OXA-48, and VIM-1) were explored in isolated microorganisms.

Results

A total of 501 strains were isolated with Staphylococcus aureus (24%) as the predominant organism. In 29% of the samples, polymicrobial infections were observed. A large proportion of Enterobacterales (59%) was resistant to carbapenems and a significantly high multiple antibiotic-resistance indexes (>0.2) were seen for 53% of organisms (P < 0.001). According to molecular analysis, the most prevalent types of ESBL and sil gene were CTX-M-1 (47%) and silE (42%), respectively. Furthermore, phenotypic silver-nitrate susceptibility testing showed significant minimum-inhibitory-concentration patterns between sil-negative and sil-positive isolates. We further observed co-occurrence of silver-resistance determinants and ESBLs (65%).

Conclusions

Notably, this is the first-time detection of silver-resistance along with its co-detection with ESBLs in Bangladesh. This research highlights the need for selecting appropriate treatment strategies and developing new alternative therapies to minimize microbial infection in wounds.

Genomic landscape of prominent XDR Acinetobacter clonal complexes from Dhaka, Bangladesh

BACKGROUND

Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones.

RESULTS

Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes (CCs): the globally dominant CC1 and CC2, and CC10; one strain had a novel sequence type (ST). AMR phenotype-genotype agreement was observed and the genomes contained various beta-lactamase genes including bla_OXA-23 (n = 12), bla_OXA-66 (n = 6), and bla_NDM-1 (n = 3). All genomes displayed roughly similar virulomes, however some virulence genes such as the Acinetobactin bauA and the type IV pilus gene pilA displayed high genetic variability. CC2 strains carried highest levels of plasmidic gene content and possessed conjugative elements carrying AMR genes, virulence factors and insertion sequences.

CONCLUSION

This study presents the first comparative genomic analysis of XDR clinical Acinetobacter spp. from Bangladesh. It highlights the prevalence of different classes of beta-lactamases, mobilome-derived heterogeneity in genetic architecture and virulence gene variability in prominent Acinetobacter clonal complexes in the country. The findings of this study would be valuable in understanding the genomic epidemiology of A. baumannii clones and their association with closely related pathogenic species like A. nosocomialis in Bangladesh.

Extended Spectrum- and Carbapenemase-Based β-Lactam Resistance in the Arabian Peninsula-A Descriptive Review of Recent Years

Antimicrobial resistance (AMR) is a global problem that also includes countries of the Arabian Peninsula. Of particular concern, is the continuing development of extended-spectrum β-lactamases (ESBLs) in the countries of this region. Additionally, antibiotic treatment options for ESBL-producing bacteria are becoming limited, primarily due to the continuing development of carbapenem resistance (CR), carbapenems being frequently used to treat such infections. An overview of recent publications (2018-2021) indicates the presence of ESBL and/or CR in patients and hospitals in most countries of the Arabian Peninsula, although the delay between microbial isolation and publication inevitably makes an accurate analysis of the current situation rather difficult. However, there appears to be greater emphasis on CR (including combined ESBL and CR) in recent publications. Furthermore, although publications from Saudi Arabia are the most prevalent, this may simply reflect the increased interest in ESBL and CR within the country. Enhanced ESBL/CR surveillance is recommended for all countries in the Arabian Peninsula.