One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings

Genomic characterization of Pseudomonas aeruginosa from canine otitis highlights the need for a One Health approach to this opportunistic pathogen

In humans, Pseudomonas aeruginosa is well known as a prominent opportunistic pathogen associated with antimicrobial resistance (AMR), which presents a major challenge to successful treatment. This is also the case in animals, particularly in companion dogs where P. aeruginosa is a common cause of otitis. Despite its clinical significance, little data are available on the genomics and epidemiology of P. aeruginosa in dogs. To address this, we have genome-sequenced 34 canine otitis P. aeruginosa isolates from a veterinary referral hospital and analysed these along with a further 62 publicly available genomes from canine isolates. Phylogenetic analysis revealed that all three P. aeruginosa phylogroups, A-C, are represented amongst a diverse bacterial population isolated from dogs. We identify examples of persistent or recurrent infection by the same strain of up to 309 days between sampling, demonstrating the difficulty of successfully eradicating infection. Isolates encoded a variety of AMR genes with genomic and phenotypic AMR correlating poorly for β-lactams but showing complete concordance between fluoroquinolone resistance and quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV. Pangenome-wide analysis between 80 canine otitis isolates (34 newly sequenced here and a further 46 publicly available) and a reference collection of 491 human isolates found no genes which were over-represented or specific to either host species, indicating similar strains infect both humans and dogs. This agrees with the sharing of multilocus sequence types between dogs and humans, including the isolation here of ST235 from three dogs, a lineage prominent among the multidrug resistant (MDR) and extensively drug-resistant (XDR) international high-risk clones of P. aeruginosa causing human infections. The presence of such 'high-risk' clones in companion dogs is concerning given their potential impact on animal health and the potential for zoonotic spread. These data provide new insight into this difficult-to-treat veterinary pathogen and promote the need for a One Health approach to tackling it.

One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings

BACKGROUND

WGS can potentially be routinely used in clinical microbiology settings, especially with the increase in sequencing accuracy and decrease in cost. Escherichia coli is the most common bacterial species analysed in those settings, thus fast and accurate diagnostics can lead to reductions in morbidity, mortality and healthcare costs.

OBJECTIVES

To evaluate WGS for diagnostics and surveillance in a collection of clinical E. coli; to examine the pool of antimicrobial resistance (AMR) determinants circulating in Denmark and the most frequent STs; and to evaluate core-genome MLST (cgMLST) and SNP-based clustering approaches for detecting genetically related isolates.

METHODS

We analysed the genomes of 699 E. coli isolates collected throughout all Danish Clinical Microbiology Laboratories. We used rMLST and KmerFinder for species identification, ResFinder for prediction of AMR, and PlasmidFinder for plasmid identification. We used Center for Genomic Epidemiology MLST, cgMLSTFinder and CSI Phylogeny to perform typing and clustering analysis.

RESULTS

Genetic AMR determinants were detected in 56.2% of isolates. We identified 182 MLSTs, most frequently ST-69, ST-73, ST-95 and ST-131. Using a maximum 15-allele difference as the threshold for genetic relatedness, we identified 23 clusters. SNP-based phylogenetic analysis within clusters revealed from 0 to 13 SNPs, except two cases with 111 and 461 SNPs.

CONCLUSIONS

WGS data are useful to characterize clinical E. coli isolates, including predicting AMR profiles and subtyping in concordance with surveillance data. We have shown that it is possible to adequately cluster isolates through a cgMLST approach, but it remains necessary to define proper interpretative criteria.

Genomic Diversity, Virulome, and Resistome of Streptococcus agalactiae in Northeastern Brazil: Are Multi-Host Adapted Strains Rising?

Streptococcus agalactiae, known as group B streptococci (GBS), colonizes the digestive and genitourinary tracts and causes neonatal diseases and infections in immunocompromised and elderly individuals. GBS neonatal disease prevention includes intrapartum antibiotic prophylaxis. We characterized 101 GBS isolates obtained from patients in João Pessoa, northeastern Brazil, owing to the need to develop and implement vaccines to prevent GBS infections. Capsular types were determined using multiplex-PCR, and antibiotic susceptibility profiles were determined using disc diffusion or the gradient strip method. Clonal diversity was evaluated using pulsed-field gel electrophoresis. Fourteen selected isolates had the genome sequenced and evaluated for virulence and resistance genes. The GBS population had high clonal diversity, with serotype Ia and V prevalence. Among the sequenced isolates, we detected antibiotic resistance genes (ant(6)-Ia, catA8, ermA, ermB, lsaE, lsnuB, mefA/msrD, tetM, tetO, and tetS), several virulence genes, and mobile genetic elements integrated into the chromosome. The most frequent Sequence Type (ST) was ST144, followed by ST196, ST28, ST19, ST12, ST23, ST103, and the new ST1983 (CC103). Phylogenetically, ST103 and ST1983 were distant from the other STs. Our data revealed highly virulent GBS strains in this population and a new ST that could be related to a zoonotic origin.

Clinical considerations on antimicrobial resistance potential of complex microbiological samples

Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.

Multidrug-resistant Gram-negative bacterial infections

Multidrug-resistant Gram-negative bacterial infections cause significant morbidity and mortality globally. These pathogens easily acquire antimicrobial resistance (AMR), further highlighting their clinical significance. Third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales (eg, Escherichia coli and Klebsiella spp), multidrug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii are the most problematic and have been identified as priority pathogens. In response, several new diagnostic technologies aimed at rapidly detecting AMR have been developed, including biochemical, molecular, genomic, and proteomic techniques. The last decade has also seen the licensing of multiple antibiotics that have changed the treatment landscape for these challenging infections.

Integrative genomics would strengthen AMR understanding through ONE health approach

Emergence of drug-induced antimicrobial resistance (AMR) forms a crippling health and economic crisis worldwide, causing high mortality from otherwise treatable diseases and infections. Next Generation Sequencing (NGS) has significantly augmented detection of culture independent microbes, potential AMR in pathogens and elucidation of mechanisms underlying it. Here, we review recent findings of AMR evolution in pathogens aided by integrated genomic investigation strategies inclusive of bacteria, virus, fungi and AMR alleles. While AMR monitoring is dominated by data from hospital-related infections, we review genomic surveillance of both biotic and abiotic components involved in global AMR emergence and persistence. Identification of pathogen-intrinsic as well as environmental and/or host factors through robust genomics/bioinformatics, along with monitoring of type and frequency of antibiotic usage will greatly facilitate prediction of regional and global patterns of AMR evolution. Genomics-enabled AMR prediction and surveillance will be crucial - in shaping health and economic policies within the One Health framework to combat this global concern.

Evaluation of phenotypic and genotypic methods for the identification and characterization of bacterial isolates recovered from catheter-associated urinary tract infections

AIMS

Urinary tract infections are the most common hospital-acquired infection, 80% of which are associated with catheterization. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital.

METHODS AND RESULTS

We compared five bacterial identification methods, including biochemical testing, matrix-assisted laser desorption/ionization biotyping, and genome sequencing, finding differences in genus- or species-level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design.

CONCLUSIONS

This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body.

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.

Rapid Phenotypic Antibiotics Susceptibility Analysis by a 3D Printed Prototype

One of the most important public health concerns is the increase in antibiotic-resistant pathogens and corresponding treatment of associated infections. Addressing this challenge requires more efficient use of antibiotics, achievable by the use of evidence-based, effective antibiotics identified by antibiotic susceptibility testing (AST). However, the current standard method of phenotypic AST used for this purpose requires 48 h or more from sample collection to result. Until results are available, broad-spectrum antibiotics are used to avoid delaying treatment. The turnaround time must therefore be shortened in order for the results to be available before the second administration of antibiotics. The phenotypic electrochemical AST method presented here identifies effective antibiotics within 5-10 h after sampling. Spiked serum samples, including polymicrobial samples, with clinically relevant pathogens and respective concentrations commonly found in bloodstream infections (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa) are used. Direct loading of the test with diluted serum eliminates the need for a pre-culture, as required by existing methods. Furthermore, by combining several electrochemical measurement procedures with computational analysis, allowing the method to be used both online and offline, the AST achieves a sensitivity of 94.44% and a specificity of 95.83% considering each replicate individually.

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.

Genomic surveillance for antimicrobial resistance - a One Health perspective

Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.

Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis

IMPORTANCE

The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.

Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital

Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3 month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which ST357 and ST773 are considered to be high-risk clones. Antimicrobial resistance (AMR) testing according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines showed that the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)] and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422 938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms and were predicted to encode virulence genes associated with adherence, antimicrobial activity, anti-phagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.

Serotype distribution and antibiogram of Streptococcus parauberis isolated from fish in South Korea

Streptococcus parauberis is the dominant etiological agent of streptococcosis, the most devastating bacterial disease in the olive flounder farming industry in South Korea. In this study, the distribution of serotypes, antimicrobial susceptibility, and presence of antimicrobial resistance genes (ARGs) in S. parauberis isolates obtained between 1999 and 2021 was thoroughly investigated to gain insight into the dynamics of their presence and the relationship between serotypes and antimicrobial resistance. Disk diffusion testing of 103 isolates against 10 antimicrobial agents was performed, and epidemiological cut-off values generated through normalized resistance interpretation analysis were used to classify wild-type (WT) and non-wild-type (NWT) populations. Principal component analysis and hierarchical clustering were implemented to achieve an understanding on the relationship between serotypes and antimicrobial resistance patterns. PCR-based serotyping showed that serotype Ia (67.1%) was the most prevalent in South Korea, followed by serotypes Ib/Ic (25.2%) and II (7.7%). The highest proportion of isolates was assigned to NWT against amoxicillin (80.6%), followed by oxytetracycline (77.7%) and erythromycin (48.5%). The time-scale data showed that recently obtained serotypes Ib/Ic and II isolates tended to be categorized as NWT populations resistant to more antibiotics, possibly due to microbial adaptation to antibiotic pressure. ARGs responsible for resistance to oxytetracycline and erythromycin were found only in NWT populations in serotype Ia [tet(S) and erm(B), respectively], and serotype II [tet(M) and mef(J)-msr(I), respectively]. We also found that the mef-msr gene pair in S. parauberis serotype II might be involved in low-level resistance to erythromycin. IMPORTANCE This study presents serotype distribution and antimicrobial susceptibility data along with the antimicrobial resistance genes (ARGs) of Streptococcus parauberis, which is an important bacterial fish pathogen worldwide. In particular, almost all oxytetracycline and erythromycin non-wild-type (NWT) populations harbored tet(S) or tet(M), and erm(B) or mef(J)-msr(I), respectively. Interestingly, these ARGs were distributed in a highly serotype-dependent manner, resulting in a clear correlation between the antibiogram and serotype distribution. Moreover, recent isolates belonging to serotypes Ib/Ic and II tended to be more frequently categorized as NWT against antimicrobials, including amoxicillin and cefalexin compared to old isolates, while a dramatic decrease in erythromycin and clindamycin NWT frequencies was observed in recent serotype Ia isolates, which lacked erm(B). These variations might be attributed to shifts in the antibiotics employed in South Korean aquaculture over time. The overall findings would provide important background knowledge for understanding the epidemiology of S. parauberis infection in aquaculture.

Hospital and community wastewater as a source of multidrug-resistant ESBL-producing Escherichia coli

Introduction

Hospitals and wastewater are recognized hot spots for the selection and dissemination of antibiotic-resistant bacteria to the environment, but the total participation of hospitals in the spread of nosocomial pathogens to municipal wastewater treatment plants (WWTPs) and adjacent rivers had not previously been revealed.

Methods

We used a combination of culturing and whole-genome sequencing to explore the transmission routes of Escherichia coli from hospitalized patients suffering from urinary tract infections (UTI) via wastewater to the environment. Samples were collected in two periods in three locations (A, B, and C) and cultured on selective antibiotic-enhanced plates.

Results

In total, 408 E. coli isolates were obtained from patients with UTI (n=81), raw hospital sewage (n=73), WWTPs inflow (n=96)/outflow (n=106), and river upstream (n=21)/downstream (n=31) of WWTPs. The majority of the isolates produced extended-spectrum beta-lactamase (ESBL), mainly CTX-M-15, and showed multidrug resistance (MDR) profiles. Seven carbapenemase-producing isolates with GES-5 or OXA-244 were obtained in two locations from wastewater and river samples. Isolates were assigned to 74 different sequence types (ST), with the predominance of ST131 (n=80) found in all sources including rivers. Extraintestinal pathogenic lineages frequently found in hospital sewage (ST10, ST38, and ST69) were also found in river water. Despite generally high genetic diversity, phylogenetic analysis of ST10, ST295, and ST744 showed highly related isolates (SNP 0-18) from different sources, providing the evidence for the transmission of resistant strains through WWTPs to surface waters.

Discussion

Results of this study suggest that 1) UTI share a minor participation in hospitals wastewaters; 2) a high diversity of STs and phylogenetic groups in municipal wastewaters derive from the urban influence rather than hospitals; and 3) pathogenic lineages and bacteria with emerging resistance genotypes associated with hospitals spread into surface waters. Our study highlights the contribution of hospital and municipal wastewater to the transmission of ESBL- and carbapenemase-producing E. coli with MDR profiles to the environment.

Co-Harboring of Beta-Lactamases and mcr-1 Genes in Escherichia coli and Klebsiella pneumoniae from Healthy Carriers and Backyard Animals in Rural Communities in Ecuador

Few studies have addressed drug resistance of Enterobacterales in rural communities in developing countries. This study aimed to determine the coexistence of extended-spectrum β-lactamase (ESBL) and carbapenemase genes in Escherichia coli and Klebsiella pneumoniae strains carrying the mcr-1 gene in rural communities in Ecuador from healthy humans and their backyard animals. Sixty-two strains, thirty E. coli and thirty-two K. pneumoniae strains carrying the mcr-1 gene were selected from a previous study. PCR were performed for the presence of ESBLs and carbapenemase genes. The strains were further characterized, and the genetic relationship was studied with multi-locus sequencing typing (MLST) of seven housekeeping genes. Fifty-nine of the sixty-two mcr-1 isolates (95%) harbored at least on β-lactam resistance gene. The most prevalent ESBL genes were the bla_TEM genes (present in in 80% of the E. coli strains) and the bla_SHV gene (present in 84% of the K. pneumoniae strains). MSLT analysis revealed 28 different sequence types (ST); 15 for E. coli and 12 for K. pneumoniae, with most ST never described in humans and animals. The coexistence of mcr-1 and β-lactams resistant genes in E. coli and K. pneumoniae strains is alarming and threatens the efficacy of last-resort antibiotics. Our findings highlight backyard animals as a reservoir of mcr-1/β-lactams resistant genes.

Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives

Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).