Global mapping of antibiotic resistance rates among clinical isolates of Stenotrophomonas maltophilia: a systematic review and meta-analysis.

INTRODUCTION: Infections caused by Stenotrophomonas maltophilia are clinically important due to its intrinsic resistance to a broad range of antibiotics. Therefore, selecting the most appropriate antibiotic to treat S. maltophilia infection is a major challenge. AIM: The current meta-analysis aimed to investigate the global prevalence of antibiotic resistance among S. maltophilia isolates to the develop more effective therapeutic strategies. METHOD: A systematic literature search was performed using the appropriate search syntax after searching Pubmed, Embase, Web of Science and Scopus databases (May 2023). Statistical analysis was performed using Pooled and the random effects model in R and the metafor package. A total of 11,438 articles were retrieved. After a thorough evaluation, 289 studies were finally eligible for inclusion in this systematic review and meta-analysis. RESULT: Present analysis indicated that the highest incidences of resistance were associated with doripenem (97%), cefoxitin (96%), imipenem and cefuroxime (95%), ampicillin (94%), ceftriaxone (92%), aztreonam (91%) and meropenem (90%) which resistance to Carbapenems is intrinsic. The lowest resistance rates were documented for minocycline (3%), cefiderocol (4%). The global resistance rate to TMP-SMX remained constant in two periods before and after 2010 (14.4% vs. 14.6%). A significant increase in resistance to tigecycline and ceftolozane/tazobactam was observed before and after 2010. CONCLUSIONS: Minocycline and cefiderocol can be considered the preferred treatment options due to low resistance rates, although regional differences in resistance rates to other antibiotics should be considered. The low global prevalence of resistance to TMP-SMX as a first-line treatment for S. maltophilia suggests that it remains an effective treatment option.

Performance of an innovative culture-based digital dipstick for detection of bacteriuria.

IMPORTANCE: In this study, we explore the transformative potential of UTI-lizer, an emerging technology not yet commercially available. Our manuscript shows that UTI-lizer is a promising alternative for detecting the five main pathogens that cause urinary tract infections (UTIs). The results also indicate that digital dipsticks have the potential to uniquely provide UTI diagnostic quality on par with that of gold-standard testing, with the added benefits of ease of testing, rapid test handling time, and simple test equipment. This technology can be helpful in quickly ruling out bacterial infections and reducing the unnecessary use of antibiotics, especially in primary care settings or at the point of care. Moreover, the UTI-lizer test can reduce the number of negative urine samples sent to central laboratories, thus easing the burden of UTI diagnostics on the healthcare system. We believe our study, as well as current and upcoming research based on this technology, is highly relevant for clinical microbiologists, microbiology scientists, general practitioners, and urologists.

Expert guidance on target product profile development for AMR diagnostic tests.

Diagnostics are widely considered crucial in the fight against antimicrobial resistance (AMR), which is expected to kill 10 million people annually by 2030. Nevertheless, there remains a substantial gap between the need for AMR diagnostics versus their development and implementation. To help address this problem, target product profiles (TPP) have been developed to focus developers' attention on the key aspects of AMR diagnostic tests. However, during discussion between a multisectoral working group of 51 international experts from industry, academia and healthcare, it was noted that specific AMR-related TPPs could be extended by incorporating the interdependencies between the key characteristics associated with the development of such TPPs. Subsequently, the working group identified 46 characteristics associated with six main categories (ie, Intended Use, Diagnostic Question, Test Description, Assay Protocol, Performance and Commercial). The interdependencies of these characteristics were then identified and mapped against each other to generate new insights for use by stakeholders. Specifically, it may not be possible for diagnostics developers to achieve all of the recommendations in every category of a TPP and this publication indicates how prioritising specific TPP characteristics during diagnostics development may influence (or not) a range of other TPP characteristics associated with the diagnostic. The use of such guidance, in conjunction with specific TPPs, could lead to more efficient AMR diagnostics development.

High frequency of carbapenemase in extensively drug-resistant Acinetobacter baumannii isolates in central Iran.

OBJECTIVES: We assessed the frequency of occurrence for infections caused by wild-type A. baumannii, multidrug-resistant (MDR) or XDR A. baumannii, and CRAB. We detected different antibiotic resistance genes in the genomes of infectious A. baumannii strains from central Iran. METHODS: This study investigated 546 clinical patient samples for the presence of A. baumannii by using conventional culture methods and PCR. Antibiotic resistance profiles, and the phenotypic and genotypic characteristics of various antibiotic genes were analyzed. RESULTS: Out of 546 samples, 87 (15.9%) A. baumannii isolates were obtained using culture and all culture positive samples were also positive by PCR. The most effective antibiotics were polymyxin B (n = 84 strains) (96.6% susceptibility), colistin (n = 81) (93.1%), and ampicillin/sulbactam (n = 18) (20.7%). All clinical A. baumannii isolates were ESBL-positive. The number of CRAB was 84 (96.5%). All CRAB isolates were both MDR and XDR. Of all CRAB isolates, 78 out of 84 (92.4%) produced metallo-ß-lactamase (MBL) by phenotypic diagnosis. The most abundant genes were blaPER (32/87; 36.7%), blaTEM (29/87; 33.3%), blaVEB (26/87; 29.8%) for ESBL and Ambler class D ß -lactamases included blaOXA-23 (69/84; 82.1%), blaOXA-24 (46/84; 54.7%), MBLs included blaVIM (51/84; 60.7%), and blaIMP (28/84; 33.3%) for carbapenemase. CONCLUSION: High frequencies of XDR A. baumannii and CRAB (96.5%) were detected in central Iran. Quick and accurate diagnosis, appropriate isolation of patients colonized or infected by CRAB isolates, application of accurate and effective infection control policies and programs, and appropriate preventive measures are deemed helpful in preventing the further spread of these resistant and clinically highly relevant strains.

The effect of aging on the epidemiology of blood transfusions in North Khorasan province, Iran.

PURPOSE: Additional knowledge on the epidemiology and recipients of blood transfusions will help health-care managers to estimate the future needs. The study was performed to define the blood transfusion rate based on gender, sex, and clinical features of patients receiving blood products in all hospitals of the North Khorasan province of Iran. METHODS: Data on blood transfusion implementation were extracted from blood bank documents. The data for all patients who received at least one blood product were collected from March 2018 to March 2019. RESULTS: Among blood transfused patients, the highest transfusion rate was for packed red blood cells (PRBC) (47.7%). The two other most frequently used products were fresh frizzed plasma (FFP) (27.2%) and platelets (PLT) (21.9%). The patients in the age group of 51-80 years received the majority of PRBCs and FFPs. Patients aged 21-40 and 61-70 yrs had the highest transfusion rates for PLT. Elderly female patients (57.4%) received more blood products than their male counterparts. The highest blood transfusion rates were among patients with neoplasms, anemia, gastrointestinal bleeding, and gastric diseases. CONCLUSION: The primary Iranian blood recipients were elderly patients. Population aging is associated with an increase in the number of blood recipients and simultaneously declines the blood donors pool. It highlights the need for optimizing the use of blood in hospitals and having better strategies for overcoming the shortage of blood.

Improving antimicrobial stewardship with penicillin allergy testing: a review of current practices and unmet needs.

Penicillin allergy, the most frequently reported drug allergy, has been associated with suboptimal antibiotic therapy, increased antimicrobial resistance, increased rates of Clostridioides difficile colonization and infection, as well as extended hospital length of stay and increased cost. Although up to 10% of all patients may report penicillin allergy, most penicillin allergies are not confirmed. As such, most patients with a penicillin allergy can still safely use penicillin and related drugs following a more precise assessment. Herein, we review the current practices and unmet needs in penicillin allergy testing. The diagnostic algorithm is mostly based on a clinical history assessment followed by in vivo testing, i.e. skin test and/or drug challenge. As these tests are labour and resource intensive, there is increased interest in point-of-care penicillin allergy de-labelling solutions incorporated into Antimicrobial Stewardship Programmes including digital assessment tools. These can be locally parameterized on the basis of characteristics of target populations, incidence of specific allergies and local antibiotic usage to perform clinical risk stratification. Safely ruling out any residual risk remains essential and in vivo drug challenge and/or skin testing should be systematically encouraged. Gradual understanding and convergence of the risk stratification of the clinical presentation of penicillin allergy is enabling a wider implementation of this essential aspect of antimicrobial stewardship through digitalized decision tools and in vivo testing. More research is needed to deliver point of care in vitro diagnostic tools to democratize this de-labelling practice, which would be highly beneficial to patient care. This progress, together with better education of patients and clinicians about the availability, efficacy and safety of penicillin allergy testing, will increase the dissemination of penicillin allergy assessment as an important component of Antimicrobial Stewardship Programmes.

Common Etiological Agents in Adult Patients with Gastroenteritis from Central Iran.

Aims: This study represents the first analysis from Iran for both the frequency of the most common causes of infectious diarrhoea and their antibiotic resistance patterns in adult patients. Methods: Adult stool specimens (n = 211) were analyzed. Stool specimens were analyzed using standard microbiological, polymerase chain reaction, and reverse transcription polymerase chain reaction tests to identify bacterial, parasitic, and viral enteropathogens. Antibiotic resistance profiles were determined. Results: Enteropathogens were identified in 46.4% (98/211) of the surveyed samples. This included 33.1% (70/211) bacterial infections, including 9.9% (21/211) diarrheagenic Escherichia coli (DEC) and 8.5% (18/211) Shigella spp. We detected 7.1% (15/211) parasitic infections (mostly Giardia lamblia) and 6.1% (13/211) viral infections (mostly adenovirus). The DEC and Shigella spp. isolates included many multi-drug resistant (MDR) isolates (95.2% and 77.7%, respectively), and extended spectrum-ß-lactamase (ESBL) genes were often present (57.1% and 61.1%, respectively). The most commonly identified ESBL genes in the DEC and Shigella spp. isolates were blaTEM (100% in both species), blaCTX-M15 (91.6% and 100%, respectively), AmpC blaCIT (80% and 100%, respectively), and blaDHA (80% and 100%, respectively). Conclusions: Bacterial infection was the primary cause of infectious diarrhea, affecting one-third of the adults. The frequency of DEC and Shigella spp. was higher than for other enteropathogens. The high prevalence of MDR, the elevated incidence of ESBL genes among Shigella spp. and DEC isolates, and the presence of quinolone resistance in the Salmonella spp. isolates represent a significant challenge for gastroenteritis diagnosis and treatment in this region.

Whole Genome Multi-Locus Sequence Typing and Genomic Single Nucleotide Polymorphism Analysis for Epidemiological Typing of Pseudomonas aeruginosa From Indonesian Intensive Care Units.

We have previously studied carbapenem non-susceptible Pseudomonas aeruginosa (CNPA) strains from intensive care units (ICUs) in a referral hospital in Jakarta, Indonesia (Pelegrin et al., 2019). We documented that CNPA transmissions and acquisitions among patients were variable over time and that these were not significantly reduced by a set of infection control measures. Three high risk international CNPA clones (sequence type (ST)235, ST823, ST357) dominated, and carbapenem resistance was due to carbapenemase-encoding genes and mutations in the porin OprD. Pelegrin et al. (2019) reported core genome analysis of these strains. We present a more refined and detailed whole genome-based analysis of major clones represented in the same dataset. As per our knowledge, this is the first study reporting Single Nucleotide Polymorphisms (wgSNP) analysis of Pseudomonas strains. With whole genome-based Multi Locus Sequence Typing (wgMLST) of the 3 CNPA clones (ST235, ST357 and ST823), three to eleven subgroups with up to 200 allelic variants were observed for each of the CNPA clones. Furthermore, we analyzed these CNPA clone clusters for the presence of wgSNP to redefine CNPA transmission events during hospitalization. A maximum number 35350 SNPs (including non-informative wgSNPs) and 398 SNPs (ST-specific_informative-wgSNPs) were found in ST235, 34,570 SNPs (including non-informative wgSNPs) and 111 SNPs (ST-specific_informative-wgSNPs) in ST357 and 26,443 SNPs (including non-informative SNPs) and 61 SNPs (ST-specific_informative-wgSNPs) in ST823. ST-specific_Informative-wgSNPs were commonly noticed in sensor-response regulator genes. However, the majority of non-informative wgSNPs was found in conserved hypothetical proteins or in uncharacterized proteins. Of note, antibiotic resistance and virulence genes segregated according to the wgSNP analyses. A total of 8 transmission chains for ST235 strains followed by 9 and 4 possible transmission chains for ST357 and ST823 were traceable on the basis of pairwise distances of informative-wgSNPs (0 to 4 SNPs) among the strains. The present study demonstrates the value of detailed whole genome sequence analysis for highly refined epidemiological analysis of P. aeruginosa.

High-level seroprevalence against Leptospira interrogans serovars among wild foxes, jackals and stray dogs in the North Khorasan Province, Iran.

BACKGROUND: Leptospirosis is an important, neglected zoonotic disease that affects people and animals in humid (sub)tropical regions. Wild canines carry the pathogen and may contaminate natural resources which may then act as a source of human infection. OBJECTIVES: The study was designed to understand the seroprevalence of leptospirosis among domestic and wild canines in Bojnurd County, Northeast Iran. METHODS: A total of 77 serum samples, comprising 29 sera from asymptomatic wild canines [foxes (n = 25) and jackals (n = 4)] and 48 sera from asymptomatic stray dogs, was investigated. Serovars were identified and antibody titres were measured by standard microscopic agglutination test (MAT) using serial serum dilutions. RESULTS: Among all serum samples, 44.1% reacted positively to a Leptospira interrogans serovars. The average percentage of positive reactions was higher in stray dogs than in wild canines although this did not reach statistical significance (55.2% and 37.5%, p = 0.159). Positive reactions with L. i. Pomona, L. i. Australis and L. i. Tarasovi was detected only among jackals and foxes. Among the stray dogs, the highest number of positive sera were for L. i. Grippotyphosa (61.1%) and L. i. Canicola (50%). The highest titre detected was for L. i. canicola (1:1600) in two stray dogs and against L. i. Icterohaemorrhagiae and L. i. Pomona (1:800) in a single jackal. CONCLUSIONS: The study revealed that leptospirosis is endemic among various canine species in the North Khorasan Province of Iran. Detailed monitoring of canines is necessary for better understanding the epidemiology of infection in our and other Iranian regions.

Murine Model for Measuring Effects of Humanized-Dosing of Antibiotics on the Gut Microbiome.

There is a current need for enhancing our insight in the effects of antimicrobial treatment on the composition of human microbiota. Also, the spontaneous restoration of the microbiota after antimicrobial treatment requires better understanding. This is best addressed in well-defined animal models. We here present a model in which immune-competent or neutropenic mice were administered piperacillin-tazobactam (TZP) according to human treatment schedules. Before, during and after the TZP treatment, fecal specimens were longitudinally collected at established intervals over several weeks. Gut microbial taxonomic distribution and abundance were assessed through culture and molecular means during all periods. Non-targeted metabolomics analyses of stool samples using Quadrupole Time of Flight mass spectrometry (QTOF MS) were also applied to determine if a metabolic fingerprint correlated with antibiotic use, immune status, and microbial abundance. TZP treatment led to a 5-10-fold decrease in bacterial fecal viability counts which were not fully restored during post-antibiotic follow up. Two distinct, relatively uniform and reproducible restoration scenarios of microbiota changes were seen in post TZP-treatment mice. Post-antibiotic flora could consist of predominantly Firmicutes or, alternatively, a more diverse mix of taxa. In general, the pre-treatment microbial communities were not fully restored within the screening periods applied. A new species, closely related to Eubacterium siraeum, Mageeibacillus indolicus, and Saccharofermentans acetigenes, became predominant post-treatment in a significant proportion of mice, identified by 16S rRNA gene sequencing. Principal component analysis of QTOF MS of mouse feces successfully distinguished treated from non-treated mice as well as immunocompetent from neutropenic mice. We observe dynamic but distinct and reproducible responses in the mouse gut microbiota during and after TZP treatment and propose the current murine model as a useful tool for defining the more general post-antibiotic effects in the gastro-intestinal ecosystem where humanized antibiotic dosing may ultimately facilitate extrapolation to humans.

Natural and Synthetic Sortase A Substrates Are Processed by Staphylococcus aureus via Different Pathways.

Endogenous Staphylococcus aureus sortase A (SrtA) covalently incorporates cell wall anchored proteins equipped with a SrtA recognition motif (LPXTG) via a lipid II-dependent pathway into the staphylococcal peptidoglycan layer. Previously, we found that the endogenous S. aureus SrtA is able to recognize and process a variety of exogenously added synthetic SrtA substrates, including K(FITC)LPMTG-amide and K(FITC)-K-vancomycin-LPMTG-amide. These synthetic substrates are covalently incorporated into the bacterial peptidoglycan (PG) of S. aureus with varying efficiencies. In this study, we examined if native and synthetic substrates are processed by SrtA via the same pathway. Therefore, the effect of the lipid II inhibiting antibiotic bacitracin on the incorporation of native and synthetic SrtA substrates was assessed. Treatment of S. aureus with bacitracin resulted in a decreased incorporation of protein A in the bacterial cell wall, whereas incorporation of exogenous synthetic substrates was increased. These results suggest that natural and exogenous synthetic substrates are processed by S. aureus via different pathways.

Contemporary diagnostics for medically relevant fastidious microorganisms belonging to the genera Anaplasma,Bartonella,Coxiella,OrientiaandRickettsia.

Many of the human infectious pathogens-especially the zoonotic or vector-borne bacteria-are fastidious organisms that are difficult to cultivate because of their strong adaption to the infected host culminating in their near-complete physiological dependence on this environment. These bacterial species exhibit reduced multiplication rates once they are removed from their optimal ecological niche. This fact complicates the laboratory diagnosis of the disease and hinders the detection and further characterization of the underlying organisms, e.g. at the level of their resistance to antibiotics due to their slow growth. Here, we describe the current state of microbiological diagnostics for five genera of human pathogens with a fastidious laboratory lifestyle. For Anaplasma spp., Bartonella spp., Coxiella burnetii, Orientia spp. and Rickettsia spp., we will summarize the existing diagnostic protocols, the specific limitations for implementation of novel diagnostic approaches and the need for further optimization or expansion of the diagnostic armamentarium. We will reflect upon the diagnostic opportunities provided by new technologies including mass spectrometry and next-generation nucleic acid sequencing. Finally, we will review the (im)possibilities of rapidly developing new in vitro diagnostic tools for diseases of which the causative agents are fastidiously growing and therefore hard to detect.

Novel strategies to diagnose prosthetic or native bone and joint infections.

INTRODUCTION: Bone and Joint Infections (BJI) are medically important, costly and occur in native and prosthetic joints. Arthroplasties will increase significantly in absolute numbers over time as well as the incidence of Prosthetic Joint Infections (PJI). Diagnosis of BJI and PJI is sub-optimal. The available diagnostic tests have variable effectiveness, are often below standard in sensitivity and/or specificity, and carry significant contamination risks during the collection of clinical samples. Improvement of diagnostics is urgently needed. AREAS COVERED: We provide a narrative review on current and future diagnostic microbiology technologies. Pathogen identification, antibiotic resistance detection, and assessment of the epidemiology of infections via bacterial typing are considered useful for improved patient management. We confirm the continuing importance of culture methods and successful introduction of molecular, mass spectrometry-mediated and next-generation genome sequencing technologies. The diagnostic algorithms for BJI must be better defined, especially in the context of diversity of both disease phenotypes and clinical specimens rendered available. EXPERT OPINION: Whether interventions in BJI or PJI are surgical or chemo-therapeutic (antibiotics and bacteriophages included), prior sensitive and specific pathogen detection remains a therapy-substantiating necessity. Innovative tests for earlier and more sensitive and specific detection of bacterial pathogens in BJI are urgently needed.

Multicenter Clinical Evaluation of ETEST Plazomicin (PLZ) for Susceptibility Testing of Enterobacterales.

Plazomicin (PLZ), brand name ZEMDRI (Cipla Therapeutics), is a novel aminoglycoside antibiotic approved by the U.S. Food and Drug Administration (FDA) for treatment of complicated urinary tract infections including pyelonephritis. ETEST® is a gradient diffusion method that represents an alternative to the more laborious broth micro-dilution (BMD) method for performing antimicrobial susceptibility testing (AST). A multi-center evaluation of the performance of the new ETEST PLZ (bioMérieux) was conducted in comparison with BMD following FDA and International Standards Organization (ISO) recommendations using FDA-defined breakpoints. Clinical isolates of Enterobacterales (n = 598) were included. Fifty-three isolates were resistant to PLZ according to BMD. Overall, the ETEST PLZ demonstrated 99.0% essential agreement (EA), 92.8% category agreement (CA), 1.9% very major errors (VME), 0% major errors (ME), and 7.0% minor errors (mE) with both clinical and challenge isolates of Enterobacterales. The VME was found for a single Serratia marcescens strain. Individual species demonstrated EA rates ≥ 90%. In conclusion, we report that ETEST PLZ represents an accurate tool for performing PLZ AST of Enterobacterales.

Recent Advances in Rapid Antimicrobial Susceptibility Testing.

BACKGROUND: Antimicrobial susceptibility testing (AST) is classically performed using growth-based techniques that essentially require viable bacterial matter to become visible to the naked eye or a sophisticated densitometer. CONTENT: Technologies based on the measurement of bacterial density in suspension have evolved marginally in accuracy and rapidity over the 20th century, but assays expanded for new combinations of bacteria and antimicrobials have been automated, and made amenable to high-throughput turn-around. Over the past 25 years, elevated AST rapidity has been provided by nucleic acid-mediated amplification technologies, proteomic and other "omic" methodologies, and the use of next-generation sequencing. In rare cases, AST at the level of single-cell visualization was developed. This has not yet led to major changes in routine high-throughput clinical microbiological detection of antimicrobial resistance. SUMMARY: We here present a review of the new generation of methods and describe what is still urgently needed for their implementation in day-to-day management of the treatment of infectious diseases.

The Global Prevalence of Daptomycin, Tigecycline, and Linezolid-Resistant Enterococcus faecalis and Enterococcus faecium Strains From Human Clinical Samples: A Systematic Review and Meta-Analysis.

Background and Aim: The predominant species of the Enterococcus, Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium) cause great variety of infections. Therefore, the expansion of antimicrobial resistance in the Enterococcus is one of the most important global concerns. This study was conducted to investigate the prevalence of resistance to linezolid, tigecycline, and daptomycin among enterococcal strains isolated from human clinical specimens worldwide. Methods: Several databases including Web of Science, EMBASE, and Medline (via PubMed), were carefully searched and reviewed for original research articles available in databases and published between 2000 and 2020. A total of 114 studies worldwide that address E. faecalis and E. faecium resistance to linezolid, tigecycline, and daptomycin were analyzed by STATA software. Results: The overall prevalence of antibiotic-resistant E. faecalis and E. faecium was reported to be 0.9 and 0.6%, respectively. E. faecalis and E. faecium were more resistant to the linezolid (2.2%) and daptomycin (9%), respectively. The prevalence of tigecyline-resistant E. facium (1%) strains was higher than E. faecalis strains (0.3%). Accordingly, the prevalence of linezolid-resistant E. faecalis was higher in Asia (2.8%), while linezolid-resistant E. faecium was higher in the America (3.4%). Regarding tigecycline-resistance, a higher prevalence of E. faecalis (0.4%) and E. faecium (3.9%) was reported in Europe. Conclusion: In conclusion, this meta-analysis shows that there is an emerging resistance in Enterococcus strains. Despite the rising resistance of enterococci to antibiotics, our results demonstrate that tigecycline, daptomycin, and linezolid can still be used for the treatment of enterococcal infections worldwide.

Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens.

Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen-surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin-ligand interaction, supported by present high-throughput "omics" technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.

Reply to Fabre et al. Comment on "Tanmoy et al. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes 2020, 11, 1365".

We respectfully thank Fabre et al. [...].

Biofilm associated genotypes of multiple antibiotic resistant Pseudomonas aeruginosa.

BACKGROUND: Pseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its presence in biofilms formed on indwelling device surfaces. Biofilm promotes adhesion to, and survival on surfaces, protects from desiccation and the actions of antibiotics and disinfectants. RESULTS: We examined the genetic basis for biofilm production on polystyrene at room (22 °C) and body temperature (37 °C) within 280 P. aeruginosa. 193 isolates (69 %) produced more biofilm at 22 °C than at 37 °C. Using GWAS and pan-GWAS, we found a number of accessory genes significantly associated with greater biofilm production at 22 °C. Many of these are present on a 165 kb region containing genes for heavy metal resistance (arsenic, copper, mercury and cadmium), transcriptional regulators and methytransferases. We also discovered multiple core genome SNPs in the A-type flagellin gene and Type II secretion system gene xpsD. Analysis of biofilm production of isolates of the MDR ST111 and ST235 lineages on stainless-steel revealed several accessory genes associated with enhanced biofilm production. These include a putative translocase with homology to a Helicobacter pylori type IV secretion system protein, a TA system II toxin gene and the alginate biosynthesis gene algA, several transcriptional regulators and methytransferases as well as core SNPs in genes involved in quorum sensing and protein translocation. CONCLUSIONS: Using genetic association approaches we discovered a number of accessory genes and core-genome SNPs that were associated with enhanced early biofilm formation at 22 °C compared to 37 °C. These included a 165 kb genomic island containing multiple heavy metal resistance genes, transcriptional regulators and methyltransferases. We hypothesize that this genomic island may be associated with overall genotypes that are environmentally adapted to survive at lower temperatures. Further work to examine their importance in, for example gene-knockout studies, are required to confirm their relevance. GWAS and pan-GWAS approaches have great potential as a first step in examining the genetic basis of novel bacterial phenotypes.