Microbiology Spectrum

ObjectiveUrine cultures are frequently requested at an early stage in primary care and outpatient settings, often without a comprehensive clinical assessment. This practice increases healthcare costs and laboratory workload and may lead to misleading results due to asymptomatic bacteriuria and specimen contamination. This study aimed to evaluate whether routinely reported microscopic urinary leukocyte findings can predict urine culture positivity under real-world clinical conditions. The distribution of isolated microorganisms and the frequency of mixed or contaminated growth were assessed. MethodsThis retrospective, laboratory-based diagnostic accuracy study included all urine samples sent for culture over a one-year period at a tertiary care hospital, provided concurrent microscopic urinalysis was available. No additional clinical exclusion criteria were applied to reflect the routine practice. Leukocyte findings were reported semi-quantitatively and analyzed both categorically and as approximate numerical values. The urine culture results were classified as positive, negative, or mixed/contaminated growth. The diagnostic performance was evaluated using receiver operating characteristic (ROC) curve analysis. ResultsA total of 8,478 urine samples were analyzed in this study. Urine culture positivity was detected in 2,666 (31.4%) samples, whereas 5, 812 (68.6%) showed no growth. Culture positivity increased significantly with higher leukocyte levels (p < 0.001), ranging from 13.1% in the lowest category to 83.1% in samples with abundant leukocytes. ROC analysis demonstrated an acceptable discriminative performance (AUC = 0.747). The Youden index identified an optimal threshold of approximately 5.5 leukocytes per high-power field, with a sensitivity of 60.4% and a specificity of 77.8%. Mixed or contaminated growth was the most common finding among culture-positive samples (43.5%), followed by Escherichia coli (29.5%). ConclusionMicroscopic urinary leukocyte findings were significantly associated with urine culture positivity and demonstrated acceptable predictive performance in real-world clinical practice settings. Although leukocyte microscopy alone is not diagnostic, it may support more selective urine culture ordering, reduce contamination, and contribute to rational diagnosis and antimicrobial management in primary care.

2.Metagenomic approaches to diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adaptive sampling (AS) can be used to preferentially sequence more of the infecting organism. Here, we evaluate AS using clinical samples from infected prosthetic joints to determine the absolute fold enrichment achieved. We found that AS achieved a range of 1.61 to 1.96-fold higher absolute fold enrichment for bacterial sequenced bases using AS over control pores. In this limited sample set, AS did not impact bacterial diagnosis overall but led to a modest increase in the bacterial sequence available without any obvious cost. 3. Impact statementMetagenomic approaches offer the possibility to rapidly detect the cause of an infection and to provide information on drug susceptibility. Implementing this technique is challenging because samples collected from patients contain high levels of human DNA which can obscure detection of bacterial DNA. Reducing the amount of human DNA sequenced would allow easier detection of bacteria. This study assessed a sequencing protocol that rejects human DNA during the sequencing process known as adaptive sampling (AS), specifically as concerns samples from patients with joint infections. Our findings demonstrate that AS can increase bacterial sequencing efficiency. However, these modest improvements did not significantly enhance bacterial identification in our small sample set, although we did not detect additional costs associated with using AS. The study confirms modest utility of AS in real-world clinical samples and extends current literature by applying AS to joint infection. The implications of this method extend to clinical microbiology, where rapid and accurate pathogen detection can significantly impact patient outcomes. 4. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article, through supplementary data files, or in publicly accessible repositories. Nanopore sequencing fastq data are available in the ENA under project accession: PRJEB78709.

Introductory paragraphInfectious osteomyelitis is a potentially severe disease with an increased incidence of 10% over the last 10 years (1, 2) and a 20% recurrence rate creating chronic infections (3). Diagnosis and pathogen identification remain challenging, with culture-negative results in 7-39% of cases (4-6), of which 14-27% are PCR-positive from drained fluids (7). Of recent intensive research focus, osteomyelitis associated with Prosthetic Joint Infection (PJI) is a serious and growing complication of orthopaedic joint replacement surgery, with a failure to cure rate within 2-years internationally of between 15-46% (8, 9). Osteocytes act as potential long-term reservoirs for intracellular Staphylococcus aureus, protecting it against the immune responses and antimicrobial treatment (10-15). However, the intra-osteocytic adaptation mechanisms by S. aureus remain understudied, and it is unknown why so many infections are culture-negative but PCR-positive. Here, we found that in chronic intra-osteocytic infections, S. aureus consistently adopts a viable but non-culturable (VBNC) state. Whole genome sequencing of parental and a revertant strain indicated that initially, S. aureus cells possessing TarP and a complete T7SS dominate the bacterial community but these cell numbers declined with genetic rearrangements seemingly linked with the shift to a VBNC state. The subsequent acquisition of a single nucleotide polymorphism (SNP) in srrB was associated with resuscitation to a culturable state, suggesting at least one mechanism underlying entrance and exit from the intracellular VBNC state.

Breast implant-associated infections (BIAIs) are a common complication following breast prostheses placement and account for [~]100,000 infections annually. The frequency, high cost of treatment, and morbidity make BIAIs a significant health burden for women. Thus, effective BIAI prevention strategies are urgently needed. This study tests the efficacy of one infection prevention strategy: the use of a triple antibiotic pocket irrigant (TAPI) against Staphylococcus aureus, the most common cause of BIAIs. TAPI, which consists of 50,000 U bacitracin, 1 g cefazolin, and 80 mg gentamicin diluted in 500 mL of saline, is used to irrigate the breast implant pocket during surgery. We used in vitro and in vivo assays to test the efficacy of each antibiotic in TAPI, as well as TAPI at the concentration used during surgery. We found that planktonically grown S. aureus BIAI isolates displayed susceptibility to gentamicin, cefazolin, and TAPI. However, TAPI treatment enhanced biofilm formation of BIAI strains. Furthermore, we compared TAPI treatment of a S. aureus reference strain (JE2) to a BIAI isolate (117) in a mouse BIAI model. TAPI significantly reduced infection of JE2 at 1- and 7-days post infection (dpi). In contrast, BIAI strain 117 displayed high bacterial burdens in tissues and implants, which persisted out to 14-dpi despite TAPI treatment. Lastly, we demonstrated that TAPI was effective against P. aeruginosa reference (PAO1) and BIAI strains in vitro and in vivo. Together, these data suggest S. aureus BIAI strains employ unique mechanisms to resist antibiotic prophylaxis treatment and promote chronic infection.

Parenteral drugs must meet strict release criteria to ensure patient safety upon administration. Sterility is a critical requirement, and is typically assessed using the compendial U.S. Pharmacopoeia (USP) <71> sterility test. However, with the growing demand to reduce batch release times, the tests 14-day incubation period is becoming a concern, emphasizing the need for more rapid alternatives. Here, we compared the performance of the calScreener+ isothermal microcalorimetry (IMC) device (Symcel) to that of the compendial USP <71> sterility test, using a panel of sixteen microorganisms (six USP <71> reference strains and ten field isolates) in two inoculum sizes (100 and 5 CFU). The IMC-based method detected a higher number of positive samples compared to the compendial method (95.8% vs 87.5%; p < 0.05). Furthermore, IMC was consistently faster, reducing mean detection times from 43 hours to 19 hours at 100 CFU and from 46 hours to 28 hours at 5 CFU (p < 0.001). In conclusion, the calScreener+ IMC device shows promise as a rapid and sensitive alternative to the compendial sterility test, with the potential to speed up batch releases without compromising patient safety.

Staphylococcus aureus is a leading human pathogen associated with both hospital-acquired and community-acquired infections. The bacterium has steadily gained resistance to {beta}-lactams and other important first-line antibiotics culminating in its categorization as an urgent threat by the U.S. Centers for Disease Control and Prevention. Observations of a varying response to antimicrobial exposure as a function of media type has revealed that clinical susceptibility testing performed in standard bacteriological media might not adequately represent pharmacological responses in the patient. Such observations have encouraged research designed to identify media types that more closely mimic the in vivo environment. In this study, we examine the response of a hospital-acquired USA100 lineage methicillin-resistant, vancomycin-intermediate S. aureus (MRSA/VISA) strain (D592) to nafcillin in a bacteriological compared to a more physiological tissue culture-based medium. We performed multi-dimensional analysis including growth and bacterial cytological profiling, RNA sequencing, and exo-metabolomics measurements (both HPLC and LC/MS) to shed light on the media-dependent activity of the commonly prescribed {beta}-lactam antibiotic nafcillin. O_TBL View this table: org.highwire.dtl.DTLVardef@85b95borg.highwire.dtl.DTLVardef@14c1504org.highwire.dtl.DTLVardef@1f7e976org.highwire.dtl.DTLVardef@100598dorg.highwire.dtl.DTLVardef@1f770e9_HPS_FORMAT_FIGEXP M_TBL C_TBL

Bacteria possess the ability to enter a growth arrested state known as persistence in order to survive antibiotic exposure. Clinically, persisters are regarded as the main causative agents for chronic and recurrent infectious diseases. To combat this antibiotic-tolerant population, a better understanding of the molecular physiology of persisters is required. In this study, we collected samples at different stages of the biphasic kill curve to reveal the dynamics of the cellular molecular changes that occur in the process of persister formation. After exposure to antibiotics with different modes of action, namely vancomycin and enrofloxacin, similar persister levels were obtained. Both shared and distinct stress responses were enriched for the respective persister populations. However, the dynamics of the presence of proteins linked to the persister phenotype throughout the biphasic kill curve and the molecular profiles in a stable persistent population did show large differences depending on the antibiotic used. This suggests that persisters at the molecular level are highly stress specific, emphasizing the importance of characterizing persisters generated under different stress conditions. Additionally, although generated persisters exhibited cross-tolerance toward tested antibiotics, combined therapies were demonstrated to be a promising approach to reduce persister levels. In conclusion, this investigation sheds light on the stress-specific nature of persisters, highlighting the necessity of tailored treatment approaches and the potential of combined therapy. ImportanceBy monitoring proteome and metabolites during Staphylococcus aureus persister formation under vancomycin and enrofloxacin exposure, we revealed the dynamic information of the molecular physiology of persister formation upon exposure to two different antibiotics with different modes of action. The data shows that cells that phenotypically are similarly classified as persisters, do have several molecular characteristics in common but, remarkably so, differ substantially in a significant number of other aspects of their molecular makeup. These contrasts provided valuable insights into persister eradication, which holds considerable clinical relevance.

Pseudomonas aeruginosa is one of the microorganisms with high-risk regarding antimicrobial resistance, since it has an overwhelming capacity to acquire antibiotic resistance, mainly by mutations during persistent lung infections. Mutations in mexZ, encoding the local negative regulator of genes encoding the MexXY efflux pump, are very frequently acquired at early stages of P. aeruginosa infections, while they are rarely selected for in vitro. Although traditionally related to resistance to the first-line drug tobramycin, caused by the overproduction of the aminoglycosides MexXY efflux pump, mutations in mexZ are actually associated with low levels of aminoglycosides resistance when determined in the clinical microbiology laboratory. This very moderate but frequent phenotype suggests that these mutations may shape the infection process, beyond causing conventional resistance. Here we investigated the colonization strategy of a mexZ mutant, compared to a wild-type strain, in a human airway infection model. We observed that the mexZ mutant tends to accumulate inside the epithelial cell layer. This behaviour allows bacteria to colonise the epithelium while being more protected against diverse antibiotics. The altered colonization phenotype was caused by the overexpression of lecA, a Quorum Sensing regulated gene encoding a lectin involved in P. aeruginosa tissue invasiveness. lecA upregulation was underlied by the competition for the shared porin, OprM, between the overproduced MexXY and the MexAB efflux pump, responsible for extruding Quorum Sensing molecules. These findings suggest that standardised antimicrobial susceptibility determined in the clinic may be misleading because antibiotic resistance often depends on the infection environment.

BackgroundAn ongoing challenge for DNA sequencing of samples containing microorganisms is the ability to meaningfully compare different samples and to connect the results back to clinically relevant disease states. The reads of DNA sequence from each sample do not, in and of themselves, give sufficient information to calculate the absolute abundances of each observed organism. Using relative abundances alone is insufficient to determine whether absolute abundances have increased or decreased in the organisms of interest from one sample to the next. This is a well-studied problem in 16S sequencing, but solutions in shotgun sequencing are lacking. Here we show how spike-ins can be used in shotgun sequencing to calculate absolute abundances of organisms present. We also propose the use of the host cells already in the sample as an alternative calculation method. Mammalian host cells are typically of sufficient size that they can be easily and cheaply counted prior to sequencing by a variety of methods and combining this with sequencing data provides sufficient information to calculate the absolute abundances of microbial organisms. ResultsMicrobial abundances in the samples calculated via this method were consistent with manufacturer-stated values of microbial communities, with qPCR, and with our method tested against itself with regard the spike-in and host-cell based options. R2 values on the log10 scale in these tests ranged from 0.85 to 0.98, and the log10-RMSE ranged from 0.1 to 0.7. ConclusionsThe proposed method can consistently calculate absolute microbial abundances to within an order of magnitude. Both versions of the method, where spike-ins are added to the samples, or where host cells in the sample are counted, are viable. Calculating absolute abundances allows for direct comparisons to be made between different samples. If disease-thresholds have been identified, absolute abundances can quantify disease states.

Staphylococcus aureus can cause a variety of infections, many of which involve biofilm infections. Inside biofilms, growing and non-growing bacteria such as persisters co-exist, making it challenging to completely eradicate a persistent and recurrent infection with current treatments. Despite the clinical relevance, most of the current antibiotic treatments mainly kill the growing bacteria and have poor activity against non-growing persister bacteria and thus have limited effect on treating persistent infections including biofilm infections. We previously proposed a Yin-Yang model using a drug combination approach targeting both growing bacteria and persister bacteria for more effective clearance of persistent infections. Here, as a proof of principle, we showed that combining drugs that have high activity against growing forms, such as vancomycin or meropenem, with drugs that have robust anti-persister activity, such as clinafloxacin and oritavancin, could completely eradicate S. aureus biofilm bacteria in vitro. In contrast, single or two drugs including the current treatment for persistent S. aureus infection doxycycline plus rifampin failed to kill all biofilm bacteria in vitro. We then developed a chronic persistent skin infection mouse model with biofilm-seeded bacterial inocula demonstrating that biofilm bacteria caused more severe and persistent skin lesions than log phase S. aureus bacteria. More importantly, we found that the drug combination which eradicated biofilm bacteria in vitro is more efficacious than current treatments and completely eradicated S. aureus biofilm infection in mice. The complete eradication of biofilm bacteria is attributed to the unique high anti-persister activity of clinafloxacin, which could not be replaced by other fluoroquinolones such as moxifloxacin, levofloxacin or ciprofloxacin. Our study is the first to demonstrate that the combination of meropenem, daptomycin, plus clinafloxacin completely cleared the persistent infection, healed the lesions, and had less inflammation, while mice treated with doxycycline plus rifampin, the current clinically recommended treatment for chronic tissue infection, failed to do so. We also compared our persister drug combination with other approaches for treating persistent infections including gentamicin+fructose and ADEP4+rifampin in the S. aureus biofilm infection mouse model. Neither gentamicin+fructose nor ADEP4+rifampin could eradicate or cure the persistent biofilm infection in mice. In contrast, our drug combination regimen with persister drug clinafloxacin plus meropenem and daptomycin completely eradicated and cured the persistent biofilm infection in 7 days. An unexpected observation is that ADEP4 treatment group developed worsened skin lesions and caused more extensive pathology than the untreated control mice. Our study demonstrates an important treatment principle for persistent infections by targeting both growing and non-growing heterogeneous bacterial populations utilizing persister drugs for more effective eradication of persistent and biofilm infections. Our findings may have implications for improved treatment of many other persistent infections in general.

1The high efficacy of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI) is often attributed to the restoration of the bacterial community. However, factors beyond bacteria, such as bacteriophages (phages), may also play a critical role in FMTs success. We aimed to evaluate the preservation of the phage community (phageome) along the FMT production process following Good Manufacturing Practices (GMP) at the Lausanne University Hospital (CHUV), and the engraftment of the phages in patients receiving FMT to treat rCDI. Samples from one donor were used to test the need for amplification and to compare spin-column versus magnetic bead purification. Then, sixteen samples, from four donations of a second healthy donor, were collected at various production stages - fresh, frozen, homogenized, and encapsulated - for phageome analysis. The phage community profiles of three patients before, at 14, and 60 days after FMT were examined to evaluate donor phage engraftment. Phages were detected in all sample types, and samples clustered by donation, indicating that the pre-processing steps did not significantly alter the phage profile. The recipients phageome prior to FMT was characterized by low diversity, each recipient being dominated by a different phage. In contrast, the profile 14 days post-FMT demonstrated the engraftment of donor-derived phages, which persisted at 60 days. Most were predicted to be temperate phages of the Caudoviricetes class infecting members of the Clostridia bacterial class, and Lachnospiraceae and Oscillospiraceae bacterial families. Our findings suggest that the CHUV production process for oral FMT capsules preserves the phage community and that donor phages successfully engraft in recipients. Further larger-scale studies and intervention trials will help elucidate the mechanisms underlying the potential of phages in FMTs efficacy.

Validated inactivation procedures are required for the safe handling and downstream analysis of highly pathogenic organisms, particularly those categorized as biological select agents and toxins (BSATs). TRIzol-based extraction methods are widely used for nucleic acid and protein isolation, yet their reliability for bacterial inactivation has not been comprehensively evaluated. In this study, we assessed TRIzol-based extraction methods for sample quality and inactivation reliability across a series of mock failure scenarios using five attenuated bacterial isolates: Francisella tularensis holarctica LVS, Bacillus anthracis Sterne, Yersinia enterocolitica, Mycobacterium marinum, and Burkholderia cepacia. Dilution of TRIzol to induce incomplete cell lysis for the initial extraction step, including 0% TRIzol, consistently inactivated all surrogate organisms, suggesting that downstream precipitation and sample washing reagents, including isopropanol and 70% ethanol, were sufficient to inactivate organisms in the absence of TRIzol. Several protocol failure scenarios were then evaluated to simulate human error by omitting extraction, precipitation, and washing steps individually or in combination for the most resistant organism, B. anthracis Sterne strain. Failure-scenario testing demonstrated that reliable inactivation of B. anthracis required strict adherence to the complete protocol due to the spore-forming ability of B. anthracis. Collectively, this work provides a reference with experimental evidence supporting the use of TRIzol-based extraction as a bacterial inactivation strategy for a wide range of bacterial pathogens.

Sequencing the respiratory tract transcriptome has the potential to provide insights into infectious pathogens and the hosts immune response. While DNA-based sequencing is more standard in clinical laboratories due to its stability, RNA assays offer unique advantages. RNA reflects dynamic physiological changes, and for RNA viruses, viral RNA particles directly represent copies of the viral genome, enabling greater diagnostic sensitivity. However, RNAs susceptibility to degradation remains a significant challenge, particularly in RNase-rich specimens like saliva. To address this, we conducted a systematic, combinatorial evaluation of 24 distinct mNGS workflows, crossing eight nucleic acid extraction methods with three RNA-Seq library preparation protocols. Remnant saliva samples (n = 6) were pooled and spiked with MS2 phage as a control. The SARS-CoV-2 virus was spiked into half of the samples, which were extracted using the eight different extraction methods (n = 3) and compared using RNA Integrity Number equivalent (RINe) scores and RNA concentration. The extracted RNA was then processed across the three library construction methods and subjected to short-read sequencing to assess all 24 combinations head-to-head. We compared methods based on viral read recovery and found that RINe and concentration did not correlate with viral detection. The Zymo Quick-RNA Magbead kit and the Tecan Revelo RNA-Seq High-Sensitivity RNA library kit were the extraction and library-preparation kits that yielded the most SARS-CoV-2 reads, respectively. Importantly, our combinatorial analysis revealed that any small variability attributable to different nucleic acid extraction methods was heavily overshadowed by differences in quality attributable to the RNA-Seq library preparation methods. These findings challenge the reliance on conventional RNA quality metrics for clinical metagenomics and underscore the need to redefine extraction quality standards for mNGS applications. IMPORTANCEmNGS is a powerful and unbiased approach towards pathogen detection that has mostly been applied to blood and cerebrospinal fluid samples. However mNGS has recently been applied to more areas including the respiratory pathogen detection space, with potential applications in both in-patient diagnostics and public health surveillance. Saliva samples are an ideal sample type for these use cases since they can be collected non-invasively. However, saliva is also a challenging sample type due to its high RNase activity and often yields low-quality nucleic acid. This study explores the feasibility of using saliva specimens in mNGS with contrived SARS-CoV-2 samples to optimize the combination of two factors: nucleic acid extraction and RNA-seq library preparation. Exploration in this area could enhance the sensitivity of saliva-based mNGS assays, with the goal of future expansion of this specimen type in clinical diagnostics and public health surveillance. Key PointsO_LIThe choice of RNA-Seq library preparation kit has a greater impact on pathogen detection than the nucleic acid extraction method. C_LIO_LIThe combination of Zymo Quick-RNA Magbead extraction kit and TECAN Revelo RNA-Seq High Sensitivity RNA library kit recovered the highest percentage of total SARS-CoV-2 reads. C_LIO_LIRNA quantity and RINe score do not correlate with viral read capture, indicating a need for an alternative metric to assess RNA quality for downstream mNGS clinical diagnostics. C_LI

Although polymerase chain reaction (PCR) amplification and sequencing of the 16S rDNA region has been used in a wide range of scientific fields, it does not provide DNA methylation information. We describe a simple add-on method to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical samples or flora. Single-stranded bacterial DNA after bisulfite conversion was preferentially amplified with multiple displacement amplification (MDA) at pH neutral, and the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing. 16S rDNA bisulfite sequencing can provide clinically important bacterial DNA methylation status concurrently with intact 16S rDNA sequence information. We used this approach to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii. Next, we analyzed bacterial flora from clinical specimens of small amount and identified different methylation motifs among Enterococcus faecalis strains. The method developed here, referred to as "add-on" to the conventional 16S rDNA analysis, is the most clinically used bacterial identification genetic test, which provides additional information that could not be obtained with the conventional method. Since the relationship between drug resistance in bacteria and DNA methylation status has been reported, bacterial epigenetic information would be useful in clinical testing as well. Our analysis suggests that M. MmnI has a promotive effect on erythromycin resistance. 16S rDNA bisulfite PCR and sequencing coupled with MDA at pH neutral is a useful add-on tool for analyzing 16S meta-epigenetics.

Colistin resistance in Escherichia coli arises from outer membrane (OM) remodeling that reduces surface charge and thereby lowers drug binding affinity. In this study, we investigated the zeta potential of E. coli strains with colistin minimum inhibitory concentrations (MICs) ranging from 0.125 to 16 mg/L, following EDTA treatment to chelate divalent cations and unmask intrinsic surface charge. Zeta potential was measured across pH values from 3 to 7, revealing consistent pH-dependent trends and an average 18.5 mV reduction in surface charge with increasing MIC. At pH 7, zeta potential strongly correlated with colistin resistance (R2 = 0.919), and this correlation was further strengthened following exposure to sub-inhibitory colistin (1/8 MIC; R2 = 0.9975). Notably, resistant strains carrying mcr-1 or mcr-4 exhibited significant shifts toward less negative surface charges after sub-MIC exposure, whereas the susceptible parental strain remained unchanged. However, mcr-1 mRNA expression did not consistently increase under these conditions, highlighting a disconnect between transcriptional responses and phenotypic charge alterations. These findings suggest that regulatory pathways beyond mcr-1 transcription, including stress-induced lipid A remodeling, contribute to OM charge modulation. Overall, zeta potential profiling provides a rapid and sensitive readout of resistance-associated membrane alterations and complements molecular assays by capturing functional phenotypes. This approach offers a valuable research tool for dissecting colistin resistance mechanisms and may inform future strategies for monitoring bacterial adaptation to last-resort antibiotics.

Polymicrobial infections promote the appearance of a network of interactions that can lead to an increase in their antimicrobial tolerance or to the evasion of the host immune system. Pseudomonas aeruginosa and Burkholderia cenocepacia are two multidrug-resistant opportunistic pathogens that significantly influence host health and alter their antibiotic response when in coinfection. To characterize host-pathogen dynamics, we examined infection progression, immune responses, bacterial virulence gene expression, and antibiotic susceptibility in single and coinfections involving acute and chronic P. aeruginosa strains combined with B. cenocepacia. This work was entirely performed in vivo using G. mellonella larvae as a model. Larval survival and bacterial dissemination were monitored, revealing tissue-specific patterns of infection. Our findings indicated that coinfections increased larval lethality and worsened overall health. Notably, B. cenocepacia suppressed host melanization and immune responses, while P. aeruginosa triggered a strong immune activation. Coinfection also induced upregulation of virulence genes in both pathogens. Surprisingly, increased antibiotic susceptibility was observed in coinfected groups compared to single infections. This study advances understanding of host-pathogen interactions in polymicrobial infections and highlights the need for improved therapeutic strategies. Author summaryBacterial coinfections, such as the ones with Pseudomonas aeruginosa and Burkholderia cenocepacia are especially critical in chronic lung diseases like cystic fibrosis, where persistent polymicrobial infections drive lung damage and health decline. Coinfection can enhance pathogen survival, increase drug tolerance, and disrupt host immunity, leading to worse clinical outcomes. Understanding coinfection dynamics can help improve treatment strategies, optimize antibiotic use and improve infection monitorization. Therefore, by studying and understanding microbial interactions, researchers can develop more effective therapies, ultimately improving patient care and combating the growing challenge of multidrug-resistant bacterial infections.

Burkholderia cepacia complex (Bcc) is a collection of intrinsically drug-resistant gram-negative bacteria that cause life-threatening pulmonary disease in people with cystic fibrosis (CF). Standard antimicrobial susceptibility testing methods have poor predictive value for clinical outcomes in people with Bcc infections, likely due in part to the significant differences between in vitro testing conditions and the environment in which Bcc grow in the lungs of people with CF. We tested the activity of six commonly used antibiotics against two clinical Bcc strains grown to high density in an artificial sputum medium in order to assess their activity in conditions mimicking those found in vivo. There were major discrepancies between standard susceptibility results and activity in our model, with some antibiotics, including ceftazidime, showing minimal activity despite low MICs, while others, notably tobramycin, were more active in high-density growth conditions than in standard assays. This work underscores the urgent need to develop more clinically relevant susceptibility testing approaches for Bcc.

The emergence of Acinetobacter baumannii infections as a significant healthcare concern in hospital settings, coupled with their association with poorer clinical outcomes, has prompted extensive investigation into novel therapeutic agents and innovative treatment strategies. Proguanil and chlorhexidine, both categorized as biguanide compounds, have displayed clinical efficacy as antimalarial and topical antibacterial agents, respectively. In this study, we conducted an investigation to assess the effectiveness of combining proguanil and chlorhexidine with clarithromycin or rifampicin against both laboratory strains and clinical isolates of A. baumannii. The combination therapy demonstrated rapid bactericidal activity against planktonic multidrug-resistant A. baumannii, exhibiting efficacy in eradicating mature biofilms and impeding the development of antibiotic resistance in vitro. Additionally, when administered in conjunction with clarithromycin or rifampicin, proguanil enhanced the survival rate of mice afflicted with intraperitoneal A. baumannii infections, and chlorhexidine expedited wound healing in mice with skin infections. These findings are likely attributable to the disruption of A. baumannii cell membrane integrity by proguanil and chlorhexidine, resulting in heightened membrane permeability and enhanced intracellular accumulation of clarithromycin and rifampicin. Overall, this study underscores the potential of employing proguanil and chlorhexidine in combination with specific antibiotics to effectively combat A. baumannii infections and improve treatment outcomes in clinically challenging scenarios. IMPORTANCEA. baumannii has emerged as a globally significant nosocomial pathogen due to its remarkable ability to acquire antibiotic resistance and develop biofilms on both biotic and abiotic surfaces. Recent research has demonstrated that the antidiabetic drug metformin has a potentiation effect on doxycycline and minocycline against certain multidrug-resistant bacterial pathogens, suggesting the potential of this biguanide agent as a novel tetracyclines adjuvant. In this study, we provide evidence showing that the combination of proguanil and chlorhexidine with clarithromycin or rifampicin exhibits rapid bactericidal activities against both planktonic cells and mature biofilms of A. baumannii, the capacity to inhibit the development of antibiotic resistance and improvement of the treatment outcomes in A. baumannii-infected mice. Given the advantages of repurposing non-antibiotic drugs as antibiotic adjuvants, proguanil and chlorhexidine show promise as adjuvants of specific antibiotics in combating clinically significant pathogenic A. baumannii.

Dysregulated iron metabolism is reported in tuberculosis patients; therefore, it represents an opportunity for developing host-directed therapeutics. This study monitored the antimycobacterial properties of an iron chelator, i.e., Deferoxamine (DFO/D), and its impact on the transcript and metabolite levels of Mycobacterium tuberculosis (Mtb) in vitro. For in vivo validation, a group of mice received ferric carboxymaltose to create an iron overload condition, and controls were aerosol-infected with Mtb H37Rv. Mtb-infected mice received isoniazid (INH/H) and rifampicin (RIF/R) in combination with or without DFO before tissue-specific CFU assay, liver metabolite screening and iron quantification using mass spectrometry. DFO showed antimycobacterial properties comparable to INH in vitro. DFO treatment deregulated (log2DFO/control>{+/-}1.0) Mtb transcript (n=137) levels, the majority of which encode for iron-containing proteins and proteins involved in stress response. DFO treatment up-regulated Rv3622c (PE32), Rv2353c (PPE39) and Rv3022A (PE29) genes and conditional knocking down of ABC transporter like irtA by anhydrotetracycline (Atc) inducible CRISPR interference (CRISPRi) approach compromised Mtb growth showing their potential involvement in iron metabolism. Global Mtb metabolite analysis using GC-MS identified a set of 5 deregulated metabolites indicating a perturbed pentose phosphate pathway and inositol phosphate metabolism in the host upon DFO treatment. Iron-overloaded mice exhibited significantly higher tissue mycobacterial burden at two weeks post-infection, and the efficacy of INH and RIF were compromised, corroborating with previous reports. Iron chelation by DFO or combined with/adjunct to RIF and INH significantly reduced the lung/tissue mycobacterial burden at four weeks post-treatment, specifically in the first ([~]0.5 log) and second weeks ([~]0.5 log) of treatment. The intracellular pro-inflammatory cytokine levels in the lung CD4+ T cells of INH and RIF-treated groups with or without DFO were similar, suggesting DFO has a direct role in Mtb survival and metabolism rather than improved infection, and the efficacy of INH and RIF were compromised, corroborating with previous reports. DFO adjunct to RIF and INH treatment significantly altered liver arginine biosynthesis, which directly neutralizes ammonia and is immune-supportive. Conventionally, DFO is used for treating acute iron toxicity that is common in thalassemic patients, and this study demonstrates DFO has potential as adjunct therapeutics for tuberculosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/543389v3_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@5066fdorg.highwire.dtl.DTLVardef@99a292org.highwire.dtl.DTLVardef@80426dorg.highwire.dtl.DTLVardef@892436_HPS_FORMAT_FIGEXP M_FIG C_FIG

Decades of antibiotic overuse and misuse have placed us at the precipice of a post-antibiotic era. This rise in multidrug-resistant and pandrug-resistant bacteria poses a serious risk to public health, warranting urgent exploration of alternative treatment options for bacterial infections. One emerging method displaying promise in the field is phage-antibiotic combination therapy: the use of bacteriophages, viruses that exclusively infect bacteria, as adjuvants to antibiotics. This study investigated the synergistic effects of phage OMKO1, previously utilized in compassionate-use cases, with five antibiotics of diverse drug classes against Pseudomonas aeruginosa. Modified checkerboard assays were performed to test phage-antibiotic combination treatments across several antibiotic concentrations and phage multiplicities of infection. Synergy was achieved by four of the five phage-antibiotic pairings at sub-minimum inhibitory antibiotic concentrations. All combination treatments reduced the antibiotic minimum inhibitory concentration (MIC) by [&ge;] 2-fold and resulted in a reduction in resistant regrowth. These findings highlight the potential of phages to lower effective antibiotic concentrations and prolong their utility by slowing the rise of antimicrobial resistance.