BACKGROUND: World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuberculosis (MTB) through airborne transmission. Treatment of TB is estimated to be 85% successful, however, this drops to 57% if MTB exhibits multiple antimicrobial resistance (AMR), for which fewer treatment options are available.
RESULTS: We develop a robust machine-learning classifier using both linear and nonlinear models (i.e. LASSO logistic regression (LR) and random forests (RF)) to predict the phenotypic resistance of Mycobacterium tuberculosis (MTB) for a broad range of antibiotic drugs. We use data from the CRyPTIC consortium to train our classifier, which consists of whole genome sequencing and antibiotic susceptibility testing (AST) phenotypic data for 13 different antibiotics. To train our model, we assemble the sequence data into genomic contigs, identify all unique 31-mers in the set of contigs, and build a feature matrix M, where M[i, j] is equal to the number of times the ith 31-mer occurs in the jth genome. Due to the size of this feature matrix (over 350 million unique 31-mers), we build and use a sparse matrix representation. Our method, which we refer to as MTB++, leverages compact data structures and iterative methods to allow for the screening of all the 31-mers in the development of both LASSO LR and RF. MTB++ is able to achieve high discrimination (F-1 >80%) for the first-line antibiotics. Moreover, MTB++ had the highest F-1 score in all but three classes and was the most comprehensive since it had an F-1 score >75% in all but four (rare) antibiotic drugs. We use our feature selection to contextualize the 31-mers that are used for the prediction of phenotypic resistance, leading to some insights about sequence similarity to genes in MEGARes. Lastly, we give an estimate of the amount of data that is needed in order to provide accurate predictions.
BACKGROUND: The models and source code are publicly available on Github at https://github.com/M-Serajian/MTB-Pipeline.

In 2022, an outbreak with severe bloodstream infections caused by Serratia marcescens occurred in an adult intensive care unit (ICU) in Hungary. Eight cases, five of whom died, were detected. Initial control measures could not stop the outbreak. We conducted a matched case-control study. In univariable analysis, the cases were more likely to be located around one sink in the ICU and had more medical procedures and medications than the controls, however, the multivariable analysis was not conclusive. Isolates from blood cultures of the cases and the ICU environment were closely related by whole genome sequencing and resistant or tolerant against the quaternary ammonium compound surface disinfectant used in the ICU. Thus, S. marcescens was able to survive in the environment despite regular cleaning and disinfection. The hospital replaced the disinfectant with another one, tightened the cleaning protocol and strengthened hand hygiene compliance among the healthcare workers. Together, these control measures have proved effective to prevent new cases. Our results highlight the importance of multidisciplinary outbreak investigations, including environmental sampling, molecular typing and testing for disinfectant resistance.

UNASSIGNED: Salmonella infections are considered the most common foodborne pathogens responsible for zoonotic infections and food poisoning in humans and animal species such as birds. Antimicrobial resistance is considered a global anxiety because it causes human public health repercussions, as well as leads to an increase in animal morbidity and death.
UNASSIGNED: The aims of this study are the isolation and identification of Salmonella enterica, as well as to investigate the antimicrobial susceptibility test (AST) and the molecular characteristics using polymerase chain reaction (PCR) and sequences for isolates from chicken products (eggs, livers, and minced meat) and human in the Wasit Governorate of Iraq.
UNASSIGNED: A total of 300 samples (150 chicken product samples including eggs, livers, and minced meat, and 150 human fecal samples) were collected from the Wasit governorate of Iraq from January to December 2022. The bacterial isolation was done according to recommendations of ISO 6579 standard and the Global Foodborne Infections Network laboratory protocol. Serotyping test and AST were done by using 19 antibiotic agents according to the recommendations of the Clinical and Laboratory Standards Institute, 2022 by using disc diffusion susceptibility test and Vitik 2 test. Finally, the suspected isolates were confirmed using the conventional PCR method and sequencing for a unique rRNA gene.
UNASSIGNED: The results showed that the isolation percentage of S. enterica in chicken products was 8.66% (12% eggs, 6% livers, and 8% minced meat), while in humans it was 4.6%. Also, showed 100% of Salmonella typhi in humans. While, in chicken eggs S. typhi, Salmonella typhimurium, and Salmonella enteritidis were 50%, 33.33%, and 16.66%, respectively. Also, showed 100% of S. typhimurium in both livers and minced meat. The AST in human isolates showed resistance to Ampicillin, Cefotaxime, Ceftazidime, Cefepime, Amikacin, Gentamicin, Ciprofloxacin, Norfloxacin, and Ceftriaxone, while no resistance to Amoxicillin, Pipracillin, Ertapenem, Imipenem, Meropenem, Fosfomycin, Nitrofurantoin, Trimethoprim, Azithromycin, and Tetracycline. In chicken products, isolates were resistant with different percentages to Amikacin, Gentamicin, Tetracycline, Ciprofloxacin, Norfloxacin, Nitrofurantoin, Ampicillin, Cefotaxime, Ceftazidime, Cefepime, and Trimethoprim; while no resistance to Amoxicillin, Pipracillin, Ertapenem, Imipenem, Meropenem, Fosfomycin, Azithromycin, and Ceftriaxone. Sequencing by using rRNA gene was done for four PCR products.
UNASSIGNED: This study showed the presence of genetic mutations for S. enterica which led to variations in the molecular characteristics, and antimicrobial drug resistance of S. enterica isolated from chicken products and humans.

OBJECTIVE: The human oral microbiome, a complex ecosystem linked to oral and systemic health, harbors a diverse array of microbial populations, including antimicrobial resistance genes (ARGs). As a critical component of the One Health approach to tackle antibiotic resistance, comprehending the oral resistome\'s composition and diversity is imperative. The objective of this study was to investigate the impact of chemical cell lysis treatment using MetaPolyzyme on the detectability of the oral microbiome, resistome, and DNA quality and quantity.
METHODS: Saliva samples were collected from five healthy individuals, and each of the samples was subjected to DNA extraction with and without the treatment with MetaPolyzyme. Through metagenomic sequencing, we analyzed, assessed, and compared the microbial composition, resistome, and DNA characteristics between both groups of extracted DNA.
RESULTS: Our study revealed that MetaPolyzyme treatment led to significant shifts in the detectability of microbial composition, favoring Gram-positive bacteria, notably Streptococcus, over Gram-negative counterparts. Moreover, the MetaPolyzyme treatment also resulted in a distinct change in ARG distribution. This shift was characterized by an elevated proportion of ARGs linked to fluoroquinolones and efflux pumps, coupled with a reduction in the prevalence of tetracycline and β-lactam resistance genes when compared with the nontreated group. Alpha diversity analysis demonstrated altered species and ARG distribution without affecting overall diversity, while beta diversity analysis confirmed significant differences in the taxonomical composition and oral resistome between treated and nontreated groups.
CONCLUSIONS: These findings underscore the critical role of cell lysis treatment in optimizing oral metagenomic studies and enhance our understanding of the oral resistome\'s dynamics in the context of antimicrobial resistance.

Purpose: Cutaneous infection in epidermolysis bullosa (EB) can cause significant morbidity, mortality, and dangerous sequelae. This review article aims to delve into the known epidemiology of EB, highlight the disease\'s primary causative agents and their antimicrobial resistance spectrum.Materials and methods: A thorough literature search was conducted using Medline, EMBASE, JBI and PubMed to gather data on the microbial landscape of EB wounds. The focus was on identifying the most common bacteria associated with EB infections and assessing their antimicrobial resistance profiles.Results: The analysis revealed that Staphylococcus aureus is the most frequently identified bacterium in EB wounds, with a notable prevalence of methicillin-resistant strains (MRSA). Specific studies on mupirocin resistance further indicated rising rates of mupirocin-resistant Staphylococcus aureus, with one study reporting rates as high as 16.07%. Additionally, high resistance to other antibiotics, such as levofloxacin and trimethoprim/sulfamethoxazole, was observed in MRSA isolates.Conclusions: The findings highlight the critical need for regular resistance surveillance and the prudent use of mupirocin to manage infections effectively in EB. The multi-drug resistant nature of pathogens in EB presents a significant challenge in treatment, highlighting the importance of antimicrobial stewardship. Ultimately, given the sparse literature and the rarity of large-scale studies, further longitudinal research on the antimicrobial resistance profile of bacteria isolated from EB wounds is essential.

OBJECTIVE: Bloodstream infections in patients with COVID-19 are linked to higher mortality rates, whilst data on epidemiology and resistance patterns remains scarce to guide management and prevent antibiotic resistance. This research focuses on the prevalence, clinical features, causative microorganisms, and antimicrobial susceptibility of bacterial and fungal secondary bloodstream co-infections in hospitalized patients with COVID-19.
METHODS: In this retrospective study analysis of 230 patients with COVID-19 from Central Taiwan (June 2021 to June 2022), pathogens were identified via MALDI-TOF MS and Vitek 2 system with Clinical & Laboratory Standards Institute (CLSI) standards.
RESULTS: In the cohort, 17.8% experienced bloodstream infections, resulting in a total of 45 isolates from the 41 bloodstream infection patients: predominantly gram-positive bacteria (Staphylococcus and Enterococcus) at 69%, gram-negative at 29% (Escherichia coli and Klebsiella pneumoniae), and fungi at 2%. Infected patients showed significantly elevated levels of white blood count (WBC), C-reactive protein (CRP) and procalcitonin (PCT). Of note, resistance to common antibiotics, such as fluoroquinolones, cephalosporins, and oxacillin was significant, especially in K. pneumoniae, Acinetobacter species, and S. aureus infections.
CONCLUSIONS: Our study highlights the influence of bacterial infections in hospitalized patients with COVID-19. The bacterial infections were discovered to impact the clinical trajectory of COVID-19, potentially exacerbating or mitigating its symptoms, severity and fatality. These insights are pivotal to addressing clinical challenges in COVID-19 management and underscoring the need for tailored medical interventions. Understanding these co-infections is thus essential for optimizing patient care and improving overall outcomes in the post COVID-19 pandemic era.

Background Gonorrhoea infections and antimicrobial resistance are rising in many countries, particularly among men who have sex with men, and an increasing proportion of infection is detected at extragenital sites. This study assessed trends in gonorrhoea diagnoses and antibiotic resistance at a sexual health service in New Zealand that followed national guidelines for specimen collection. Methods Routinely-collected data from Canterbury Health Laboratories of specimens taken at the Christchurch Sexual Health Service 2012-2022 were audited. Descriptive results included the number of patient testing events positive for gonorrhoea per year and site of infection (extragenital/urogenital). Annual test-positivity was calculated (number of positive patient testing events divided by total number of testing events) and the Cochran-Armitage Test for Trend was used to assess whether there was an association between test-positivity and year. Results Of 52,789 patient testing events, 1467 (2.8%) were positive for gonorrhoea (81% male). Half (49.3%) of people (57.9% of males, 12.2% of females) with a gonorrhoea infection had an extragenital infection in the absence of a urogenital infection. The number of extragenital infections increased at a faster rate than urogenital among males. Test-positivity increased from 1.3% in 2012 to 5.8% in 2022 (P Conclusions This study highlights the importance of extragenital sampling and maintaining bacterial culture methods for accurate diagnosis and treatment. The observation that gonorrhoea positivity rate and antimicrobial resistance rates are rising in New Zealand calls for urgent action.

The misuse of antibiotics and the emergence of antimicrobial resistance (AMR) is a concern in the aquaculture industry because it contributes to global health risks and impacts the environment. This study analyzed the AMR of sentinel bacteria associated with striped catfish (Pangasisanodon hypophthalmus) and giant snakehead (Channa micropeltes), the two main fish species reared in the pond culture in Cambodia. Phenotypic and genotypic characterization of the recovered isolates from fish, water, and sediment samples revealed the presence of bacteria, such as 22 species belonging to families Aeromonadaceae, Enterobacteriaceae, and Pseudomonadaceae. Among 48 isolates, Aeromonas caviae (n = 2), Aeromonas hydrophila (n = 2), Aeromonas ichthiosmia (n = 1), Aeromonas salmonicida (n = 4) were detected. A. salmonicida and A. hydrophilla are known as fish pathogens that occur worldwide in both fresh and marine water aquaculture. Antibiotic susceptibility testing revealed antibiotic resistance patterns of 24 (50 %) isolates among 48 isolates with higher multiple antibiotic resistance index (> 0.2). All the isolates of Enterobacteriaceae were susceptible to ciprofloxacin. Ciprofloxacin is a frontline antibiotic that is not recommended to use in aquaculture. Therefore, its use has to be strictly controlled. This study expands our knowledge of the AMR status in aquaculture farms which is very limited in Cambodia.

CONCLUSIONS: Effective antimicrobials play an important element in modern medicine\'s success in treating infections, without which the patients would be put at risk. Along with the naturally occurring process of antibiotic resistance, the misuse/overuse of these antibiotics also leads to them losing their effectiveness. It limits the treatment options as the microbe that had previously been sensitive becomes resistant. This bibliometric study was performed by searching the Scopus database according to a specific search strategy. A total of 4200 articles were retrieved from the search, and after applying inclusion and exclusion criteria, 1355 articles were included in the study. All of the bibliometric variables examined in this study revealed significant growth in this research field, especially during COVID-19, in terms of increasing scientific output and research collaboration. The study findings indicate an adequate quality and amount of antimicrobial resistance (AMR) research on microbiology and pharmacodynamics in India, whereas more research needs to be conducted on measures to tackle AMR, its public health, and policy aspects.

Background and Objective: Enterococci are typically found in a healthy human gastrointestinal tract but can cause severe infections in immunocompromised patients. Such infections are treated with antibiotics. This study addresses the rising concern of antimicrobial resistance (AMR) in Enterococci, focusing on the prevalence of vancomycin-resistant enterococcus (VRE) strains. Materials and Methods: The pilot study involved 140 Enterococci isolates collected between 2021 and 2022 from two multidisciplinary hospitals (with and without local therapeutic drug monitoring protocol of vancomycin) in Latvia. Microbiological assays and whole genome sequencing were used. AMR gene prevalence with resistance profiles were determined and the genetic relationship and outbreak evaluation were made by applying core genome multi-locus sequence typing (cgMLST). Results: The acquired genes and mutations were responsible for resistance against 10 antimicrobial classes, including 25.0% of isolates expressing resistance to vancomycin, predominantly of the vanB type. Genetic diversity among E. faecalis and E. faecium isolates was observed and seven potential outbreak clusters were identified, three of them containing sequence types ST6, ST78 and ST80. The prevalence of vancomycin resistance was highest in the hospital without a therapeutic drug-monitoring protocol and in E. faecium. Notably, a case of linezolid resistance due to a mutation was documented. Conclusions: The study illustrates the concerning prevalence of multidrug-resistant Enterococci in Latvian hospitals, showcasing the rather widespread occurrence of vancomycin-resistant strains. This highlights the urgency of implementing efficient infection control mechanisms and the need for continuous VRE surveillance in Latvia to define the scope and pattern of the problem, influencing clinical decision making and planning further preventative measures.