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Introduction. Antibacterial resistance and the increasing number of infections caused by multidrug-resistant bacteria threaten human health worldwide. The coronavirus disease 2019 (COVID-19) pandemic may have influenced antibacterial resistance patterns through changes in infection control practices and antibiotic prescribing. Aim. This single-centre, retrospective study aimed to describe changes in bacterial distribution, antibacterial resistance and antibiotic consumption in a university research and practice hospital before and during the COVID-19 pandemic. Methods. We analysed routine microbiology and pharmacy records from hospitalized patients between 01 April 2018 and 31 March 2022. The 2 years before 01 April 2020 was defined as the pre-pandemic period and the 2 years after 01 April 2020 as the pandemic period. Bacteria isolated from blood, urine and lower respiratory tract cultures, together with their antimicrobial susceptibility profiles, were compared between periods according to EUCAST criteria. Antibiotic consumption was calculated as defined daily doses per 1,000 inpatient days for commonly used agents. No patient-level clinical data or ward/ICU stratification was available. Results. A total of 7,275 isolates from 47,729 culture samples were obtained in the pre-pandemic period and 5,794 isolates from 47,210 samples during the pandemic. Coagulase-negative staphylococci remained the most frequently isolated species from blood cultures, Escherichia coli from urine cultures and Acinetobacter baumannii from lower respiratory tract cultures in both periods. Extended-spectrum β-lactamase (ESBL) rates and carbapenem resistance in E. coli and Klebsiella pneumoniae increased significantly during the pandemic, whereas teicoplanin and linezolid resistance in coagulase-negative staphylococci decreased. Carbapenem resistance in A. baumannii also decreased. Overall antibiotic consumption increased for most agents, particularly cephalosporins, carbapenems, aminoglycosides and fluoroquinolones, while vancomycin use decreased. Conclusion. In this single-centre, retrospective analysis, the overall distribution of major bacterial species remained largely stable before and during the COVID-19 pandemic, whereas important changes were observed in antimicrobial resistance profiles and antibiotic consumption. The increase in ESBL and carbapenem resistance in Enterobacterales, together with higher use of broad-spectrum antibiotics, underlines the need for strengthened antimicrobial stewardship and continuous local surveillance.

Introduction. Typhoid fever, caused by Salmonella enterica serovar Typhi, is a systemic infection. Approximately 40 cases occur annually in Japan, most of which are imported. In August 2023, a researcher engaged in phage typing of S. Typhi was diagnosed with typhoid fever. Case Presentation. A 48-year-old man presented with high fever, diarrhoea, malaise and loss of appetite. Initial findings, including liver dysfunction and severe inflammation, led to a suspected diagnosis of autoimmune disease. However, blood cultures identified S. Typhi, confirming typhoid fever. Comparative genomic analysis demonstrated clonality between the strain handled in the laboratory and the patient isolates, indicating a laboratory-acquired infection. Conclusion. This case underscores the need for ongoing vigilance regarding the risk of laboratory-acquired infections and highlights the value of whole-genome sequencing for tracking. It would be also emphasized that this is the first reported case in Japan linked to phage typing, a conventional typing method for S. Typhi. This raises the urgency of transitioning from phage typing to genotyping and recommends mandatory typhoid vaccination for laboratory personnel working with S. Typhi to minimize infection risk.

Background. Extended-spectrum β-lactamase (ESBL)-producing bacteria pose a global challenge because of resistance developing against a wide range of antimicrobial agents, complicating available treatment options. Thus, identifying the prevalent bacterial species producing ESBL enzymes and understanding how they are susceptible to antibiotics is necessary to inform effective treatment guidelines. Objective. We sought to characterize ESBL-producing bacteria isolated from pregnant women's urine at Itojo Hospital, Ntungamo district, Southwestern Uganda. Methods. We conducted a cross-sectional study where we collected and analysed 340 urine samples from 340 pregnant women. We did antimicrobial susceptibility testing using the Kirby-Bauer disc diffusion method. Isolates were screened for ESBL production and confirmed using the combination disc test. Genotypic characterization was confirmed using multiplex PCR to detect blaTEM, blaCTX-M and blaSHV genes. Results. The prevalence of ESBL-producing bacteria was 29.7% (101/340). Escherichia coli 36/101 (35.6%) and Klebsiella species 33/101 (32.7%) were predominant ESBL producers. Genotypic analysis revealed blaTEM 50/101 (49.5%) and blaCTX-M 31/101 (30.7%) as the most prevalent genes, while blaSHV was less common, 8/101 (7.9%) Conclusion. The high prevalence of ESBL-producing bacteria and their resistance to commonly used antibiotics highlighted the need for targeted antibiotic therapy, antimicrobial stewardship and regular molecular surveillance.

Antimicrobial resistance (AMR) increasingly compromises food safety and public health worldwide. Poultry products are major vectors for AMR bacteria in the food supply. We conducted the first preliminary survey of non-typhoidal Salmonella (NTS) and Escherichia coli on imported poultry in the Maldives. A total of 30 frozen whole chicken samples (15 processed as whole and 15 separated into meat and skin) and 3 pooled egg samples (10 eggs per pool) were obtained from supermarkets and grocery stores in Greater Malé between June 2022 and July 2022. Standard culture methods (Food and Drug Administration Bacteriological Analytical Manual) were used to isolate NTS and E. coli, and isolates were tested for susceptibility to five antibiotics (ampicillin, ceftriaxone, ciprofloxacin, tetracycline and trimethoprim-sulphamethoxazole) by disc diffusion [European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines]. NTS was recovered from 10 of 30 (33.3%) chicken samples, predominantly from skin (9/15) versus meat (3/15); E. coli was found in 15 of 30 (50%) samples, more often in meat. One pooled egg sample (33%) was positive for E. coli. Among 13 NTS isolates, 69% (9/13) were resistant to tetracycline, and 38% (5/13) to ciprofloxacin, ampicillin and ceftriaxone. Thirty-eight per cent (5/13) of NTS were classified by EUCAST as susceptible, increased exposure to ciprofloxacin. Overall, 9 of 13 (69.2%) NTS isolates were multidrug-resistant (MDR; non-susceptible to ≥3 classes). In E. coli, resistance was most common to ampicillin (8/19; 42.1%), followed by tetracycline (5/19; 26.3%), trimethoprim-sulphamethoxazole (4/19; 21.1%), ciprofloxacin (1/19; 5.3%) and ceftriaxone (1/19; 5.3%), with 26.3% (5/19) of E. coli being MDR. These results indicate a substantial prevalence of MDR foodborne bacteria in imported poultry and underscore critical food safety and One Health concerns. Strengthened microbiological surveillance, risk-based import inspection and enhanced regulatory coordination (aligned with the Maldives' AMR Action Plan) are urgently needed to protect public health.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance is crucial for understanding viral evolution and guiding public health responses. However, many countries, particularly in Central America, have limited sequencing capacity, resulting in scarce and delayed data. This study addresses this gap by analysing 320 SARS-CoV-2 genomes sequenced from a major diagnostic centre in Guatemala City, Guatemala, between April and August 2021. Clade 21J (Delta) was predominant (46.2%), followed by 19B (29.4%) and 20J (Gamma, 6.6%). The most reported symptoms were cough, headache, malaise and myalgia/arthralgia. Among patients infected with the Delta variant, 39.9% reported being contacts from a confirmed case, less than reported by the patients infected with non-Delta variants (53.2%, P=0.017). The proportion of signs and symptoms was similar among these two groups, except for the history of fever, which was increased by ~twofold in the Delta group. This research contributes valuable genomic and epidemiological data to elucidate SARS-CoV-2 variant dynamics in Central America and emphasizes the importance of global genomic surveillance for pandemic preparedness and response.

Xanthomonas spp. are increasingly recognized as a global threat to agriculture, impacting a broad range of economically important crops. We report the whole-genome sequences of six Xanthomonas strains isolated from tomato and pepper plants in Turkey that were experiencing symptoms of bacterial spot disease. Phylogenomic analysis with representative Xanthomonas genomes from each species revealed that three of these strains belonged to Xanthomonas perforans, two to Xanthomonas euvesicatoria and one to Xanthomonas campestris. We then analysed the phylogenomic relatedness of these strains with other strains from these respective species and characterized their type III secreted effector content. These genomic data represent a valuable resource for understanding the genetic diversity and local epidemiology of bacterial spot disease in Turkey.

Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occasional wastewater contamination. Restricted water exchange also allows for occasional summer heat spells with elevated water temperatures. Thus, infections stemming from wastewater contamination and seasonal opportunistic pathogens are potential health threats to recreational users of the fjord. In this pilot study, we assess the suitability of sequencing-based surveillance for the detection of pathogens at a popular urban location for recreational water activities, employing both long- and short-read sequencing platforms, paired with selective culturing. We find both metagenomic and full-length 16S sequencing to be promising tools for surveillance of seasonal opportunistic Vibrio pathogens. Furthermore, we identified Rhodoferax abundance to be a potentially attractive indicator of sewage contamination using low to medium-depth full-length 16S sequencing. Selective plating revealed minimal abundance of culturable extended-spectrum β-lactam-resistant bacteria, of which none were detected by metagenomic sequencing. Metagenomic analyses did, however, pick up several other β-lactamases in various bacterial taxa, including some that were closely related to those identified by selective plating and sequencing.

Vibrio parahaemolyticus is a foodborne pathogen commonly present in seafood. Of the various V. parahaemolyticus serotypes reported, O3:K6, O1:K25, O1:KUT and O4:K68 represent the major serotypes among pandemic clones that emerged from 1995 onward. However, new molecular markers of pandemic clones remain unidentified, and limited genomic sequence data are available for non-pandemic strains. Therefore, we aimed to identify novel genetic markers specific to pandemic V. parahaemolyticus strains by comparing non-pandemic and pandemic strains using whole-genome sequencing. Phylogenetic analysis of 163 V. parahaemolyticus strains revealed high genomic diversity within the species. The analysis also revealed a pandemic clade consisting of serotypes O3:K6, O1:K25, O1:KUT and O4:K68 strains isolated after 1995. We identified the genomic island GI-110 (VPaI-5) as a potential marker exclusive to the pandemic clade. Multiplex PCR detection of VPaI-5 demonstrated high specificity for pandemic strains, outperforming the detection of existing markers. The capacity of multiplex PCR for VPaI5 in distinguishing between pandemic and non-pandemic strains was confirmed using clinical isolates from Thailand. Our findings provide valuable insights into the genetic diversity of V. parahaemolyticus and establish a reliable method for monitoring pandemic strains.

The type I IFN response is crucial for cells to restrict viral replication during infection. Many viruses, including human cytomegalovirus (HCMV), have evolved mechanisms to antagonize the type I IFN response. We have previously observed an increase in protein expression of certain IFN-stimulated genes when comparing the high-passage HCMV strain AD169 to the low-passage strain HCMV Merlin, suggesting that AD169 is defective in its ability to inhibit type I IFN function. To better understand HCMV interaction with the type I IFN response, we examined expression of cellular and viral proteins expressed in Merlin- and AD169-infected cells associated with IFN production and signalling. HCMV IFN antagonists expressed by both viruses had differences in amino acids throughout their protein sequences, although analysis using AlphaFold revealed that there was likely to be no obvious differences in the overall structure of these proteins. Analysis of quantitative mass spectrometry datasets showed modest differences in the expression of cellular IFN-associated proteins between strains. Contrary to previously reported data, we found no obvious loss of IRF3 expression, though this may be due to experimental differences between studies. These data revealed that multiplicity of infection was an important factor in IRF3 expression. We found little or no statistical difference in the production of IFN-β RNA between Merlin- and AD169-infected cells in reverse transcriptase quantitative PCR assays and little or no statistical difference in replication of AD169 and Merlin in virus replication assays. Overall, these data suggest that different strains of HCMV have different, albeit modest, abilities to influence the expression of type I IFN pathway proteins during infection. However, this had no overall impact on the ability of different strains to produce a type I IFN or to replicate.