Causative Strain Research Articles

Relationship between clarithromycin MICs and treatment responses in Mycobacterium avium complex pulmonary disease.

Mycobacterium avium complex pulmonary disease (MAC-PD) is a chronic lung condition with rapidly increasing prevalence worldwide. Macrolides like azithromycin and clarithromycin are the backbone of long-term antibiotic therapy for progressive MAC-PD. The impact of minimum inhibitory concentrations (MICs), especially within the susceptible range, for macrolides on treatment responses remains unclear. We analyzed adult patients who started treatment for MAC-PD between 1 March 2009 and 1 March 2022 at Seoul National University Hospital. Patients were categorized into four groups according to the clarithromycin MICs of their causative strains at treatment initiation. Logistic regression was employed to evaluate the impact of clarithromycin MICs on the microbiological cure rate. Companion drugs and their MICs, alongside clinical characteristics like age, sex, body mass index, cavity presence, acid-fast bacilli smear positivity, causative species, and erythrocyte sedimentation rate were adjusted in multivariable analysis. Four-hundred thirty-six patients (median age, 65 years; 34% men) were included. Microbiological cure rates were 51.8%, 51.9%, 50.0%, and 18.2% for patients with clarithromycin MICs ≤0.5, 1-2, 4-8, and ≥32 µg/mL, respectively (P=0.181). No significant differences in microbiological cure rates were observed across varying levels of clarithromycin MICs within the susceptible range (≤8 µg/mL). Relative to patients with clarithromycin-susceptible strains, patients with MICs ≥32 µg/mL had an odds ratio of 0.25 for achieving microbiological cure (95% confidence interval, 0.06-1.07; P=0.06). Treatment responses were comparable among patients with strains having clarithromycin MICs within the susceptible range, but were likely to be worse for patients with strains having MICs ≥32 µg/mL.

Virulence of Burkholderia pseudomallei ATS2021 Unintentionally Imported to United States in Aromatherapy Spray.

In the United States in 2021, an outbreak of 4 cases of Burkholderia pseudomallei, the etiologic agent of melioidosis and a Tier One Select Agent (potential for deliberate misuse and subsequent harm), resulted in 2 deaths. The causative strain, B. pseudomallei ATS2021, was unintentionally imported into the United States in an aromatherapy spray manufactured in India. We established that ATS2021 represents a virulent strain of B. pseudomallei capable of robust formation of biofilm at physiologic temperatures that may contribute to virulence. By using mouse melioidosis models, we determined median lethal dose estimates and analyzed the bacteriologic and histopathologic characteristics of the organism, particularly the potential neurologic pathogenesis that is probably associated with the bimABm allele identified in B. pseudomallei strain ATS2021. Our data, combined with previous case reports and the identification of endemic B. pseudomallei strains in Mississippi, support the concept that melioidosis is emerging in the United States.

Prevalence of Urinary Tract Infections in Hospitalized Diabetic Patients: Insights from a Guntur-A Case Study

Background: The existence of evidence was always given when diabetes predisposes individuals to a higher likelihood of experiencing asymptomatic bacteriuria and urinary tract infections. Urinary tract infections(UTIs) are highly prevalent among individuals with diabetes, emerging as the foremost type of bacterial infection within this demographic. Objective: This study was done to establish the prevalence of urinary tract infections in hospitalized diabetics and the most common causative strains. Materials and Methods: The research samples are consisted of 649 individuals diagnosed with 373 being women and 276 being men. These patients were admitted to the Government General Hospital (GGH), Guntur in various departments such as Urology, Nephrology, and the general ward between January and December 2023. We gathered individuals' personal medical information and conducted urine cultures. For statistical analysis we used Graph Pad Prism 10.2.3; the significance of the difference between the percentage values was assessed using Fisher’s exact test. Results: Among the patients studied, 110 (17%) had positive urine cultures. Of these 110 urinary tract infections, 86 (78.3%) were cases of asymptomatic bacteriuria. Escherichia coli was the most commonly identified bacterium, responsible for 68.9% of the infections. Conclusion: Urinary tract infections are prevalent among diabetic individuals. Given the significant number of asymptomatic cases, it is advisable to conduct urine cultures for all hospitalized diabetic patients.

Association between Exposure to Leptospira spp. and Abortion in Mares in Croatia.

Leptospirosis is one of the most common zoonotic infections and a major problem in terms of both veterinary medicine and public health. However, the disease is under-recognised and under-diagnosed worldwide, particularly in horses. Clinical leptospirosis in horses is mainly associated with recurrent uveitis (ERU), which has recently been studied more intensively, and reproductive disorders, the epidemiology of which is still relatively poorly understood. To enhance our comprehension of abortions caused by leptospirosis in horses and to identify the causative strains, a serological study was carried out with subsequent molecular characterisation of the isolate obtained. Using the microscopic agglutination test (MAT), serum samples from mares that aborted and foetal fluids (when available) were tested for antibodies against Leptospira spp. Furthermore, bacteria isolation from kidney cultures was conducted. Of 97 mare serum samples, 21 (21.64%) tested positive, with Grippotyphosa and Pomona being the most frequently detected serogroups. A significantly higher seroprevalence was found in aborting mares compared to the healthy horse population from the same geographical area, as well as a pronounced seasonal variation. Leptospiral antibodies were not detected in any of the foetal fluids, but isolation was successful in 1 case out of 39 (2.56%). Genotyping by multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) identified the obtained isolate as Leptospira kirschneri, serogroup Pomona, serovar Mozdok. Further surveillance and molecular typing of Leptospira strains causing abortion in horses would be invaluable in understanding the prevalence and impact of leptospirosis on equine reproductive health in Europe.

Complete genome sequences of two avian pathogenic Escherichia coli strains isolated from broilers exhibiting colibacillosis in Mississippi.

We report the whole-genome sequences of Escherichia coli strains APEC-O2-MS1266 and APEC-O2-MS1657 isolated from the liver and heart of infected broilers in Mississippi State, US. The genomic information of these two causative strains may provide a valuable reference for comparative studies of avian pathogenic E. coli.

A combination of GRA3, GRA6 and GRA7 peptides offer a useful tool for serotyping type II and III Toxoplasma gondii infections in sheep and pigs.

The clinical consequences of toxoplasmosis are greatly dependent on the Toxoplasma gondii strain causing the infection. To better understand its epidemiology and design appropriate control strategies, it is important to determine the strain present in infected animals. Serotyping methods are based on the detection of antibodies that react against segments of antigenic proteins presenting strain-specific polymorphic variations, offering a cost-effective, sensitive, and non-invasive alternative to genotyping techniques. Herein, we evaluated the applicability of a panel of peptides previously characterized in mice and humans to serotype sheep and pigs. To this end, we used 51 serum samples from experimentally infected ewes (32 type II and 19 type III), 20 sheep samples from naturally infected sheep where the causative strain was genotyped (18 type II and 2 type III), and 40 serum samples from experimentally infected pigs (22 type II and 18 type III). Our ELISA test results showed that a combination of GRA peptide homologous pairs can discriminate infections caused by type II and III strains of T. gondii in sheep and pigs. Namely, the GRA3-I/III-43 vs. GRA3-II-43, GRA6-I/III-213 vs. GRA6-II-214 and GRA6-III-44 vs. GRA6-II-44 ratios showed a statistically significant predominance of the respective strain-type peptide in sheep, while in pigs, in addition to these three peptide pairs, GRA7-II-224 vs. GRA7-III-224 also showed promising results. Notably, the GRA6-44 pair, which was previously deemed inefficient in mice and humans, showed a high prediction capacity, especially in sheep. By contrast, GRA5-38 peptides failed to correctly predict the strain type in most sheep and pig samples, underpinning the notion that individual standardization is needed for each animal species. Finally, we recommend analyzing for each animal at least 2 samples taken at different time points to confirm the obtained results.

Outbreak of Streptococcus pyogenes emm89 ST646 in a head and neck surgical oncology ward.

This study describes an outbreak of Streptococcus pyogenes that occurred in a ward caring for patients with head and neck cancer and tracheostomies. Many cases of invasive infections occurred in a short period, and extensive empiric antimicrobial administration on patients and healthcare workers was performed to control the outbreak. Whole-genome sequencing analysis of the causative strains confirmed that it was a monoclonal transmission of strains belonging to emm89/clade 3. The epidemiology and clinical characteristics of S. pyogenes infections have changed with the replacement of the prevalent clones worldwide. In the 1980s, there was a reemergence of S. pyogenes infections in high-income countries due to the spread of hypervirulent emm1 strains. emm89/clade 3 has recently been spreading worldwide and shares common features with emm1, including increased production of two toxins, NADase, and streptolysin O. The outbreak reported here may reflect the high spreading potential and virulence of emm89/clade 3.

Study of the circulation and properties of the West Nile virus in Russia in 2022

Introduction. The relevance of the study is due to the need to assess the real expansion of West Nile fever (WNF) in Russia, analyze the manifestations of epizootic and epidemic processes and study the population structure of West Nile virus (WNV).
 Aim. To obtain objective data on the intensity of WNV circulation in certain territories of Russia and study the properties of the isolated strains of the pathogen.
 Materials and methods. 4564 samples of field material from 23 subjects of the Russian Federation and 1547 samples of clinical material from 12 subjects of the Russian Federation were examined. A set of laboratory diagnostic methods was used: ELISA, RT-PCR, virological, sequencing.
 Results. In 20 out of 1331 (1.5%) examined febrile patients, IgM antibodies to WNV were detected, including positive cases identified for the first time in the Karachay-Cherkess Republic, Tver and Vladimir regions. The presence of immunity to WNV was found on average in 8.6% of 11 federal subjects' population with high seroprevalence rates in Zaporozhye (24,5%), Tula (15,4%) and Kursk (11,1%) regions. Low-avidity IgG antibodies were detected in 44 (33,1%) samples from a population of 9 federal subjects. Intensive circulation of WNV lineage 2 in the epizootic cycle in the southern part of European Russia was confirmed. 12 WNV isolates were obtained, including those isolated for the first time in the Republic of Crimea, the Karachay-Cherkess Republic and the Stavropol Territory. The heterogeneity of circulating WNF causative agent's strains related to the two clades of the WNV lineage 2 formed in 2021 and 2022 was established.
 Conclusion. In the course of comprehensive monitoring studies, a new northern border of the WNF range was established, which as of 2022 passes through the territory of the Tver region. Data from seroepidemiological studies, including the detection of low-avidity IgG antibodies, confirm fairly intense, but undiagnosed contact of the population of the European part of Russia with the WNF pathogen. In the southern region of the European part of Russia, WNV genotype 2 predominantly circulates, belonging to at least two clades formed in 2021 and 2022.

A search strategy for detecting duodenoscope-associated infections: a retrospective observational study

Duodenoscope-associated infections (DAIs) are exogenous infections resulting from the use of contaminated duodenoscopes. Though numerous outbreaks of DAI have involved multidrug-resistant micro-organisms (MDROs), outbreaks involving non-MDROs are also likely to occur. Detection challenges arise as these infections often resolve before culture or because causative strains are not retained for comparison with duodenoscope strains. To identify and analyse DAIs spanning a seven-year period in a tertiary care medical centre. This was a retrospective observational study. Duodenoscope cultures positive for gastrointestinal flora between March 2015 and September 2022 were paired with duodenoscope usage data to identify patients exposed to contaminated duodenoscopes. Analysis encompassed patients treated after a positive duodenoscope culture and those treated within the interval from a negative to a positive culture. Patient identification numbers were cross-referenced with a clinical culture database to identify patients developing infections with matching micro-organisms within one year of their procedure. A 'pair' was established upon a species-level match between duodenoscope and patient cultures. Pairs were further analysed via antibiogram comparison, and by whole-genome sequencing (WGS) to determine genetic relatedness. Sixty-eight pairs were identified; of these, 21 exhibited matching antibiograms which underwent WGS, uncovering two genetically closely related pairs categorized as DAIs. Infection onset occurred up to two months post procedure. Both causative agents were non-MDROs. This study provides crucial insights into DAIs caused by non-MDROs and it highlights the challenge of DAI recognition in daily practice. Importantly, the delayed manifestation of the described DAIs suggests a current underestimation of DAI risk.

A normalized parameter for comparison of biofilm dispersants in vitro

Dispersal of infectious biofilms increases bacterial concentrations in blood. To prevent sepsis, the strength of a dispersant should be limited to allow the immune system to remove dispersed bacteria from blood, preferably without antibiotic administration. Biofilm bacteria are held together by extracellular polymeric substances that can be degraded by dispersants. Currently, comparison of the strength of dispersants is not possible by lack of a suitable comparison parameter. Here, a biofilm dispersal parameter is proposed that accounts for differences in initial biofilm properties, dispersant concentration and exposure time by using PBS as a control and normalizing outcomes with respect to concentration and time. The parameter yielded near-identical values based on dispersant-induced reductions in biomass or biofilm colony-forming-units and appeared strain-dependent across pathogens. The parameter as proposed is largely independent of experimental methods and conditions and suitable for comparing different dispersants with respect to different causative strains in particular types of infection.

Outbreaks of bovine mastitis caused by specific Mycoplasma bovis strains recurring at multi-year intervals.

Mycoplasma bovis is a major cause of bovine mastitis. Intermittent shedding of the organism for many months is a feature of cows with intramammary infection. A dairy farm in Japan experienced a mastitis outbreak caused by M. bovis in 2016, as well as 2 additional outbreaks and 1 case in 2020-2021. The causative strains in the 3 outbreaks shared a common and identical genetic feature, the insertion of a transposase gene at the same site within the phosphate acetyltransferase-2 gene. Additionally, all isolates were genotyped to closely related sequence types (ST21 and ST141) by multilocus sequence typing, and had similar pulsopatterns by pulsed-field gel electrophoresis. Our results indicate that infection with the same causative strain remained in this herd and environment for 4 y. Treatment with fluoroquinolones, guided by antimicrobial susceptibility test results, eliminated M. bovis from 16 of 20 M. bovis-infected cows, as confirmed by culture and somatic cell counts. However, mastitis caused by other bacteria occurred in 9 M. bovis-free cows within 2 mo of the last treatment.

On the onset and dispersal of a major MDR TB clone among HIV-negative patients, Tunisia

BackgroundTo carry out a whole genome sequencing (WGS)-based investigation on the emergence and spread of the largest multidrug-resistant tuberculosis (MDR TB) outbreak that has been thriving among HIV-negative patients, Tunisia, since the early 2000s.MethodsWe performed phylogeographic analyses and molecular dating based on a WGS dataset representing 68 unique Mycobacterium tuberculosis isolates, covering almost the entire MDR TB outbreak for the time period 2001–2016.ResultsThe data indicate that the ancestor of the MDR TB outbreak emerged in the region of Bizerte, as early as 1974 (95% CI 1951–1985), from where it spread to other regions by 1992 (95% CI 1980–1996). Analysis of a minimum spanning tree based on core genome Multilocus Sequence Typing (cgMLST) uncovered the early spill-over of the fitness-compensated MDR TB strain from the prison into the general population. Indeed, cases with history of incarceration were found to be directly or indirectly linked to up to 22 new outbreak cases (32.35%) among the non-imprisoned population. By around 2008, the MDR TB outbreak strain had acquired additional resistance, leading to an XDR phenotype.ConclusionsWGS allowed refining our understanding of the emergence and evolution of the largest MDR TB outbreak in Tunisia, whose causative strain has been circulating silently for almost 26 years before. Our study lends further support to the critical role of prisons-related cases in the early spread of the outbreak among the general population. The shift to an XDR phenotype of such an epidemic clone prompts an urgent need to undertake drastic control measures.

Clinical and Bacterial Characteristics of Bloodstream Infections Caused by Listeria monocytogenes in Western China.

Bloodstream infections (BSIs) caused by Listeria monocytogenes are linked to high mortality of the patients. Case-specific details related to this disease and causative strains in different districts remain to be characterized. In this study, medical data of BSIs admitted to West China Hospital from October 2017 to March 2023 were retrieved from the hospital information system. The in vitro antimicrobial susceptibility testing and whole-genome sequencing were performed for L. monocytogenes strains isolated from blood specimens. The genetic relationship of these strains with those in public databases was also analyzed. The in-hospital mortality of L. monocytogenes BSIs was 25.7% (9/35). The changes in consciousness and elevated serum C-reactive protein (CRP) level were found to be the differential factors of L. monocytogenes BSIs (P < 0.05). All the 27 strains studied were susceptible to ampicillin, meropenem, and erythromycin. Only 22.2% of them were susceptible to trimethoprim-sulfamethoxazole. The Listeria pathogenicity islands 1 (LIPI-1), truncated LIPI-2, and multiple virulence-related genes outside the LIPIs were determined from these strains. Also, 12 sequence types (STs) and 12 clonal complexes (CCs) were identified and classified into clonal lineages I (9/27, 33.3%) and lineages II (18/27, 66.7%), demonstrating genetic differences with the strains in the database. ST451/CC11 (5/27, 18.5%) and ST8/CC8 (4/27, 14.8%) were the common genotypes. The consciousness change and elevated serum CRP level were found to be the differential factors of L. monocytogenes BSIs. Considering the high virulence of the strains, it is needed to pay more attention to the dissemination of the predominant genotype.

Clinical Study of 162 Cases of Peritonsillar Abscess Diagnosed by Contrast-Enhanced Computed Tomography

AbstractIn this retrospective clinical study of peritonsillar abscesses, we reviewed the data of 162 patients (116 males and 46 females) with peritonsillar abscess aged 8 to 86 years (mean age, 37.0 years) who had been diagnosed by contrast-enhanced computed tomography (CT), hospitalized, and treated for the abscess between January 2017 and December 2022. The abscess occurred on the left side in 72 (44.4%) patients, on the right side in 80 (49.4%) patients, and bilaterally in 10 (6.2%) patients. The abscess was of the superior oval type on 85 (49.4%) sides, the superior cap type on 41 (23.8%) sides, the inferior oval type on 25 (14.5%) sides, and the inferior cap type on 21 (12.2%) sides. Among 111 patients, bacteriological examination of the abscess fluid for the causative bacteria yielded 78 causative strains, including 24 strains of aerobic bacteria, predominantly Streptococcus pyogenes (51.6%), and 47 strains of anaerobic bacteria; the remainder were mixed bacterial strains. Bacterial resistance rates to antibiotics were as follows: 5.8% for piperacillin, 3.4% for ceftriaxone, 2.6% for meropenem, 11.5% for clindamycin, 28.6% for levofloxacin, and 15.4% for minocycline. Of the 162 patients, 83 (48.3%) were treated by incision, 25 (14.5%) by puncture, 62 (36.0%) with antibiotics, and 2 (1.2%) via abscess tonsillectomy. The most frequently used antibiotics (87.2% cases) were ampicillin/sulbactam combined with clindamycin and/or dexamethasone. The peritonsillar abscess recurred in 14 (8.6%) patients, and the recurrence occurred within 3 months of the initial onset in 8 (57.1%) of these patients. In conclusion, contrast-enhanced CT should be performed to accurately diagnose the location, size, and shape of a peritonsillar abscess and select the optimal treatment.

The virulence of Dichelobacter nodosus, measured by the elastase test, is an important predictor for virulent footrot diagnosis in New South Wales sheep flocks.

Ovine footrot is a contagious bacterial disease that causes foot lesions, and depending on the virulence of the causative strains, may lead to severe underrunning of the hoof and lameness. Virulent footrot can be identified, treated and controlled more effectively than less virulent benign forms. The in vitro elastase test for virulence of the causative bacteria, Dichelobacter nodosus, has been used to support clinical diagnosis. However, not all laboratory-designated virulent D. nodosus strains cause clinical signs of virulent footrot. This study evaluated retrospectively how well the elastase test supported clinical footrot diagnosis in 150 sheep flocks examined for suspect footrot in New South Wales between August 2020 and December 2021. Flocks were included if measures of clinical disease, environmental conditions and the virulence of D. nodosus isolates were available. Variation in the elastase activity result between D. nodosus isolated from the same flock made bacterial virulence hard to interpret, but calculating the mean elastase rate for all isolates from the same flock made correlations between bacterial virulence and flock footrot diagnosis possible. Simplifying bacterial virulence into whether there were any elastase-positive D. nodosus isolates before 12 days increased the predictive value of elastase results for virulent diagnosis, compared with using the first day that any isolate was elastase positive or the percentage of elastase-positive isolates by 12 days, but not all clinically virulent flocks had isolates with elastase activity before 12 days. Logistic regression models were fitted to identify the minimum number of predictors for virulent footrot diagnosis, with models suggesting that virulent footrot diagnosis was best predicted by adding the elastase test result and environmental conditions to the prevalence of severe foot lesions (score 4 and 5). However, performing the same analysis with different breeds, ages of sheep and seasons might highlight other factors important in the diagnosis of virulent footrot.

Isolation and Identification of Bacterial Soft-Rot-Causing Isolates from Cassava, Homa-Bay County, Kenya

Cassava bacterial soft rot is of great importance to economically valuable crop varieties. Commonly, bacterial soft rot strains cause destructive vegetable and potato diseases worldwide. The strain act similar to other species of the family Enterobacteriaceae that cause soft rot in plants. However, the disease has spread in a wide range of environment with its prevalence and causative strains less known to most agroecological zones of Kenya. Generally, aim of this study was to isolate, characterize and identify bacterial soft rot causative strains in cassava, Homa-Bay County. At the Sub County level, 104 farms were identified through a simple random method and symptomatic cassava plants sampled along laid transect in each farm. Rotten cassava tubers were then randomly sampled, packed and taken to the laboratory for pathogen identification. The bacterial strains were isolated in Nutrient Agar at 37˚c for 24 hours to obtain pure cultures. Identification was done using morphological, biochemical and 16S rRNA analysis method. The study identified: two Pectobacterium carotovorum, three Bacillus species: Bacillus amyloliquefaciens, Bacillus subtilis, and Bacillus tropicus, and three Achromobacter species: Achromobacter marplatensis, Verticiella sediminum, and Achromobacter xylosoxidans, pathogenic strains causing cassava bacterial soft rot. In this study, characterization and identification of cassava bacterial soft rot in Homa Bay County was done for the first time. The results can not only be used in the characterization enzymes produced by cassava bacterial soft rot strains but also in the development of effective control strategy.

Marked reduction in the incidence of transfusion-transmitted hepatitis B virus infection after the introduction of antibody to hepatitis B core antigen and individual donation nucleic acid amplification screening in Japan.

In Japan, 41 million blood donations have been screened for hepatitis B virus (HBV) during the past 8.4 years using individual donation nucleic acid amplification testing (ID-NAT) and antibody to hepatitis B core antigen (anti-HBc) screening. Transfusion-transmitted HBV infection (TT-HBV) incidence was examined. Donated blood implicated in TT-HBV was analyzed for infection stage and DNA levels. Causative HBV strains were phylogenetically analyzed. Among 5162 (0.013%) ID-NAT positives, window period (WP) and occult HBV infection (OBI) accounted for 3.4% (176) and 11.5% (594), respectively. No OBI-related TT-HBV occurred. Seven blood donations caused eight TT-HBV cases, six of which were in the pre-ID-NAT WP, leaving one with an unresolved infection stage. Seven cases were caused by platelet concentrate (180 mL plasma) and one case by fresh-frozen plasma (200 mL plasma), which contained estimated infectious doses varying between 2 and 2300 HBV virions. HBV subgenotypes in five cases were HBV/A2. Complete genome sequences of the transmitting A2 strains were nearly identical (99.6%-100%) and clustered in a group that included HBV/HIV-1 coinfections and a higher proportion of donors in the acute infection phase (69%) than the other group of HBV/A2 sequences (5%). The incidence of observed TT-HBV cases has significantly reduced to 0.19 per million in the ID-NAT screening period. OBI-related TT-HBV was eliminated by anti-HBc screening. Established TT-HBV cases were caused by blood products with large plasma volumes containing extremely low HBV concentrations derived from blood donors at a very early infection stage.

Microbial isolates and antibiotic sensitivity in patients hospitalized with odontogenic infections at a tertiary center over 10 years.

This study investigated causative strains and their antibiotic sensitivity in patients who were hospitalized for maxillofacial odontogenic infections at a tertiary center in South Korea over the past 10 years with the aim of providing guidelines for the selection of appropriate empirical antibiotics. Patients with head and neck fascial space abscesses due to odontogenic infections who underwent incision and drainage surgery with pus culture tests between 2013 and 2022 at the Department of Oral and Maxillofacial Surgery, Dankook University Hospital were included. The bacterial isolates and antibiotic sensitivity of each strain were analyzed for 2013-2022, 2013-2017, and 2018-2022. The affected fascial spaces were classified into primary, secondary, and deep neck spaces. In the 192 patients included in this study, 302 strains were detected. Viridans streptococcus had the highest frequency (51.7%), followed by Prevotella spp. (16.9%), Staphylococcus spp. (5.6%), and Klebsiella pneumoniae (4.6%). The identification rate of viridans streptococcus significantly increased from 41.8% in 2013-2017 to 60.9% in 2018-2022. Viridans streptococcus showed an antibiotic sensitivity of 80.5% to ampicillin; the sensitivity to penicillin antibiotics decreased over the study period. Antibiotic susceptibility was approximately 94% for third-generation cephalosporins. K. pneumoniae, which was identified at a high percentage in patients with deep neck space infection, showed increasing antibiotic resistance to most antibiotics over the study period. Viridans streptococcus was identified in head and neck fascial space abscesses with the highest frequency. Empirical antibiotics should be effective against this strain; penicillin antibiotics are considered inappropriate. For effective treatment of deep neck space abscesses, bacterial culture and antibiotic sensitivity tests performed as soon as possible are essential.

Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

Plague, caused by Yersinia pestis, is a zoonotic disease that can reemerge and cause outbreaks following decades of latency in natural plague foci. However, the genetic diversity and spread pattern of Y. pestis during these epidemic-silent cycles remain unclear. In this study, we analyze 356 Y. pestis genomes isolated between 1952 and 2016 in the Yunnan Rattus tanezumi plague focus, China, covering two epidemic-silent cycles. Through high-resolution genomic epidemiological analysis, we find that 96% of Y. pestis genomes belong to phylogroup 1.ORI2 and are subdivided into two sister clades (Sublineage1 and Sublineage2) characterized by different temporal-spatial distributions and genetic diversity. Most of the Sublineage1 strains are isolated from the first epidemic-silent cycle, while Sublineage2 strains are predominantly from the second cycle and revealing a west to east spread. The two sister clades evolved in parallel from a common ancestor and independently lead to two separate epidemics, confirming that the pathogen responsible for the second epidemic following the silent interval is not a descendant of the causative strain of the first epidemic. Our results provide a mechanism for defining epidemic-silent cycles in natural plague foci, which is valuable in the prevention and control of future plague outbreaks.

Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains.

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.