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Infectious Bovine Keratoconjunctivitis (IBK) is a widespread ocular disease that affects dairy and beef cattle worldwide, caused by Gram-negative bacteria from the genus Moraxella . It is the most common eye disease in cattle, with symptoms including tearing, ocular pain, corneal opacity, photophobia, ulceration, and, in severe cases, permanent blindness. This study focused on characterizing Moraxella species in a 2022 IBK outbreak in Minas Gerais, Brazil. Ocular swabs from 18 symptomatic Holstein cattle were analyzed through colony isolation, physiological tests, and molecular techniques, including PCR-RFLP and sequencing. Results revealed one isolate of Moraxella bovoculi genotype 1 and five isolates of Moraxella oculi , marking the first report of the latter species in Brazil. This study represents the second report of Moraxella oculi isolation and the first in a country different from the initial report. Notably, Moraxella bovis was not isolated in this outbreak. All isolates exhibited susceptibility to the tested antibiotics. Comparative genomic analysis between the Brazilian Moraxella oculi isolate and the American strain (Tifton 1) revealed 99.5% similarity in the 16–23 S rRNA locus and 99.0% average nucleotide identity.

Abstract Rationale Many bacterial pathogens causing respiratory infections in children are common residents of the respiratory tract. Insight into bacterial colonization patterns and microbiota stability at a young age might elucidate healthy or susceptible conditions for development of respiratory disease. Objectives To study bacterial succession of the respiratory microbiota in the first 2 years of life and its relation to respiratory health characteristics. Methods Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12, and 24 months were characterized by 16S-based pyrosequencing. We determined consecutive microbiota profiles by machine-learning algorithms and validated the findings cross-sectionally in an additional cohort of 140 children per age group. Measurements and Main Results Overall, we identified eight distinct microbiota profiles in the upper respiratory tract of healthy infants. Profiles could already be identified at 1.5 months of age and were associated with microbiota stability and change over the first 2 years of life. More stable patterns were marked by early presence and high abundance of Moraxella and Corynebacterium/Dolosigranulum and were positively associated with breastfeeding in the first period of life and with lower rates of parental-reported respiratory infections in the consecutive periods. Less stable profiles were marked by high abundance of Haemophilus or Streptococcus. Conclusions These findings provide novel insights into microbial succession in the respiratory tract in infancy and link early-life profiles to microbiota stability and respiratory health characteristics. New prospective studies should elucidate potential implications of our findings for early diagnosis and prevention of respiratory infections. Clinical trial registered with www.clinicaltrials.gov (NCT00189020).

The airway microbiome has an important role in asthma pathophysiology. However, little is known on the relationships between the airway microbiome of asthmatic children, loss of asthma control, and severe exacerbations. Here we report that the microbiota’s dynamic patterns and compositions are related to asthma exacerbations. We collected nasal blow samples (n = 319) longitudinally during a clinical trial at 2 time-points within one year: randomization when asthma is under control, and at time of early loss of asthma control (yellow zone (YZ)). We report that participants whose microbiota was dominated by the commensal Corynebacterium   +   Dolosigranulum cluster at RD experience the lowest rates of YZs (p = 0.005) and have longer time to develop at least 2 episodes of YZ (p = 0.03). The airway microbiota have changed from randomization to YZ. A switch from the Corynebacterium   +   Dolosigranulum cluster at randomization to the Moraxella- cluster at YZ poses the highest risk of severe asthma exacerbation (p = 0.04). Corynebacterium’s relative abundance at YZ is inversely associated with severe exacerbation (p = 0.002). How the airway microbiome influences asthma pathophysiology remains unclear. Here, the authors analyse nasal samples of cohort of school-age children with persistent asthma and find that the microbiota’s patterns and composition at time of early loss of asthma control associate with severe asthma exacerbations.

Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. To investigate the population structure of M. catarrhalis , we developed a core-genome multilocus sequence typing (cgMLST) scheme using 1319 core genes, and a life identification number (LIN) barcode classification system. Whole-genome analyses of nearly 2000 genomes confirmed divergent seroresistant (SR) and serosensitive (SS) M. catarrhalis lineages with distinct evolutionary trajectories. SR genomes are more conserved, while SS genomes exhibited greater genetic variability. Virulence gene analyses revealed lineage-specific variations in ubiquitous surface proteins (UspA1 and UspA2) and lipooligosaccharide (LOS) types. The bro β-lactamase, and mcb bacteriocin cluster, are more common in SR lineages, which suggested different selective pressures and adaptation. Here, we show that this cgMLST scheme and LIN code system provide a robust method for characterising M. catarrhalis , distinguish between SR and SS lineages, and offer a unified framework for population structure analyses. This study introduces a genomic typing system for Moraxella catarrhalis , revealing two major lineages with distinct evolution, variability, and virulence traits.

Background The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. Results In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp , are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria (“superbugs”) existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such “cutotypes” was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development. Conclusions The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. 7R3iiahnQ7D7AnHo8QeReb Video abstract

To investigate the etiology and clinical characteristics of Moraxella catarrhalis infections in the lower respiratory tract among pediatric patients in southwestern Shandong Province, China. This study aims to enhance early identification and diagnostic accuracy for laboratory physicians, while providing evidence to guide clinical diagnosis and treatment of Moraxella catarrhalis-related infections. This retrospective cohort study analyzed pediatric patients with Moraxella catarrhalis lower respiratory tract infections in southwestern Shandong Province, China. Clinical isolates were obtained through standardized sputum/bronchoalveolar lavage collection protocols and subjected to microbiological identification, antimicrobial susceptibility testing, and molecular characterization of β-lactamase production and bro gene variants. Epidemiological patterns and clinical profiles were systematically evaluated using electronic medical record data spanning January 2020 to December 2023. During the 4-year surveillance period (2018–2021), Moraxella catarrhalis was isolated from 848 pediatric cases of lower respiratory tract infections, representing a 7.81% overall detection rate. Age-stratified analysis revealed the highest prevalence in infants aged 28 days to 1 year (9.69%), with significant seasonal variation peaking in the fourth quarter (11.58%, p  < 0.05). Monomicrobial infections predominated (79.72%, 676/848), while polymicrobial cases (20.28%, 172/848) predominantly co-occurred with Streptococcus pneumoniae and Haemophilus influenzae. All isolates were confirmed through parallel testing using automated biochemical analyzers and MALDI-TOF mass spectrometry. Antimicrobial susceptibility profiling demonstrated complete susceptibility to ceftazidime, cefepime, and imipenem (100%), with ≥ 95% susceptibility rates to ciprofloxacin (98.2%), levofloxacin (97.6%), ceftriaxone (96.8%), cefuroxime (96.1%), tetracycline (95.4%), and chloramphenicol (95.1%). A concerning temporal escalation in erythromycin resistance was observed (69.73% in 2018 vs. 90.57% in 2021, χ²=41.32, p  < 0.001), while ampicillin and clindamycin resistance remained persistently high (> 93% across all years).β-lactamase production was detected in 96.58% (819/848) of isolates, with molecular characterization identifying bro-1 (94.51%, 774/819) and bro-2 (5.49%, 45/819) gene variants. The β-lactamase-negative subgroup (3.42%, 29/848) showed no significant epidemiological clustering. Our surveillance study demonstrates that Moraxella catarrhalis lower respiratory tract infections in southwestern Shandong Province predominantly affect infants aged 28 days to 1 year, with significantly elevated seasonal incidence during the fourth quarter. Notably, we observed a concerning temporal escalation in erythromycin resistance and persistently high resistance rates to ampicillinand clindamycin throughout the 2018–2021 surveillance period. Crucially, β-lactamase hyperproduction particularly BRO-1 gene carriage emerged as the principal resistance mechanism against β-lactams, while maintained susceptibility to expanded-spectrum cephalosporins and carbapenems suggests preserved therapeutic options. These findings underscore the necessity for: Avoidance of macrolides and β-lactam/β-lactamase inhibitor combinations in empirical therapy; Continuous monitoring of BRO gene evolution patterns; Age-specific antimicrobial stewardship programs targeting infant populations.

Moraxella catarrhalis is an exclusively human pathogen and is a common cause of otitis media in infants and children, causing 15%-20% of acute otitis media episodes. M. catarrhalis causes an estimated 2–4 million exacerbations of chronic obstructive pulmonary disease in adults annually in the United States. M. catarrhalis resembles commensal Neisseria species in culture and, thus, may be overlooked in samples from the human respiratory tract. The prevalence of colonization of the upper respiratory tract is high in infants and children but decreases substantially in adulthood. Most strains produce β-lactamase and are thus resistant to ampicillin but susceptible to several classes of oral antimicrobial agents. Recent work has elucidated mechanisms of pathogenesis and focused on vaccine development to prevent otitis media in children and respiratory tract infections caused by M. catarrhalis in adults with chronic obstructive pulmonary disease.

Moraxella is an ocular bacterial pathogen isolated in cases of keratitis, conjunctivitis, and endophthalmitis. Gram-negative brick-shaped diplobacilli from ocular specimens, and slow growth in culture, are early indications of Moraxella ocular infection; however, identifying Moraxella to species can be complex and inconsistent. In this study, bacteria consistent with Moraxella were identified to species using: (1) DNA sequencing coupled with vancomycin susceptibility, (2) MALDI-TOF mass spectrometry, and (3) the Biolog ID system. Study samples consisted of nine ATCC Moraxella controls, 82 isolates from keratitis, 21 isolates from conjunctivitis, and 4 isolates from endophthalmitis. The ATCC controls were correctly identified. For keratitis, 66 (80.5%) were identified as M. nonliquefaciens, 7 (9.0%) as M. lacunata, 5 (6%) as M. osloensis, 2 (2.5%) as Acinetobacter lwoffii, 1 (1.0%) as M. bovis/nonliquefaciens, and 1 (1.0%) as M. osloensis/nonliquefaciens. For conjunctivitis, 9 (43.0%) were identified as M. osloensis, 6 (29.0%) as M. nonliquefaciens, 3 (14.3%) as Roseomonas, 2 (9.5%) as Acinetobacter (parvus, junii), and 1 (4.5%) as M. catarrhalis/nonliquefaciens. From endophthalmitis, 3 of 4 of the isolates were M. nonliquefaciens. Overall, M. nonliquefaciens and M. osloensis were identified in 70% (75 of 107) and 13% (14 of 107) of cases, respectively, totaling 83% (89 of 107). M. nonliquefaciens and M. osloensis are important bacterial pathogens of the eye as determined by DNA sequencing, MALDI-TOF MS, and Biolog. Although Moraxella catarrhalis is a clinical pathogen, other species of Moraxella appear to have a prominent role in eye infections.

Background Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed. Methods We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing. Results The healthy subjects harbored primarily Streptococcus , whereas the patients showed an enrichment of Haemophilus or Moraxella . Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis. Conclusions This study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens.

Phages use anti-CRISPR proteins to deactivate the CRISPR–Cas system. The mechanisms for the inhibition of type I and type II systems by anti-CRISPRs have been elucidated. However, it has remained unknown how the type V CRISPR–Cas12a (Cpf1) system is inhibited by anti-CRISPRs. Here we identify the anti-CRISPR protein AcrVA5 and report the mechanisms by which it inhibits CRISPR–Cas12a. Our structural and biochemical data show that AcrVA5 functions as an acetyltransferase to modify Moraxella bovoculi (Mb) Cas12a at Lys635, a residue that is required for recognition of the protospacer-adjacent motif. The AcrVA5-mediated modification of MbCas12a results in complete loss of double-stranded DNA (dsDNA)-cleavage activity. In contrast, the Lys635Arg mutation renders MbCas12a completely insensitive to inhibition by AcrVA5. A cryo-EM structure of the AcrVA5-acetylated MbCas12a reveals that Lys635 acetylation provides sufficient steric hindrance to prevent dsDNA substrates from binding to the Cas protein. Our study reveals an unprecedented mechanism of CRISPR–Cas inhibition and suggests an evolutionary arms race between phages and bacteria.Zhiwei Huang and colleagues report structural and biochemical data showing that the anti-CRISPR protein AcrVA5 functions as an acetyltransferase, modifying MbCas12a at Lys635, a residue required for PAM recognition. Acetylation of Lys635 creates a steric clash that prevents binding of target DNA.