Carriage Isolates Research Articles

Hidden Perils: Diagnosing Asymptomatic Disease Carriers

COVID-19, a disease induced by SARS-CoV-2, became a worldwide pandemic while SARS, a disease induced by a closely related virus, SARS-CoV, was successfully contained. This is because COVID-19, unlike SARS, can be spread by people who do not display any symptoms of disease, either because they are in the early stages of the infection or because their infection remains clinically silent. This research article traces the complex history of the diagnosis of symptom-free (or asymptomatic) carriers of pathogens, a term inseparably linked to the rise of the laboratory diagnosis of pathogens. Only such a diagnosis can reveal that an apparently healthy individual harbours dangerous bacteria, parasites, or viruses. The article begins with the iconic story of ‘Typhoid Mary’, a New York cook found to be an asymptomatic carrier of typhoid fever microbes. It then discusses divergent approaches to the treatment of symptom-free carriers of hookworm and controversies around the screening of HIV carriers, especially before the development of anti-retroviral treatments. It concludes with a presentation of the debates on the role of asymptomatic carriers in the spread of COVID-19 and of the differences between the approaches of countries seeking to eliminate this disease, a goal that itself entails tracing and isolation of all asymptomatic carriers of coronavirus, and those trying to contain it, an approach that tolerates the presence of a limited number of ‘invisible’ virus carriers.

Genomic Diversity of Haemophilus influenzae Serotype a in an Outbreak Community-Alaska, 2018.

Haemophilus influenzae serotype a (Hia) can cause severe invasive disease, especially in young children. In 2018, 4 invasive Hia cases occurred in an Alaska community. We used whole-genome sequencing (WGS) to evaluate the relationship of the bacteria from this community and other Alaska patients with invasive Hia. All carriage (n = 15) and invasive (n = 4) Hia isolates from the outbreak community, together with 15 nonoutbreak Alaska invasive Hia surveillance isolates from 2018, were tested for antimicrobial susceptibility and characterized using WGS. Phylogenetic analysis of both invasive and carriage Hia isolates revealed 2 major clades that differed by an average of 300 core single-nucleotide polymorphisms (SNPs). All isolates from the outbreak community were clustered in 1 subclade, within a larger clade containing 3 nonoutbreak invasive Hia isolates. Comparative genomics did not reveal any genetic mutations that distinguished carriage from invasive isolates. Three (20%) community isolates were rifampin resistant and had a previously unreported mutation in the rpoB gene. In the outbreak community, Hia isolates from carriers were indistinguishable from the invasive Hia isolates. Overall, invasive Hia isolates from Alaska in 2018 were genetically similar. The rifampin resistance mutation is concerning as rifampin is the first-line medication for Hia prophylaxis.

Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.

Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses-including isolates recovered from individual horses sampled repeatedly-to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.

The Israeli national policy for discontinuation of isolation of carbapenem-resistant Enterobacterales carriers by carbapenemase type: a retrospective cohort study

ObjectivesThe Israeli national policy for containing carbapenemase-producing Enterobacterales (CPE) includes a protocol allowing for discontinuation of carrier status following spontaneous decolonization. We examined the strategy's effectiveness based on carbapenemase type. MethodsWe performed a retrospective cohort study comparing individuals colonized with KPC- or NDM-producing Enterobacterales who underwent the process of isolation discontinuation. The primary outcome was reversion of carrier status, i.e. re-identification of the same CPE species following isolation discontinuation. We used survival analysis to estimate overall hazard ratio and performed competing-risks analysis using a Fine–Gray subdistribution hazard model and cause-specific hazard ratios. ResultsBetween 1 January 2006 and 1 January 2019 we identified 1694 individuals who met inclusion criteria, including 1337 (78.9%) carriers of KPC-producing Enterobacterales, 305 (18.0%) carriers of NDM-producing Enterobacterales and 52 (3.1%) carriers of dual KPC-/NDM-producing Enterobacterales. A total of 134 individuals (7.9%) had reversion of carrier status: 9.1% (121/1337) and 4.3% (13/305) of individuals with KPC- and NDM-producing Enterobacterales, respectively. The subdistribution hazard ratio of status reversion was not increased among carriers of NDM producers compared with KPC producers (0.567, 95% CI 0.320–1.000], p 0.052). Cause-specific hazard ratios yielded similar results (0.522, 95% CI 0.291–0.937, p 0.029. ConclusionsCarriage of NDM-producing Enterobacterales was not associated with higher rates of reversion to carrier status following spontaneous decolonization than was carriage of KPC-producing Enterobacterales.

Whole-genome analysis uncovers loss of blaZ associated with carriage isolates belonging to methicillin-resistant Staphylococcus aureus (MRSA) clone ST5-VI in Cape Verde

Surveillance studies for Staphylococcus aureus carriage are a primary tool to survey the prevalence of methicillin-resistant S. aureus (MRSA) in the general population, patients and healthcare workers. We have previously reported S. aureus carriage in various African countries, including Cape Verde. Whole-genome sequences of 106 S. aureus isolates from Cape Verde were determined. Staphylococcus aureus carriage isolates in Cape Verde show high genetic variability, with the detection of 27 sequence types (STs) and three primary genetic clusters associated with ST152, ST15 and ST5. One transmission event with less than eight core-genome single nucleotide polymorphisms (cgSNP) differences was detected among the ST5-VI MRSA lineage. Genetic analysis confirmed the phenotypic resistance and allowed the identification of six independent events of plasmid or transposon loss associated with the deletion of blaZ in nine isolates. In the four ST5 MRSA isolates, loss of the blaZ plasmid coincided with the acquisition of SCCmec type VI and an unusual penicillin phenotype with a minimum inhibitory concentration (MIC) at the breakpoint, indicating an adaptation trend in this endemic lineage. Similar events of blaZ plasmid loss, with concomitant acquisition SCCmec elements, were detected among ST5 isolates from different geographical origins. Overall, the genome data allowed to place isolates in a phylogenetic context and to identify different blaZ gene deletions associated with plasmid or transposon loss. Genomic analysis unveiled adaptation and evolution trends, namely among emerging MRSA lineages in the country, which deserve additional consideration in the design of future infection control protocols.

Genetic Diversity of Meningococcal Serogroup B Vaccine Antigens among Carriage Isolates Collected from Students at Three Universities in the United States, 2015-2016.

ABSTRACTCarriage evaluations were conducted during 2015 to 2016 at two U.S. universities in conjunction with the response to disease outbreaks caused by Neisseria meningitidis serogroup B and at a university where outbreak and response activities had not occurred. All eligible students at the two universities received the serogroup B meningococcal factor H binding protein vaccine (MenB-FHbp); 5.2% of students (181/3,509) at one university received MenB-4C. A total of 1,514 meningococcal carriage isolates were obtained from 8,905 oropharyngeal swabs from 7,001 unique participants. Whole-genome sequencing data were analyzed to understand MenB-FHbp’s impact on carriage and antigen genetic diversity and distribution. Of 1,422 isolates from carriers with known vaccination status (726 [51.0%] from MenB-FHbp-vaccinated, 42 [3.0%] from MenB-4C-vaccinated, and 654 [46.0%] from unvaccinated participants), 1,406 (98.9%) had intact fHbp alleles (716 from MenB-FHbp-vaccinated participants). Of 726 isolates from MenB-FHbp-vaccinated participants, 250 (34.4%) harbored FHbp peptides that may be covered by MenB-FHbp. Genogroup B was detected in 122/1,422 (8.6%) and 112/1,422 (7.9%) isolates from MenB-FHbp-vaccinated and unvaccinated participants, respectively. FHbp subfamily and peptide distributions between MenB-FHbp-vaccinated and unvaccinated participants were not statistically different. Eighteen of 161 MenB-FHbp-vaccinated repeat carriers (11.2%) acquired a new strain containing one or more new vaccine antigen peptides during multiple rounds of sample collection, which was not statistically different (P = 0.3176) from the unvaccinated repeat carriers (1/30; 3.3%). Our findings suggest that lack of MenB vaccine impact on carriage was not due to missing the intact fHbp gene; MenB-FHbp did not affect antigen genetic diversity and distribution during the study period.

Prevalence and Characterization of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Major Hospitals in Gabon.

In Gabon, few data exist on extended-spectrum beta-lactamases-producing Enterobacteriaceae (ESBL-PE). This study investigated ESBL-PE prevalence and the associated resistance genes in clinical samples (n = 5,956) and anal swabs (n = 78) analyzed in eight hospitals and a medical analysis laboratory in Gabon from January 2016 to March 2018. Matrix-Assisted Laser Desorption Ionization-Time Of Flight (MALDI-TOF) mass spectrometry analysis identified 790 Enterobacteriaceae isolates (n = 712 clinical samples and n = 78 fecal samples). ESBL-PE prevalence (Müller-Hinton agar disk diffusion method and double-disk synergy test) was 11.8% (84/712) in clinical samples (15.5% from inpatients and 7.1% from outpatients; p < 0.05) and 16.7% (13/78) in carriage isolates. Most ESBL-PE were isolated from urine samples (46/84). In clinical and carriage ESBL-PE isolates, Escherichia coli was predominant (42.8% and 61.5%; phylogroups A, B1, B2, and D), followed by Klebsiella pneumoniae (41.7% and 23.1%). Multiplex PCR and bi-directional sequencing showed that CTX-M group 1 (blaCTX-M-15) was predominant in clinical and carriage ESBL-PE (94% and 92.3%) among which 85.7% and 92.3% also harbored one to three β-lactamase-encoding genes (blaTEM-1, blaOXA-1, or blaSHV-1). Resistance genes were detected in all hospitals in Gabon. ESBL-PE prevalence in Gabon has not reached alarming levels yet, but corrective and monitoring measures are needed to curb their emergence.

Fatal exudative dermatitis in island populations of red squirrels (Sciurus vulgaris): spillover of a virulent Staphylococcus aureus clone (ST49) from reservoir hosts.

Fatal exudative dermatitis (FED) is a significant cause of death of red squirrels (Sciurus vulgaris) on the island of Jersey in the Channel Islands where it is associated with a virulent clone of Staphylococcus aureus, ST49. S. aureus ST49 has been found in other hosts such as small mammals, pigs and humans, but the dynamics of carriage and disease of this clone, or any other lineage in red squirrels, is currently unknown. We used whole-genome sequencing to characterize 228 isolates from healthy red squirrels on Jersey, the Isle of Arran (Scotland) and Brownsea Island (England), from red squirrels showing signs of FED on Jersey and the Isle of Wight (England) and a small number of isolates from other hosts. S. aureus was frequently carried by red squirrels on the Isle of Arran with strains typically associated with small ruminants predominating. For the Brownsea carriage, S. aureus was less frequent and involved strains associated with birds, small ruminants and humans, while for the Jersey carriage S. aureus was rare but ST49 predominated in diseased squirrels. By combining our data with publicly available sequences, we show that the S. aureus carriage in red squirrels largely reflects frequent but facile acquisitions of strains carried by other hosts sharing their habitat (‘spillover’), possibly including, in the case of ST188, humans. Genome-wide association analysis of the ruminant lineage ST133 revealed variants in a small number of mostly bacterial-cell-membrane-associated genes that were statistically associated with squirrel isolates from the Isle of Arran, raising the possibility of specific adaptation to red squirrels in this lineage. In contrast there is little evidence that ST49 is a common carriage isolate of red squirrels and infection from reservoir hosts such as bank voles or rats, is likely to be driving the emergence of FED in red squirrels.

Evolving epidemiology of carbapenemase-producing Enterobacterales: one hospital's infection prevention and control response over nine years

Preventing carbapenemase-producing Enterobacterales (CPE) transmission is a significant challenge for hospital infection prevention and control teams (IPCTs). Control measures include screening at-risk patients, contact tracing, and the isolation of carriers with contact precautions. The evolution of infection prevention and control measures was assessed in a tertiary acute care hospital with predominately multi-bedded patient accommodation, from 2011 to 2019 as cases of CPE increased. The implications for, and the response and actions of, the IPCT were also reviewed. CPE data collected prospectively from our laboratory, IPCT, and outbreak meeting records were reviewed to assess how the IPCT adapted to the changing epidemiology, from sporadic cases, to outbreaks and to localized endemic CPE. Of 178 cases, 152 (85%) were healthcare-associated and there was a marked increase in cases from 2017. The number of screening samples tested annually increased from 1190 in 2011 to 16,837 in 2019, and six outbreaks were documented, with larger outbreaks identified in later years. OXA-48 carbapenemase was detected in 88% of isolates and attendance at outbreak meetings alone accounted for 463.5 h of IPCT members, and related staff time. Despite considerable efforts and time invested by the IPCT, the number of CPE cases is increasing year-on-year, with more outbreaks being reported in later years, albeit partly in response to increased screening requirements. Infrastructural deficits, the changing epidemiology of CPE, and national policy are major factors in the increasing number of cases.

Frequency of beta toxin and phage Sa3 genes of Staphylococcus aureus in multiple sclerosis patients and healthy nasal carriers

The incidence of Staphylococcus aureus infection is alarming as a significant public health problem. This bacterium contributes to the development of multiple sclerosis (MS) disorder in young and adult individuals. This research aimed to determine the frequency of hlb, int of phi3, and mecA genes in S. aureus isolates collected from MS-patients and healthy nasal carriers. Four hundred nasal swabs were collected from MS patients (140) and healthy nasal carriers (260). The isolates were identified by phenotypic tests including catalase, coagulase, growth on mannitol salt agar, and DNase activity. Antibiotic susceptibility was conducted by disk diffusion agar method. Besides, PCR was done to the detection of hlb, int of phi3, nuc, and mecA genes. One hundred thirty isolates were identified as S. aureus from MS patients (65 isolates) and healthy nasal carriers (65 isolates). The highest resistance rate was to erythromycin in MS patients (47.7%) and healthy nasal carriers (55.4%) isolates. All isolates of healthy nasal carriers and 64 (98.5%) isolates of MS patients were susceptible to linezolid. The percentage of isolates containing the hlb, int of phi3, and mecA in MS patients was 15%, 40%, 17% and in healthy nasal carriers 9.2%, 18.5%, 21.5%, respectively. The frequency rate of hlb, int of phi3 genes in MS-patients isolates is remarkably high in comparison to healthy nasal carrier's isolates. These findings imply that S. aureus has the potency to the development and exacerbation of MS.

Water-Stable Zn(II) Coordination Polymers Regulated by Polysubstituted Benzenes and Their Photocatalytic Performance toward Methylene Blue Degradation Dominated by Ligand-Field Effects

Photodegradation of organic dyes over coordination polymer (CP) photocatalysts has become one of the effective strategies for the prevention and control of water pollution, in which the energy band structures manipulated by the ligand field of the catalytically active metal play extremely vital roles in enhancing the photocatalytic activity. To better rationalize the ligand-field function on the band structure, a series of six 2,4,6-tris(4-pyridyl)-1,3,5-triazine (tpt)-based Zn(II)-CPs have been hydrothermally prepared by transforming the types, numbers, and locations of the coordinative substitutes attached on benzene. All of these Zn(II)-CPs have been fully structurally and photophysically characterized and used as photocatalysts for methylene blue (MB) decontamination by UV light illumination. Single-crystal structural analyses reveal that isomeric 1,2,4 (H3L1)- and 1,3,5-benzenetricarboxylates (H3L2) have assembled the ternary system into the gridlike framework {[Zn(tpt)(HL1)]·H2O}n (1), ribbon-to-connector aligned sheet [Zn3(H2O)(tpt)2(L1)2]n (2), and hexagonal dimer based double layer [Zn3(H2O)2(tpt)(L2)2]n (3). 1,2,4,5-Tetrasubstituted phenyl and diphenyl coligands have assisted in honeycomb-shaped, pillared-layer, and cuboid-like frameworks via synergetic binding of carboxylate, sulfonate and hydroxyl moieties: {[Zn2(tpt)(H2L3)(L3)0.5]·0.5H2O}n (4, H4L3 = 2,5-dihydroxyltelephthalic acid), {[Zn2.5(tpt)(μ-OH)(L4)]·1.5H2O}n (5, H4L4 = 5-sulfobenzene-1,2,4-tricarboxylic acid), and {[Zn3(H2O)0.5(tpt)2(μ-OH)(L5)1.25]·5H2O}n (6, H4L5 = 3,3′-disulfonyl-4,4′-biphenyldicarboxylic acid). More significantly, the changeable donor surroundings around the Zn(II) ions have optimized the ligand-field geometries, giving rise to variable band gaps and band potentials. Resulting from the effective isolation and migration of the charge carriers and much stronger oxidizing ability of the valence band, the cuboid-shaped framework 6 has exhibited the best photodegradation activity toward the MB pollutant, up to 89% after 4 h UV illumination. These observations have systematically revealed the consequence of the ligand field on the CP photocatalysts in organic dye photodecomposition.

Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity

ABSTRACT Antibiotic resistant Klebsiella pneumoniae is a leading public health threat and gastrointestinal carriage is an established risk factor for subsequent infections during hospitalization. Our study contributes new knowledge of risk factors for gastrointestinal carriage and the genomic population structure of K. pneumoniae colonizing humans in a representative sample of a general population in a community setting. Altogether, 2,975 participants (54% women) >40 y in the population-based Tromsø Study: Tromsø7, Norway (2015–2016) were included. Fecal samples were screened for K. pneumoniae, which were characterized using whole-genome sequencing. Risk factors for carriage were analyzed using multivariable logistic regression on data from questionnaires and the Norwegian Prescription Database. Prevalence of K. pneumoniae gastrointestinal carriage was 16.3% (95% CI 15.0–17.7, no gender difference). Risk factors associated with carriage included age ≥60 y, travel to Greece or Asia past 12 months (adjusted odds ratio 1.49, 95% CI 1.11–2.00), Crohn’s disease/ulcerative colitis (2.26, 1.20–4.27), use of proton pump inhibitors (1.62, 1.18–2.22) and non-steroidal anti-inflammatory drugs past 6 months (1.38, 1.04–1.84), and antibiotic use the last month (1.73, 1.05–2.86). Prevalence was higher among those having used combinations of drug classes and decreased over time with respect to preceding antibiotic use. The K. pneumoniae population was diverse with 300 sequence types among 484 isolates distributed across four phylogroups. Only 5.2% of isolates harbored acquired resistance and 11.6% had virulence factors. Identification of risk factors for gastrointestinal carriage allows for identification of individuals that may have higher risk of extraintestinal infection during hospitalization. The findings that specific diseases and drugs used were associated with carriage show an impact of these possibly through modulating the human gut microbiota promoting colonization. The diverse population structure of carriage isolates reflects the ecologically adaptive capacity of the bacterium and challenges for vaccine prospects and the identification of reservoirs as a potential source for human colonization.

641. Carriage and Genetics of Haemophilus influenzae Serotype A (Hia) in Alaska, 2018

Background Haemophilus influenzae serotype a (Hia) is an important cause of infection among Alaska Native children. In 2018, 4 invasive Hia cases (iHia) occurred in an Alaska community. Our response aimed to prevent more iHia and evaluate Hia carriage in the community. Whole genome sequencing (WGS) was performed to compare Hia from iHia patients across Alaska in 2018, and from healthy outbreak community members.MethodsWe collected oropharyngeal (OP) samples from outbreak community members. Children aged < 10 years and people in close contact with cases (contacts) were offered rifampin prophylaxis. A second set of OP samples was collected 8 weeks later. Isolates from iHia from across the state were collected as part of the state surveillance. Hia was detected by PCR and culture, then characterized by antimicrobial susceptibility and WGS.ResultsAt baseline, contacts had a higher prevalence of Hia carriage than non-contacts (4/27(14.8%) vs 7/364(1.9%), p=0.0043). Eight weeks after rifampin prophylaxis, carriage prevalence did not significantly change among contacts (5/42(11.9%) to 6/25(24%), p=0.18) or non-contacts (7/368(1.9%) to 2/114(1.8%), p=0.47). Phylogenetic analysis of 19 iHia isolates and 15 isolates from healthy outbreak community members, revealed two major clades that differed by an average of 300 core single nucleotide polymorphisms (SNPs). Invasive and carriage isolates from the outbreak community were clustered in one clade, along with 3 non-outbreak iHia isolates. Isolates from this community differed from each other by an average of 1.2 core SNPs. Comparative genomics did not reveal any genetic mutations that distinguished carriage from invasive isolates. Three (20%) community isolates were rifampin-resistant and had a previously unreported mutation in the rpoB gene.ConclusionWe found Hia carriage prevalence was highest among persons in contact with iHia cases. Long-term community carriage was not affected by rifampin prophylaxis, possibly due to staggered prophylaxis. In the outbreak community, Hia isolates from carriers were nearly genetically identical to iHia isolates. Overall, iHia isolates from Alaska in 2018 were genetically similar. The mutation conferring rifampin resistance is concerning, as rifampin is used to prophylax contacts of iHia cases.Disclosures All Authors: No reported disclosures

Carrier capture kinetics, deep levels, and isolation properties of β -Ga2O3 Schottky-barrier diodes damaged by nitrogen implantation

In this paper, we analyze the stability of the performance of β-Ga2O3 Schottky barrier diodes (SBDs) damaged by nitrogen implantation, based on electrical characterization and deep-level spectroscopy. We demonstrate that N-implanted SBDs show a high level of isolation, which can be further improved by electron trapping promoted by current flow and temperature. Charge trapping leads to a shift in the current–voltage curve to more positive bias, a positive effect lasting for hundreds of seconds at room temperature and fully recovered only after 200 s even at 350 K. This charge trapping process takes place in the depletion region of the Schottky diode, in a defect located 0.72 eV below the conduction band, possibly related to gallium vacancies. A model for explaining the trapping kinetics and processes is proposed, based on differential rate equations, highlighting two capture processes: charge injection from the n-type Ga2O3 into the space charge region and thermionic emission from the anode metal to the deep level.

Post-Vaccination Streptococcus pneumoniae Carriage and Virulence Gene Distribution among Children Less Than Five Years of Age, Cape Coast, Ghana.

In 2012, Ghana introduced PCV13 into its childhood immunization program. To monitor the pneumococcus after PCV13 vaccination, we analyzed serotypes, antibiotic resistance, and virulence genes of pneumococcal carriage isolates among children under five years of age. We obtained nasopharyngeal swabs from 513 children from kindergartens and immunization centers in Cape Coast, Ghana. Pneumococcal serotypes were determined by multiplex-PCR and Quellung reaction. Antibiotic resistance and virulence genes prevalence were determined by disc diffusion and PCR respectively. Overall, carriage prevalence was 29.4% and PCV13 coverage was 38.4%. Over 60% of the isolates were non-PCV13 serotypes and serotype 23B was the most prevalent. One isolate showed full resistance to penicillin, while 35% showed intermediate resistance. Resistance to erythromycin and clindamycin remained low, while susceptibility to ceftriaxone, levofloxacin and vancomycin remained high. Penicillin resistance was associated with PCV13 serotypes. Forty-three (28.5%) strains were multidrug-resistant. Virulence genes pavB, pcpA, psrP, pilus-1, and pilus-2 were detected in 100%, 87%, 62.9%, 11.9%, and 6.6% of the strains, respectively. The pilus islets were associated with PCV13 and multidrug-resistant serotypes. PCV13 vaccination had impacted on pneumococcal carriage with a significant increase in non-PCV13 serotypes and lower penicillin resistance. Including PcpA and PsrP in pneumococcal protein-based vaccines could be beneficial to Ghanaian children.

Genomic analysis of the meningococcal ST-4821 complex-Western clade, potential sexual transmission and predicted antibiotic susceptibility and vaccine coverage.

IntroductionThe ST-4821 complex (cc4821) is a leading cause of serogroup C and serogroup B invasive meningococcal disease in China where diverse strains in two phylogenetic groups (groups 1 and 2) have acquired fluoroquinolone resistance. cc4821 was recently prevalent among carriage isolates in men who have sex with men in New York City (USA). Genome-level population studies have thus far been limited to Chinese isolates. The aim of the present study was to build upon these with an extended panel of international cc4821 isolates.MethodsGenomes of isolates from Asia (1972 to 2017), Europe (2011 to 2018), North America (2007), and South America (2014) were sequenced or obtained from the PubMLST Neisseria database. Core genome comparisons were performed in PubMLST.ResultsFour lineages were identified. Western isolates formed a distinct, mainly serogroup B sublineage with alleles associated with fluoroquinolone susceptibility (MIC <0.03 mg/L) and reduced penicillin susceptibility (MIC 0.094 to 1 mg/L). A third of these were from anogenital sites in men who have sex with men and had unique denitrification gene alleles. Generally 4CMenB vaccine strain coverage was reliant on strain-specific NHBA peptides.DiscussionThe previously identified cc4821 group 2 was resolved into three separate lineages. Clustering of western isolates was surprising given the overall diversity of cc4821. Possible association of this cluster with the anogenital niche is worthy of monitoring given concerns surrounding antibiotic resistance and potential subcapsular vaccine escape.

Molecular insights into meningococcal carriage isolates from Burkina Faso 7 years after introduction of a serogroup A meningococcal conjugate vaccine.

In 2010, Burkina Faso completed the first nationwide mass-vaccination campaign of a meningococcal A conjugate vaccine, drastically reducing the incidence of disease caused by serogroup A meningococci. Since then, other strains, such as those belonging to serogroups W, X and C, have continued to cause outbreaks within the region. A carriage study was conducted in 2016 and 2017 in the country to characterize the meningococcal strains circulating among healthy individuals following the mass-vaccination campaign. Four cross-sectional carriage evaluation rounds were conducted in two districts of Burkina Faso, Kaya and Ouahigouya. Oropharyngeal swabs were collected for the detection of Neisseria meningitidis by culture. Confirmed N. meningitidis isolates underwent whole-genome sequencing for molecular characterization. Among 13 758 participants, 1035 (7.5 %) N . meningitidis isolates were recovered. Most isolates (934/1035; 90.2 %) were non-groupable and primarily belonged to clonal complex (CC) 192 (822/934; 88 %). Groupable isolates (101/1035; 9.8 %) primarily belonged to CCs associated with recent outbreaks in the region, such as CC11 (serogroup W) and CC10217 (serogroup C); carried serogroup A isolates were not detected. Phylogenetic analysis revealed several CC11 strains circulating within the country, several of which were closely related to invasive isolates. Three sequence types (STs) were identified among eleven CC10217 carriage isolates, two of which have caused recent outbreaks in the region (ST-10217 and ST-12446). Our results show the importance of carriage studies to track the outbreak-associated strains circulating within the population in order to inform future vaccination strategies and molecular surveillance programmes.

Novel hypercapsulation RNA thermosensor variants in Neisseria meningitidis and their association with invasive meningococcal disease: a genetic and phenotypic investigation and molecular epidemiological study

Neisseria meningitidis is the causative agent of invasive meningococcal disease and the polysaccharide capsule is one of its major virulence factors. Biosynthesis of the meningococcal capsule is controlled by an RNA thermosensor (RNAT) in the 5'-untranslated region (5'-UTR) of the cssA gene. The function of the RNAT depends on an 8-bp tandem repeat configuration. We aimed to identify and characterise novel RNATs in meningococcal isolates responsible for regulating capsule production. We investigated the allele igr_up_NEIS0055, containing the 5'-UTR of the cssA gene, in clinical meningococcal isolates for which whole-genome sequences are available on the Neisseria PubMLST database and that were isolated in Europe between Jan 1, 2010, and Dec 31, 2018. Eight isolates with different RNAT tandem repeat configurations were selected for genetic and phenotypic studies. The thermosensing capability of the RNAT and capsule production was tested with immunoblots. Bacterial survival by capsule protection was assessed with a human serum stress assay and capsule interference with bacterial cell adhesion was evaluated with a bacterial adhesion assay. The dataset of RNAT configurations was analysed for an association with invasive meningococcal disease, and was stratified to visualise the distribution of RNAT configurations within the meningococcal population. Our search of PubMLST identified 112 alleles for the igr_up_NEIS0055 locus and 7013 N meningitidis isolates. Five novel RNAT tandem repeat configurations were identified and eight RNAT tandem repeat configurations, ranging from 1 × 8-bp up to 8 × 8-bp, were characterised. The disrupted RNATs (1 × 8-bp and 3 × 8-bp to 8 × 8-bp) confer upregulated CssA expression and increased capsule production compared with the native 2 × 8-bp configuration, resulting in a hypercapsulation phenotype. Increased capsule production was associated with higher survival rates in up to 25% human serum. The prevalence of a disrupted RNAT resulting in hypercapsulation was almost twice as high in invasive meningococcal disease isolates compared with carrier isolates. Disrupted RNATs were especially attributed to isolates of capsule group B and C, and clonal complexes 23, 32, 213, and 269. Hypercapsulation in one isolate led to lower adhesion onto pharyngeal cells compared with a similar isolate with low capsule production. Six non-canonical RNAT tandem repeat variants (3 × 8-bp to 8 × 8-bp) were identified in the igr_up_NEIS0055 locus of N meningitidis that induce a hypercapsulation phenotype, thus providing the meningococci with better protection against host complement-mediated killing than does the native RNAT (2 × 8-bp). Further research is warranted to strengthen the association between hypercapsulation and the progression of invasive meningococcal disease, and to investigate the role of regulatory RNAs in meningococcal virulence and as potential markers for disease progression. Swedish Foundation for Strategic Research, Knut and Alice Wallenberg Foundation, and Swedish Research Council.

Serotyping and pathotyping of Glaesserella parasuis isolated 2012\u20132019 in Germany comparing different PCR-based methods

Glaesserella parasuis is an important pathogen in swine production. It acts as a primary pathogen in systemic Glässer´s disease and as a secondary pathogen in Porcine Respiratory Disease Complex. In this study, a collection of 308 isolates from carrier animals and individuals with respiratory or Glässer´s disease isolated 2012–2019 in Germany was analysed. Isolates were characterized for serovar implementing two different PCR methods. Additionally, two different PCR methods for pathotyping isolates were applied to the collection and results compared. Serovar 6 (p < 0.0001) and 9 (p = 0.0007) were correlated with carrier isolates and serovar 4 was associated with isolates from animals with respiratory disease (p = 0.015). In systemic isolates, serovar 13 was most frequently detected (18.9%). Various other serovars were isolated from all sites and the ratio of serovar 5 to serovar 12 was approximately 1:2. These two serovars together represented 14.3% of the isolates; only serovar 4 was isolated more frequently (24.7%). The pathotyping method based on the leader sequence (LS = ESPR of vta) was easy to perform and corresponded well to the clinical background information. Of the carrier isolates 72% were identified as non-virulent while 91% of the systemic isolates were classified as virulent (p < 0.0001). Results of the pathotyping PCR based on 10 different marker genes overall were in good agreement with clinical metadata as well as with results of the LS-PCR. However, the pathotyping PCR was more complicated to perform and analyze. In conclusion, a combination of the serotyping multiplex-PCR and the LS-PCR could improve identification of clinically relevant G. parasuis isolates, especially from respiratory samples.

Detection of Respiratory Infections Using RGB-Infrared Sensors on Portable Device.

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) has become a serious global pandemic in the past few months and caused huge loss to human society worldwide. For such a large-scale pandemic, early detection and isolation of potential virus carriers is essential to curb the spread of the pandemic. Recent studies have shown that one important feature of COVID-19 is the abnormal respiratory status caused by viral infections. During the pandemic, many people tend to wear masks to reduce the risk of getting sick. Therefore, in this paper, we propose a portable non-contact method to screen the health conditions of people wearing masks through analysis of the respiratory characteristics from RGB-infrared sensors. We first accomplish a respiratory data capture technique for people wearing masks by using face recognition. Then, a bidirectional GRU neural network with an attention mechanism is applied to the respiratory data to obtain the health screening result. The results of validation experiments show that our model can identify the health status of respiratory with 83.69% accuracy, 90.23% sensitivity and 76.31% specificity on the real-world dataset. This work demonstrates that the proposed RGB-infrared sensors on portable device can be used as a pre-scan method for respiratory infections, which provides a theoretical basis to encourage controlled clinical trials and thus helps fight the current COVID-19 pandemic. The demo videos of the proposed system are available at: https://doi.org/10.6084/m9.figshare.12028032.