Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants.

Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.

Awareness regarding antimicrobial resistance and confidence to prescribe antibiotics in dentistry: a cross-continental student survey.

BACKGROUND: The antimicrobial resistance (AMR) crisis is a major global threat and one of its biggest drivers is the overuse of antibiotics in humans. Dentists are responsible for 5-10% antibiotic prescriptions worldwide and recent data suggest that knowledge and prescribing practices need improvement. METHODS: A cross-sectional web-survey was sent to dental students from six universities in Norway, Canada, and Brazil. Topics addressed covered awareness, confidence to prescribe antibiotics, and education needs. Data were presented descriptively and statistical testing was employed to compare group means when applicable. RESULTS: In total, 562 responses were collected across the three countries with a response rate of 28.6%. 'Antibiotic resistance' was among the highest priorities (scale 1-10) with an average of 8.86 (SEM ± 0.05), together with 'Gender inequality' (8.68 ± 0.07) and 'Climate change' (8.68 ± 0.07). Only 28.8% thought that Dentistry was engaged in national/international campaigns promoting awareness on the topic and 8.9% stated to have heard about the 'One Health' concept. Final year dental students showed an average confidence to prescribe antibiotics of 7.59 (± 0.14). Most students demonstrated interest in receiving additional education on all topics listed, with the three most pressing being 'antibiotic prescription for treatment of infections' (82.9%), 'drug interactions' (80.9%), and 'spread of antibiotic resistance' (79.6%). A trend was observed between higher awareness regarding the topic and higher confidence to prescribe. CONCLUSIONS: There is a need to revisit dental education on antibiotic resistance with a global perspective and to create more stewardship initiatives that promote awareness on the topic.

Antibiotic Stewardship in Premature Infants: A Systematic Review.

INTRODUCTION: Antibiotic treatment in premature infants is often empirically prescribed, and practice varies widely among otherwise comparable neonatal intensive care units. Unnecessary and prolonged antibiotic treatment is documented in numerous studies. Recent research shows serious side effects and suggests long-term adverse health effects in prematurely born infants exposed to antibiotics in early life. One preventive measure to reduce unnecessary antibiotic exposure is implementation of antibiotic stewardship programs. Our objective was to review the literature on implemented antibiotic stewardship programs including premature infants with gestational age ≤34 weeks. METHODS: Six academic databases (PubMed [Medline], McMaster PLUS, Cochrane Database of Systematic Reviews, UpToDate, Cochrane Central Register of Controlled Trials, and National Institute for Health and Care Excellence) were systematically searched. PRISMA guidelines were applied. RESULTS: The search retrieved 1,212 titles of which 12 fitted inclusion criteria (11 observational studies and 1 randomized clinical trial). Included articles were critically appraised. We grouped the articles according to common area of implemented stewardship actions: (1) focus on reducing initiation of antibiotic therapy, (2) focus on shortening duration of antibiotic therapy, (3) various organizational stewardship implementations. The heterogeneity of cohort composition, of implemented actions and of outcome measures made meta-analysis inappropriate. We provide an overview of the reduction in antibiotic use achieved. CONCLUSION: Antibiotic stewardship programs can be effective for premature newborns especially when multifactorial and tailored to this population, focusing on reducing initiation or on shortening the duration of antibiotic therapy. Programs without specific measures were less effective.

Impact of narrow-spectrum penicillin V on the oral and faecal resistome in a young child treated for otitis media.

OBJECTIVES: Antibiotic overuse has led to the global emergence of antimicrobial-resistant bacteria, and children are among the most frequent users of antibiotics. Most studies with broad-spectrum antibiotics show a severe impact on resistome development in patients. Although narrow-spectrum antibiotics are believed to have fewer side effects, their impact on the microbiome and resistome is mostly unknown. The aim of this study was to investigate the impact of the narrow-spectrum antibiotic phenoxymethylpenicillin (penicillin V) on the microbiome and resistome of a child treated for acute otitis media. METHODS: Oral and faecal samples were collected from a 1-year-old child before (Day 0) and after (Days 5 and 30) receiving penicillin V for otitis media. Metagenomic sequencing data were analysed to determine taxonomic profiling using Kraken and Bracken software, and resistance profiling using KMA in combination with the ResFinder database. RESULTS: In the oral samples, antimicrobial resistance genes (ARGs) belonging to four classes were identified at baseline. At Day 5, the abundance of some ARGs was increased, whereas some remained unchanged and others could no longer be detected. At Day 30, most ARGs had returned to baseline levels or lower. In the faecal samples, seven ARGs were observed at baseline and five at Day 5. At Day 30, the number of ARGs had increased to 21. CONCLUSIONS: Following penicillin V, we observed a remarkable enrichment of the aecal resistome, indicating that even narrow-spectrum antibiotics may have important consequences in selecting for a more resistant microbiome.

Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population.

In many countries the incidence of tuberculosis (TB) is low and is largely shaped by immigrant populations from high-burden countries. This is the case in Norway, where more than 80 % of TB cases are found among immigrants from high-incidence countries. A variable latent period, low rates of evolution and structured social networks make separating import from within-border transmission a major conundrum to TB control efforts in many low-incidence countries. Clinical Mycobacterium tuberculosis isolates belonging to an unusually large genotype cluster associated with people born in the Horn of Africa have been identified in Norway over the last two decades. We modelled transmission based on whole-genome sequence data to estimate infection times for individual patients. By contrasting these estimates with time of arrival in Norway, we estimate on a case-by-case basis whether patients were likely to have been infected before or after arrival. Independent import was responsible for the majority of cases, but we estimate that about one-quarter of the patients had contracted TB in Norway. This study illuminates the transmission dynamics within an immigrant community. Our approach is broadly applicable to many settings where TB control programmes can benefit from understanding when and where patients acquired TB.

Carriage of ESBL/AmpC-producing or ciprofloxacin non-susceptible Escherichia coli and Klebsiella spp. in healthy people in Norway.

BACKGROUND: Asymptomatic carriage has been recognised as an important risk factor for infection caused by antibiotic resistant bacteria. A 14% global prevalence of Extended-Spectrum Beta-lactamase (ESBL) carriage was recently reported, but large intra-and interregional variations were observed. We investigated the faecal carriage rates of ESBL-, AmpC-producing and ciprofloxacin non-susceptible Escherichia coli and Klebsiella spp. in healthy Norwegians. METHODS: Rectal samples were obtained from 284 volunteers, together with demographic data and information on recent travel history. The rectal samples were screened by selective plating and E. coli and Klebsiella spp. identified using MALDI-TOF. Phenotypic and molecular characterization of resistant isolates was also performed. RESULTS: ESBL- or AmpC-producing E. coli and Klebsiella spp. were isolated from 4.9% and 3.2% of the study population, respectively. Carriage of ciprofloxacin non-susceptible isolates was detected in 9.9% of the volunteers. Molecular typing of ESBL/plasmid-mediated AmpC (pAmpC)-producing isolates suggested an allodemic situation rather than the dissemination of a specific clone in the Norwegian community. In concurrence with previous findings, travel to South-East Asia was associated with increased risk of carrying resistant E. coli or Klebsiella spp., highlighting the contribution of factors such as increased global mobility in erasing the boundaries between healthcare and community settings when it comes to spread of resistant bacteria. CONCLUSIONS: Overall, our study recognised Norway as a low-incidence country for faecal carriage of resistant bacteria among healthy individuals. Furthermore, our work denoted the importance of healthy humans as a reservoir for transmission of antibiotic resistant E. coli and Klebsiella spp.

Description of the largest cluster of tuberculosis notified in Norway 1997-2011: is the Norwegian tuberculosis control programme serving its purpose for high risk groups?

BACKGROUND: Approximately 90% of new tuberculosis (TB) cases notified in Norway are asylum seekers and other immigrants from high-incidence countries. Asylum seekers are screened upon arrival at the National Immigration Centre. Other immigrants receive a letter from the Municipal Health Services requesting that they present for screening in their municipality of residence. In order to identify potential areas where the TB control programme could be better adapted for these groups, we studied the largest cluster of TB cases ("cluster X") notified in Norway until 2011. METHODS: Cases were defined as TB notifications reported to MSIS between January 1997 and December 2011 with identical IS6110 RFLP assigned to cluster X. We described the cases in cluster X by using data from the Norwegian Surveillance System for Communicable Diseases (MSIS). Missing or incomplete information in MSIS was obtained from the National Reception Centre, Oslo University Hospital and Municipal Health services. RESULTS: Of a total of 44 individuals meeting the case definition, 36 originated from Somalia and eight from other high-incidence countries. Twenty nine were asylum seekers and 15 were other immigrants. Upon arrival, 18/44 had been diagnosed with latent TB infection (LTBI), 9/44 tested negative for LTBI and 4/44 had been diagnosed with active TB. Results of TB-screening upon arrival were not available for the remaining 13/44 (one asylum seeker and 12 other immigrants). Five of the 12 other immigrants had still not been screened for TB after staying one year or longer in Norway. CONCLUSIONS: Most cases in cluster X with available results of TB-screening were already infected at arrival, indicating that their disease could be due to endogenous reactivation, rather than recent transmission after arrival to Norway. TB-status upon arrival was unknown for many of the other immigrants due to lack of initial screening. The reasons why conduction of the initial screening among other immigrants is failing should be explored and methods to simplify the TB screening at arrival should be implemented.

Towards tuberculosis elimination: an action framework for low-incidence countries.

This paper describes an action framework for countries with low tuberculosis (TB) incidence (<100 TB cases per million population) that are striving for TB elimination. The framework sets out priority interventions required for these countries to progress first towards "pre-elimination" (<10 cases per million) and eventually the elimination of TB as a public health problem (less than one case per million). TB epidemiology in most low-incidence countries is characterised by a low rate of transmission in the general population, occasional outbreaks, a majority of TB cases generated from progression of latent TB infection (LTBI) rather than local transmission, concentration to certain vulnerable and hard-to-reach risk groups, and challenges posed by cross-border migration. Common health system challenges are that political commitment, funding, clinical expertise and general awareness of TB diminishes as TB incidence falls. The framework presents a tailored response to these challenges, grouped into eight priority action areas: 1) ensure political commitment, funding and stewardship for planning and essential services; 2) address the most vulnerable and hard-to-reach groups; 3) address special needs of migrants and cross-border issues; 4) undertake screening for active TB and LTBI in TB contacts and selected high-risk groups, and provide appropriate treatment; 5) optimise the prevention and care of drug-resistant TB; 6) ensure continued surveillance, programme monitoring and evaluation and case-based data management; 7) invest in research and new tools; and 8) support global TB prevention, care and control. The overall approach needs to be multisectorial, focusing on equitable access to high-quality diagnosis and care, and on addressing the social determinants of TB. Because of increasing globalisation and population mobility, the response needs to have both national and global dimensions.

Evolution of extensively drug-resistant Mycobacterium tuberculosis from a susceptible ancestor in a single patient.

BACKGROUND: Mycobacterium tuberculosis is characterized by a low mutation rate and a lack of genetic recombination. Yet, the rise of extensively resistant strains paints a picture of a microbe with an impressive adaptive potential. Here we describe the first documented case of extensively drug-resistant tuberculosis evolved from a susceptible ancestor within a single patient. RESULTS: Genome sequences of nine serial M. tuberculosis isolates from the same patient uncovered a dramatic turnover of competing lineages driven by the emergence, and subsequent fixation or loss of single nucleotide polymorphisms. For most drugs, resistance arose through independent emergence of mutations in more than one clone, of which only one ultimately prevailed as the clone carrying it expanded, displacing the other clones in the process. The vast majority of mutations identified over 3.5 years were either involved in drug resistance or hitchhiking in the genetic background of these. Additionally, RNA-sequencing of isolates grown in the absence of drug challenge revealed that the efflux-associated iniBAC operon was up-regulated over time, whereas down-regulated genes include those involved in mycolic acid synthesis. CONCLUSIONS: We observed both rapid acquisitions of resistance to antimicrobial compounds mediated by individual mutations as well as a gradual increase in fitness in the presence of antibiotics, likely driven by stable gene expression reprogramming. The rapid turnover of resistance mutations and hitchhiking neutral mutations has major implications for inferring tuberculosis transmission events in situations where drug resistance evolves within transmission chains.

Evaluation of the ability of four ESBL-screening media to detect ESBL-producing Salmonella and Shigella.

BACKGROUND: The aim of this study was to compare the ability of four commercially available media for screening extended-spectrum beta-lactamase (ESBL) to detect and identify ESBL-producing Salmonella and Shigella in fecal samples. A total of 71 Salmonella- and 21 Shigella-isolates producing ESBL(A) and/or AmpC, were received at Norwegian Institute of Public Health between 2005 and 2012. The 92 isolates were mixed with fecal specimens and tested on four ESBL screening media; ChromID ESBL (BioMèrieux), Brilliance ESBL (Oxoid), BLSE agar (AES Chemunex) and CHROMagar ESBL (CHROMagar). The BLSE agar is a biplate consisting of two different agars. Brilliance and CHROMagar are supposed to suppress growth of AmpC-producing bacteria while ChromID and BLSE agar are intended to detect both ESBL(A) and AmpC. RESULTS: The total sensitivity (ESBL(A)+AmpC) with 95% confidence intervals after 24 hours of incubation were as follows: ChromID: 95% (90.4-99.6), Brilliance: 93% (87.6-98.4), BLSE agar (Drigalski): 99% (96.9-100), BLSE agar (MacConkey): 99% (96.9-100) and CHROMagar: 85% (77.5-92.5). The BLSE agar identified Salmonella and Shigella isolates as lactose-negative. The other agars based on chromogenic technology displayed Salmonella and Shigella flexneri isolates with colorless colonies (as expected). Shigella sonnei produced pink colonies, similar to the morphology described for E. coli. CONCLUSION: All four agar media were reliable in screening fecal samples for ESBL(A)-producing Salmonella and Shigella. However, only ChromID and BLSE agar gave reliable detection of AmpC-producing isolates. Identification of different bacterial species based on colony colour alone was not accurate for any of the four agars.

Age-related differences in symptoms, diagnosis and prognosis of bacteremia.

BACKGROUND: Elderly patients are at particular risk for bacteremia and sepsis. Atypical presentation may complicate the diagnosis. We studied patients with bacteremia, in order to assess possible age-related effects on the clinical presentation and course of severe infections. METHODS: We reviewed the records of 680 patients hospitalized between 1994 and 2004. All patients were diagnosed with bacteremia, 450 caused by Escherichia coli and 230 by Streptococcus pneumoniae. Descriptive analyses were performed for three age groups (< 65 years, 65-84 years, ≥ 85 years). In multivariate analyses age was dichotomized (< 65, ≥ 65 years). Symptoms were categorized into atypical or typical. Prognostic sensitivity of CRP and SIRS in identifying early organ failure was studied at different cut-off values. Outcome variables were organ failure within one day after admission and in-hospital mortality. RESULTS: The higher age-groups more often presented atypical symptoms (p <0.001), decline in general health (p=0.029), and higher in-hospital mortality (p<0.001). The prognostic sensitivity of CRP did not differ between age groups, but in those ≥ 85 years the prognostic sensitivity of two SIRS criteria was lower than that of three criteria. Classical symptoms were protective for early organ failure (OR 0.67, 95% CI 0.45-0.99), and risk factors included; age ≥ 65 years (OR 1.65, 95% CI 1.09-2.49), comorbid illnesses (OR 1.19, 95% CI 1.02-1.40 per diagnosis), decline in general health (OR 2.28, 95% CI 1.58-3.27), tachycardia (OR 1.50, 95% CI 1.02-2.20), tachypnea (OR 3.86, 95% CI 2.64-5.66), and leukopenia (OR 4.16, 95% CI 1.59-10.91). Fever was protective for in-hospital mortality (OR 0.46, 95% CI 0.24-0.89), and risk factors included; age ≥ 65 years (OR 15.02, 95% CI 3.68-61.29), ≥ 1 comorbid illness (OR 2.61, 95% CI 1.11-6.14), bacteremia caused by S. pneumoniae (OR 2.79, 95% CI 1.43-5.46), leukopenia (OR 4.62, 95% CI 1.88-11.37), and number of early failing organs (OR 3.06, 95% CI 2.20-4.27 per failing organ). CONCLUSIONS: Elderly patients with bacteremia more often present with atypical symptoms and reduced general health. The SIRS-criteria have poorer sensitivity for identifying organ failure in these patients. Advanced age, comorbidity, decline in general health, pneumococcal infection, and absence of classical symptoms are markers of a poor prognosis.

Genetic diversity of Mycobacterium tuberculosis Complex in Jos, Nigeria.

BACKGROUND: Nigeria has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis Complex (MTC) in the country are necessary in order to improve our understanding of the epidemic. METHODS: Isolates of MTC were isolated from cases of pulmonary tuberculosis in Jos, North Central region of Nigeria during 2006-2008. Drug susceptibility test (DST) was performed on 77 of 111 isolates by proportion method on Lowenstein Jensen (LJ) slope while genotyping of mycobacterial DNA was performed by spoligotyping. The SpolDB4 database and the model-based program 'spotclust' were used to assign isolates to families, subfamilies and variants. RESULTS: A total of 111 pulmonary isolates from consecutive tuberculosis patients in the city of Jos, Plateau State, Nigeria were spoligotyped. A total of 84 (76%) of the isolates belonged to the Latin American Mediterranean (LAM) family. Of these, 78 isolates were assigned to the LAM10 lineage. Among these, 66 exhibited identical spoligopatterns. Drug susceptibility profiles obtained were not consistently associated with any spoligopattern. CONCLUSIONS: The dominance of few M. tuberculosis lineages suggests either a high rate of transmission, frequent import of closely related strains, or a highly conserved genotype. It remains to be confirmed whether the predominance of identical LAM10 represent an outbreak.Spoligotyping was useful to gain an overall understanding of the local TB epidemic. This study demonstrated that the incidence of TB in Jos, Nigeria may be caused by a few successful M. tuberculosis families, dominated by the LAM10 family.

Molecular characterization of Mycobacterium bovis isolates from Ethiopian cattle.

BACKGROUND: Bovine Tuberculosis (BTB) is a widespread and endemic disease of cattle in Ethiopia. Information relating to genotypic characteristics of Mycobacterium bovis strains affecting the cattle population in Ethiopia is limited. We carried out molecular characterization of M. bovis strains isolated from BTB infected cattle using the spoligotyping technique. The relationship between distribution of spoligotypes and recorded variables was also investigated. A new approach that can numerically reflect the degree of genetic polymorphism in a M. bovis population was also developed. The study was conducted from July 2006 to January 2007 in cattle slaughtered at five representative abattoirs in Ethiopia. RESULTS: Forty-five M. bovis isolates were obtained from 406 pathologic tissue specimens collected from 337 carcasses with lesions compatible with BTB. Twelve spoligotypes were identified from 34 distinct strains; with SB1176 as a dominant spoligotype (41.2% of the isolates) followed by SB0133 (14.7%). Comparison of spoligotypes with an M. bovis global database http://www.mbovis.org revealed six new spoligotypes which were subsequently registered in the database with international identification codes of SB1517, SB1518, SB1519, SB1520, SB1521 and SB1522. The majority of strains were obtained from cattle slaughtered at Addis Ababa abattoir. On the basis of the Spoligotype Evolutionary Index, SEI (a numeric expression approach to make standardized comparison of spoligotype evolution), M. bovis isolates from Ethiopia were relatively more heterogeneous (SEI = 3.2) compared to isolates from other countries. This might be attributed to extensive livestock movement linked to trading or seasonal migration, high degree of livestock mingling, and also diversities of the country's agricultural and livestock ecosystems, in addition to lack of disease control measures that led to high infection prevalence. Multiple spoligotype infection was recorded in nine (50%) of infected carcasses and this may indicate the prevailing high degree of super infection. CONCLUSIONS: This study provided molecular evidence for the widespread distribution of M. bovis in the cattle population in Ethiopia. It also demonstrated a relatively high degree of genetic polymorphism of the isolates. Further molecular investigation of M. bovis strains in humans and other domestic animals is recommended in order to elucidate the zoonotic importance as well as reservoirs and pattern of transmission among various hosts.

Dominant Mycobacterium tuberculosis lineages in elderly patients born in Norway.

BACKGROUND: During the previous century Norway had a high incidence of tuberculosis, but no molecular epidemiological studies could be performed and these previously epidemic strains have been disappearing during the last decades. Currently, tuberculosis among native Norwegians is in the elimination phase, and it is still not known what type of M. tuberculosis was so efficiently controlled during the second half of the 20th century. However, many elderly Norwegian-born people still develop TB that cannot be clustered to imported or recently transmitted strains of M. tuberculosis. Thus, the majority of these cases are results of reactivation of disease that was transmitted many decades ago. METHODOLOGY/PRINCIPAL FINDINGS: A total of 213 strains of M. tuberculosis isolated during 1998-2005, from patients born in Norway before 1950 were genotyped in the current study. The findings demonstrated a highly homogenous M. tuberculosis population among the patients. A total of 40% belonged to the T-family, were 35% were assigned to T1 sub- family (T2 = 0, 93%, T3 = 1, 4% and T4 = 2, 3%). As many as 35% of the isolates belonged to the Haarlem family, were 15% were assigned to Haarlem1 and 19% to Haarlem3. The remaining 25% belonged to 15 different other families. The RFLP-patterns indicated that the isolates were not a result of recent transmission, but rather represented well established strains that apparently dominated in Norway many decades ago. CONCLUSIONS/SIGNIFICANCE: The T 1, Haarlem 1, and Haarlem 3 families of M. tuberculosis were abundant among patients born in Norway before 1950. The M. tuberculosis cases represented reactivated disease that had been acquired before 1994 and were likely to have been latent for several decades. Thus, the current study indicated that the T 1, Haarlem 1, and Haarlem 3 families may have been common in Norway, when tuberculosis represented a serious public health threat during the first half of the 20th century.