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This issue of the ECDC Communicable Disease Threats Report (CDTR) covers the period 19 - 25 November 2023 and includes updates on human infection with influenza A(H1N2)v, influenza A(H5N1), an overview of respiratory virus epidemiology in the EU/EEA, respiratory infections due to Mycoplasma pneumoniae in the EU/EEA, HIV/AIDS surveillance 2023 (2022 data), West Nile virus, SARS-CoV-2 variant classification, and poliomyelitis.

This issue of the ECDC Communicable Disease Threats Report (CDTR) covers the period 19 - 25 November 2023 and includes updates on human infection with influenza A(H1N2)v, influenza A(H5N1), an overview of respiratory virus epidemiology in the EU/EEA, respiratory infections due to Mycoplasma pneumoniae in the EU/EEA, HIV/AIDS surveillance 2023 (2022 data), West Nile virus, SARS-CoV-2 variant classification, and poliomyelitis.

Der har siden sommeren været en stigning i antallet af luftvejsinfektioner med Mycoplasma pneumoniae, og forekomsten har nu nået et epidemisk niveau med væsentlig flere tilfælde end normalt.

BackgroundPreliminary unpublished results of the survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE survey) showed the expansion of carbapenemase-producing Klebsiella pneumoniae (CPKP) sequence type (ST) 39 in 12 of 15 participating Greek hospitals in 2019. AimWe conducted a rapid survey to determine the extent of spread of CPKP high-risk clones in Greek hospitals in 2022 and compare the distribution of circulating CPKP clones in these hospitals since 2013. MethodsWe analysed whole genome sequences and epidemiological data of 310 K. pneumoniae isolates that were carbapenem-resistant or ‘susceptible, increased exposure’ from Greek hospitals that participated in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE, 2013–2014), in the CCRE survey (2019) and in a national follow-up survey (2022) including, for the latter, an estimation of transmission events. ResultsFive K. pneumoniae STs including ST258/512 (n = 101 isolates), ST11 (n = 93), ST39 (n = 56), ST147 (n = 21) and ST323 (n = 13) accounted for more than 90% of CPKP isolates in the dataset. While ST11, ST147 and ST258/512 have been detected in participating hospitals since 2013 and 2014, KPC-2-producing ST39 and ST323 emerged in 2019 and 2022, respectively. Based on the defined genetic relatedness cut-off, 44 within-hospital transmission events were identified in the 2022 survey dataset, with 12 of 15 participating hospitals having at least one within-hospital transmission event. ConclusionThe recent emergence and rapid spread of new high-risk K. pneumoniae clones in the Greek healthcare system related to within-hospital transmission is of concern and highlights the need for molecular surveillance and enhanced infection prevention and control measures. …

BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales. AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France. MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed. ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene blaNDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known blaNDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam. ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone. …

New Delhi metallo-beta-lactamase (NDM)-producing Klebsiella pneumoniae (Kp) ST147 caused a large multi-hospital outbreak in Italy from 2018 to 2021. We describe a new ST6668 NDM-producing Kp clone, belonging to CC147, which rapidly spread across hospitals in the Pavia province (Northern Italy) from February to August 2023. Genomic analyses revealed that ST6668 is different from ST147 and fast evolving. As shown here, genomic surveillance programmes are useful for tracking the spread of new clones with reduced susceptibility to most antibiotics. …

New research from Northwestern University and the University of Wisconsin, however, is pointing to bacterial pneumonia as the cause of many severe COVID deaths. WebMD Health News…

A 64-year-old woman diagnosed with pneumonia had abdominal pain, diarrhea, dry cough, and night sweats. A year of inexplicable symptoms ended in an open biopsy and a live, stringlike worm. Medscape Medical News…

Clinicians should consider all three etiologies on community-acquired pneumonia presentation to improve antimicrobial stewardship and patient outcomes. CDC Expert Commentary…

Since autumn 2022, observed numbers of paediatric invasive group A Streptococcus infections in Portugal (n = 89) were higher than in pre-COVID-19 seasons. Between September 2022 and May 2023, the dominant diagnoses were pneumonia (25/79), mostly with empyema (20/25), and sepsis (22/79). A number of cases required admission to intensive care (27/79) and surgery (35/79), and the case fatality rate was 5.1% (4/79). Genomic sequencing (n = 55) revealed multiple genetic lineages, dominated by the M1UK sublineage (26/55) and more diverse emm12 isolates (12/55). …

We describe a large Q fever outbreak reported in Spain, including 108 cases, 53 with pneumonia and 27 requiring hospitalisations. The first cases were detected in February 2021 among rock climbers visiting a cave in Bizkaia, and the last case was detected in October 2021. Most cases were notified after the Easter holiday (April–May 2021). More males (63.9%) than females (36.1%) were infected (median ages: 42 (1–68) and 39 years (6–61), respectively). We detected Coxiella burnetii by PCR in faecal, dust and/or aerosol samples taken inside the cave in March 2021, and in dust and aerosol samples collected between March 2021 and February 2023. Coxiella burnetii from dust samples were cultured on Vero cells, showing viability for 24 months. Based on serological and genotyping data, goats sheltering in the cave were the most likely source of infection. The cave was closed on 29 April 2021, movements of goats and sheep in the area were restricted (March–July 2021), and the animals were vaccinated in October 2021. Investigation of Q fever outbreaks requires a multidisciplinary One Health approach as these outbreaks can occur in unexpected places like natural sites where animals are present. …

IntroductionNational and regional carbapenemase-producing Enterobacterales (CPE) surveillance is essential to understand the burden of antimicrobial resistance, elucidate outbreaks, and develop infection-control or antimicrobial-treatment recommendations. AimThis study aimed to describe CPE and their epidemiology in Norway from 2015 to 2021. MethodsA nationwide, population-based observational study of all verified clinical and carriage CPE isolates submitted to the national reference laboratory was conducted. Isolates were characterised by antimicrobial susceptibility testing, whole genome sequencing (WGS) and basic metadata. Annual CPE incidences were also estimated. ResultsA total of 389 CPE isolates were identified from 332 patients of 63 years median age (range: 0–98). These corresponded to 341 cases, 184 (54%) being male. Between 2015 and 2021, the annual incidence of CPE cases increased from 0.6 to 1.1 per 100,000 person-years. For CPE-isolates with available data on colonisation/infection, 58% (226/389) were associated with colonisation and 38% (149/389) with clinical infections. WGS revealed a predominance of OXA-48-like (51%; 198/389) and NDM (34%; 134/389) carbapenemases in a diversified population of Escherichia coli and Klebsiella pneumoniae, including high-risk clones also detected globally. Most CPE isolates were travel-related (63%; 245/389). Although local outbreaks and healthcare-associated transmission occurred, no interregional spread was detected. Nevertheless, 18% (70/389) of isolates not directly related to import points towards potentially unidentified transmission routes. A decline in travel-associated cases was observed during the COVID-19 pandemic. ConclusionsThe close-to-doubling of CPE case incidence between 2015 and 2021 was associated with foreign travel and genomic diversity. To limit further transmission and outbreaks, continued screening and monitoring is essential. …

BackgroundInternational organisations are calling for One Health approaches to tackle antimicrobial resistance. In France, getting an overview of the current surveillance system and its level of integration is difficult due to the diversity of surveillance programmes. AimThis study aimed to map and describe all French surveillance programmes for antibiotic resistance (ABR), antibiotic use (ABU) and antibiotic residues, in humans, animals, food and the environment, in 2021. Another objective was to identify integration points, gaps and overlaps in the system. MethodsWe reviewed the literature for surveillance programmes and their descriptions. To further characterise programmes found, semi-directed interviews were conducted with their coordinators. ResultsIn total 48 programmes in the human (n = 35), animal (n = 12), food (n = 3) and/or the environment (n = 1) sectors were identified; 35 programmes focused on ABR, 14 on ABU and two on antibiotic residues. Two programmes were cross-sectoral. Among the 35 ABR programmes, 23 collected bacterial isolates. Bacteria most targeted were Escherichia coli (n = 17 programmes), Klebsiella pneumoniae (n = 13), and Staphylococcus aureus (n = 12). Extended-spectrum beta-lactamase-producing E. coli was monitored by most ABR programmes (15 of 35) in humans, animals and food, and is a good candidate for integrated analyses. ABU indicators were highly variable. Areas poorly covered were the environmental sector, overseas territories, antibiotic-resistant-bacterial colonisation in humans and ABU in companion animals. ConclusionThe French surveillance system appears extensive but has gaps and is highly fragmented. We believe our mapping will interest policymakers and surveillance stakeholders. Our methodology may inspire other countries considering One Health surveillance of ABR. …

BackgroundAntimicrobial resistance (AMR) is of public health concern worldwide. AimWe aimed to summarise the German AMR situation for clinicians and microbiologists. MethodsWe conducted a systematic review and meta-analysis of 60 published studies and data from the German Antibiotic-Resistance-Surveillance (ARS). Primary outcomes were AMR proportions in bacterial isolates from infected patients in Germany (2016–2021) and the case fatality rates (2010–2021). Random and fixed (common) effect models were used to calculate pooled proportions and pooled case fatality odds ratios, respectively. ResultsThe pooled proportion of meticillin resistance in Staphylococcus aureus infections (MRSA) was 7.9% with a declining trend between 2014 and 2020 (odds ratio (OR) = 0.89; 95% CI: 0.886–0.891; p 

Pneumonia -- IraqFollowing a surge in meningitis cases in Halabjah City and Sulaymaniyah governorate since mid-April 2023, an expert team from the World Health Organization (WHO) and the Ministry of Health was deployed to the affected areas to perform a joint epidemiological investigation of the reported cases and develop a swift response plan to curb the transmission of the disease.Preliminary laboratory results from 24 collected samples showed a mixture of bacterial (_Streptococcus pneumoniae_) and viral…

Hospital-Related Infection -- United StatesA bacterial outbreak at Virginia Mason Medical Center in Seattle has sickened 31 patients since October [2022]. Seven of them have since died, but it\'s unknown what caused those deaths -- the infection or the diagnoses that brought them to the hospital in the first place._Klebsiella pneumoniae_ is a bacterium usually found in health care settings, and often resistant to antibiotics. It can cause pneumonia, meningitis, and wound or bloodstream infections.Virginia Mason is working with…

Porcine Circovirus -- United StatesThe latest Swine Disease Reporting System report has some people scratching their heads. For the 1st time in recent memory, porcine circovirus type 2 (PCV2) jumped into the top 10 most-diagnosed diseases list at the Iowa State University Veterinary Diagnostic Lab. At No. 9, it surpassed porcine epidemic diarrhea virus and came in just behind _Mycoplasma hyopneumoniae_.Porcine-circovirus-associated disease (PCVAD) can be caused by any PCV2 strain. When PCVAD 1st showed up in the US in…

Meningitis -- NigeriaBetween 1 Oct 2022 and 16 Apr 2023, Nigeria reported a total of 1686 suspected cases of meningitis, including 124 deaths, for a case fatality ratio (CFR) of 7%.Meningitis is a serious infection of the meninges, the membranes covering the brain and spinal cord. It is a devastating disease and a major public health challenge. _Neisseria meningitidis_ (meningococcus), _Streptococcus pneumoniae_ (pneumococcus), _Haemophilus influenzae_ [serotype b or Hib] and _Streptococcus agalactiae_ (group…

Klebsiella pneumoniae -- United StatesFour patients at a downtown Seattle hospital are dead in connection to an outbreak of a bacterium often found in healthcare settings that has developed resistance to some antibiotics.The [31] infected patients, who contracted _Klebsiella_, were hospitalized in various departments, including inpatient medical beds, an ICU, and an operating room at Virginia Mason Medical Center, the hospital said in a statement released Wednesday [26 Apr 2023].Beginning in October 2022, hospital staff…

A hypervirulent Klebsiella pneumoniae SL218 (ST23-KL57), phylogenetically distinct from the classical hypervirulent SL23 (ST23-KL1) lineage, was transmitted between hospitalised patients in Denmark in 2021. The isolate carried a hybrid resistance and virulence plasmid containing blaNDM-1 and a plasmid containing blaOXA-48 (pOXA-48); the latter plasmid was horizontally transferred within-patient to Serratia marcescens. The convergence of drug resistance and virulence factors in single plasmids and in different lineages of K. pneumoniae is concerning and requires surveillance. …