Antibiotic and antimicrobial resistance

Antimicrobial resistance (AMR) of Mycoplasma genitalium (MG) is a growing concern worldwide and surveillance is needed. In Belgium, samples are sent to the National Reference Centre of Sexually Transmitted Infections (NRC-STI) on a voluntary basis and representative or robust national AMR data are lacking.

We aimed to estimate the occurrence of resistant MG in Belgium.

Between July and November 2022, frozen remnants of MG-positive samples from 21 Belgian laboratories were analysed at the NRC-STI. Macrolide and fluoroquinolone resistance-associated mutations (RAMs) were assessed using Sanger sequencing of the 23SrRNA and parC gene. Differences in resistance patterns were correlated with surveillance methodology, socio-demographic and behavioural variables via Fisher’s exact test and logistic regression analysis.

Of the 244 MG-positive samples received, 232 could be sequenced for macrolide and fluoroquinolone RAMs. Over half of the sequenced samples (55.2%) were resistant to macrolides. All sequenced samples from men who have sex with men (MSM) (24/24) were macrolide-resistant. Fluoroquinolone RAMs were found in 25.9% of the samples and occurrence did not differ between socio-demographic and sexual behaviour characteristics.

Although limited in sample size, our data suggest no additional benefit of testing MG retrieved from MSM for macrolide resistance in Belgium, when making treatment decisions. The lower occurrence of macrolide resistance in other population groups, combined with emergence of fluoroquinolone RAMs support macrolide-resistance testing in these groups. Continued surveillance of resistance in MG in different population groups will be crucial to confirm our findings and to guide national testing and treatment strategies.

The COVID-19 pandemic resulted in adaptation in infection control measures, increased patient transfer, high occupancy of intensive cares, downscaling of non-urgent medical procedures and decreased travelling.

To gain insight in the influence of these changes on antimicrobial resistance (AMR) prevalence in the Netherlands, a country with a low AMR prevalence, we estimated changes in demographics and prevalence of six highly resistant microorganisms (HRMO) in hospitalised patients in the Netherlands during COVID-19 waves (March–June 2020, October 2020–June 2021, October 2021–May 2022 and June–August 2022) and interwaves (July–September 2020 and July–September 2021) compared with pre-COVID-19 (March 2019–February 2020).

We investigated data on routine bacteriology cultures of hospitalised patients, obtained from 37 clinical microbiological laboratories participating in the national AMR surveillance. Demographic characteristics and HRMO prevalence were calculated as proportions and rates per 10,000 hospital admissions.

Although no significant persistent changes in HRMO prevalence were detected, some relevant non-significant patterns were recognised in intensive care units. Compared with pre-COVID-19 we found a tendency towards higher prevalence of meticillin-resistant Staphylococcus aureus during waves and lower prevalence of multidrug-resistant Pseudomonas aeruginosa during interwaves. Additionally, during the first three waves, we observed significantly higher proportions and rates of cultures with Enterococcus faecium (pooled 10% vs 6% and 240 vs 120 per 10,000 admissions) and coagulase-negative Staphylococci (pooled 21% vs 14% and 500 vs 252 per 10,000 admissions) compared with pre-COVID-19.

We observed no substantial changes in HRMO prevalence in hospitalised patients during the COVID-19 pandemic.

Preliminary 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.

We 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.

We 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.

Five 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.

The 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.

Since 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.

We investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.

All 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.

The 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.

Highly 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.

Multidrug-resistant (MDR) bacteria are among chief causes of healthcare-associated infections (HAIs). In Spain, studies addressing multidrug resistance based on epidemiological surveillance systems are lacking.

In this observational study, cases of HAIs by MDR bacteria notified to the epidemiological surveillance system of Andalusia, Spain, between 2014−2021, were investigated. Notified cases and their spatiotemporal distribution were described, with a focus on social determinants of health (SDoH).

New cases during the study period of HAIs caused by extended-spectrum β-lactamase (ESBL)-/carbapenemase-producing Enterobacterales, MDR Acinectobacter baumannii, MDR Pseudomonas aeruginosa or meticillin resistant Staphylococcus aureus were considered. Among others, notification variables included sex and age, while socio-economic variables comprised several SDoH. Cases’ spatial distribution across municipalities was assessed. The smooth standardised incidence ratio (sSIR) was obtained using a Bayesian spatial model. Association between municipalities’ sSIR level and SDoH was evaluated by bivariate analysis.

In total, 6,389 cases with a median age of 68 years were notified; 61.4% were men (n = 3,921). The most frequent MDR bacteria were ESBL-producing Enterobacterales (2,812/6,389; 44.0%); the main agent was Klebsiella spp. (2,956/6,389; 46.3%). Between 2014 and 2021 case numbers appeared to increase. Overall, up to 15-fold differences in sSIR between municipalities were observed. In bivariate analysis, there appeared to be an association between municipalities’ sSIR level and deprivation (p = 0.003).

This study indicates that social factors should be considered when investigating HAIs by MDR bacteria. The case incidence heterogeneity between Andalusian municipalities might be explained by SDoH, but also possibly by under-notification. Automatising reporting may address the latter.

In Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.

This study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.

We collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999–2004 and 2015–2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.

Via the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015–2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3–6 months.

We validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.

Antimicrobial resistance (AMR) is of public health concern worldwide.

We aimed to summarise the German AMR situation for clinicians and microbiologists.

We 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.

The 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 < 0.0001), while vancomycin resistance in Enterococcus faecium (VRE) bloodstream infections increased (OR = 1.18; (95% CI: 1.16–1.21); p < 0.0001) with a pooled proportion of 34.9%. Case fatality rates for MRSA and VRE were higher than for their susceptible strains (OR = 2.29; 95% CI: 1.91–2.75 and 1.69; 95% CI: 1.22–2.33, respectively). Carbapenem resistance in Gram-negative pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Enterobacter spp. and Escherichia coli) was low to moderate (< 9%), but resistance against third-generation cephalosporins and fluoroquinolones was moderate to high (5–25%). Pseudomonas aeruginosa exhibited high resistance against carbapenems (17.0%; 95% CI: 11.9–22.8), third-generation cephalosporins (10.1%; 95% CI: 6.6–14.2) and fluoroquinolones (24.9%; 95% CI: 19.3–30.9). Statistical heterogeneity was high (I² > 70%) across studies reporting resistance proportions.

Continuous efforts in AMR surveillance and infection prevention and control as well as antibiotic stewardship are needed to limit the spread of AMR in Germany.

Since the beginning of the war in Ukraine in February 2022, Ukrainians have been seeking shelter in other European countries.

We aimed to investigate the prevalence and the molecular epidemiology of multidrug-resistant Gram-negative (MDRGN) bacteria and meticillin-resistant Staphylococcus aureus (MRSA) in Ukrainian patients at admittance to the University Hospital Frankfurt, Germany.

We performed screening and observational analysis of all patients from March until June 2022. Genomes of MDRGN isolates were analysed for antimicrobial resistance, virulence genes and phylogenetic relatedness.

We included 103 patients (median age: 39 ± 23.7 years), 57 of whom were female (55.3%; 95% confidence interval (CI): 45.2–5.1). Patients were most frequently admitted to the Department of Paediatrics (29/103; 28.2%; 95% CI: 19.7–37.9). We found 34 MDRGN isolates in 17 of 103 patients (16.5%; 95% CI: 9.9–25.1). Ten patients carried 21 carbapenem-resistant (CR) bacteria, five of them more than one CR isolate. Four of six patients with war-related injuries carried eight CR isolates. In six of 10 patients, CR isolates caused infections. Genomic characterisation revealed that the CR isolates harboured at least one carbapenemase gene, blaNDM-1 being the most frequent (n = 10). Core genome and plasmid analysis revealed no epidemiological connection between most of these isolates. Hypervirulence marker genes were found in five of six Klebsiella pneumoniae CR isolates. No MRSA was found.

Hospitals should consider infection control strategies to cover the elevated prevalence of MDRGN bacteria in Ukrainian patients with war-related injuries and/or hospital pre-treatment and to prevent the spread of hypervirulent CR isolates.

Surveillance of antimicrobial resistance (AMR) and antimicrobial use (AMU) in Europe is currently annual.

To study the feasibility and scalability of a quarterly AMR/AMU surveillance system in the European Union/European Economic Area (EU/EEA).

We conducted a longitudinal study within the scope of the EU-JAMRAI project. Seventeen partners from 11 EU/EEA countries prospectively collected 41 AMU and AMR indicators quarterly from September 2017 to May 2020 for the hospital sector (HS) and primary care (PC). Descriptive statistics and coefficients of variation (CV) analysis were performed.

Data from 8 million hospital stays and 45 million inhabitants per quarter were collected at national (n = 4), regional (n = 6) and local (n = 7) levels. Of all partners, five were able to provide data within 3 months after each preceding quarter, and eight within 3–6 months. A high variability in AMU was found between partners. Colistin was the antibiotic that showed the highest CV in HS (1.40; p < 0.0001). Extended-spectrum beta-lactamase-producing Escherichia coli presented the highest incidence in HS (0.568 ± 0.045 cases/1,000 bed-days per quarter), whereas ciprofloxacin-resistant E. coli showed the highest incidence in PC (0.448 ± 0.027 cases/1,000 inhabitants per quarter). Barriers and needs for implementation were identified.

This pilot study could be a first step towards the development of a quarterly surveillance system for AMU and AMR in both HS and PC in the EU/EEA. However, committed institutional support, dedicated human resources, coordination of data sources, homogeneous indicators and modern integrated IT systems are needed first to implement a sustainable quarterly surveillance system.

Modern laboratory methods such as next generation sequencing and MALDI-TOF allow identification of novel bacterial species. This can affect surveillance of infections and antimicrobial resistance. From 2017, increasing numbers of medical microbiology laboratories in Switzerland differentiated Klebsiella variicola from Klebsiella pneumoniae complex using updated MALDI-TOF databases, whereas many laboratories still report them as K. pneumoniae or K. pneumoniae complex.

Our study explored whether separate reporting of K. variicola and the Klebsiella pneumoniae complex affected the ANRESIS surveillance database.

We analysed antibiotic susceptibility rates and specimen types of K. variicola and non-K. variicola-K. pneumoniae complex isolates reported by Swiss medical laboratories to the ANRESIS database (Swiss Centre for Antibiotic Resistance) from January 2017 to June 2022.

Analysis of Swiss antimicrobial resistance data revealed increased susceptibility rates of K. variicola compared with species of the K. pneumoniae complex other than K. variicola in all six antibiotic classes tested. This can lead to underestimated resistance rates of K. pneumoniae complex in laboratories that do not specifically identify K. variicola. Furthermore, K. variicola strains were significantly more often reported from blood and primarily sterile specimens than isolates of the K. pneumoniae complex other than K. variicola, indicating increased invasiveness of K. variicola.

Our data suggest that refined differentiation of the K. pneumoniae complex can improve our understanding of its taxonomy, susceptibility, epidemiology and clinical significance, thus providing more precise information to clinicians and epidemiologists.

Evidence on the distribution of bacteria and therapy recommendations in male outpatients with urinary tract infections (UTI) remains insufficient.

We aimed to report frequency distributions and antimicrobial resistance (AMR) of bacteria causing UTI in men and to identify risk factors for resistance of Escherichia coli against trimethoprim (TMP) and ciprofloxacin (CIP).

We conducted a retrospective observational study using routinely collected midstream urine specimens from 102,736 adult male outpatients sent from 6,749 outpatient practices to nine collaborating laboratories from all major regions in Germany between 2015 and 2020. Resistance in E. coli was predicted using logistic regression.

The three most frequent bacteria were E. coli (38.4%), Enterococcus faecalis (16.5%) and Proteus mirabilis (9.3%). Resistance of E. coli against amoxicillin (45.7%), TMP (26.6%) and CIP (19.8%) was common. Multiple drug resistance was high (22.9%). Resistance against fosfomycin (0.9%) and nitrofurantoin (1.9%) was low. Resistance of En. faecalis against CIP was high (29.3%). Isolates of P. mirabilis revealed high resistance against TMP (41.3%) and CIP (16.6%). The CIP and TMP resistance was significantly higher among bacteria derived from recurrent UTI (p < 0.05). Age ≥ 90 years, recurrent UTI and regions East and South were independently associated with AMR of E. coli against TMP and CIP (p < 0.05).

The most frequent UTI-causing pathogens showed highresistance against TMP and CIP, empirical therapy is therefore likely to fail. Apart from intrinsically resistant pathogens, susceptibility to fosfomycin and nitrofurantoin remains sufficient. Therefore, they remain an additional option for empirical treatment of uncomplicated UTI in men.

Evidence supporting the effectiveness of single-room contact precautions (SCP) in preventing in-hospital acquisition of vancomycin-resistant enterococci (haVRE) is limited.

We assessed the impact of SCP on haVRE and their transmission.

We conducted a prospective, multicentre cohort study in German haematological/oncological departments during 2016. Two sites performed SCP for VRE patients and two did not (NCP). We defined a 5% haVRE-risk difference as non-inferiority margin, screened patients for VRE, and characterised isolates by whole genome sequencing and core genome MLST (cgMLST). Potential confounders were assessed by competing risk regression analysis.

We included 1,397 patients at NCP and 1,531 patients at SCP sites. Not performing SCP was associated with a significantly higher proportion of haVRE; 12.2% (170/1,397) patients at NCP and 7.4% (113/1,531) patients at SCP sites (relative risk (RR) 1.74; 95% confidence interval (CI): 1.35–2.23). The difference (4.8%) was below the non-inferiority margin. Competing risk regression analysis indicated a stronger impact of antimicrobial exposure (subdistribution hazard ratio (SHR) 7.46; 95% CI: 4.59–12.12) and underlying disease (SHR for acute leukaemia 2.34; 95% CI: 1.46–3.75) on haVRE than NCP (SHR 1.60; 95% CI: 1.14–2.25). Based on cgMLST and patient movement data, we observed 131 patient-to-patient VRE transmissions at NCP and 85 at SCP sites (RR 1.76; 95% CI: 1.33–2.34).

We show a positive impact of SCP on haVRE in a high-risk population, although the observed difference was below the pre-specified non-inferiority margin. Importantly, other factors including antimicrobial exposure seem to be more influential.

Hospital-acquired infections (HAI) caused by Enterococcus spp., especially vancomycin-resistant Enterococcusspp. (VRE), are of rising concern.

We summarised data on incidence, mortality and proportion of HAI caused by enterococci in the World Health Organization European Region.

We searched Medline and Embase for articles published between 1 January 2010 and 4 February 2020. Random-effects meta-analyses were performed to obtain pooled estimates.

We included 75 studies. Enterococcus spp. and VRE accounted for 10.9% (95% confidence interval (CI): 8.7–13.4; range: 6.1–17.5) and 1.1% (95% CI: 0.21–2.7; range: 0.39–2.0) of all pathogens isolated from patients with HAI. Hospital wide, the pooled incidence of HAI caused by Enterococcus spp. ranged between 0.7 and 24.8 cases per 1,000 patients (pooled estimate: 6.9; 95% CI: 0.76–19.0). In intensive care units (ICU), pooled incidence of HAI caused by Enterococcus spp. and VRE was 9.6 (95% CI: 6.3–13.5; range: 0.39–36.0) and 2.6 (95% CI: 0.53–5.8; range: 0–9.7). Hospital wide, the pooled vancomycin resistance proportion among Enterococcus spp. HAI isolates was 7.3% (95% CI: 1.5–16.3; range: 2.6–11.5). In ICU, this proportion was 11.5% (95% CI: 4.7–20.1; range: 0–40.0). Among patients with hospital-acquired bloodstream infections with Enterococcus spp., pooled all-cause mortality was 21.9% (95% CI: 15.7–28.9; range: 14.3–32.3); whereas all-cause mortality attributable to VRE was 33.5% (95% CI: 13.0–57.3; range: 14.3–41.3).

Infections caused by Enterococcus spp. are frequently identified among hospital patients and associated with high mortality.

While 20–80% of regular visitors to (sub)tropical regions become colonised by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), those hospitalised abroad often also carry other multidrug-resistant (MDR) bacteria on return; the rates are presumed to be highest for interhospital transfers.

This observational study assessed MDR bacterial colonisation among patients transferred directly from hospitals abroad to Helsinki University Hospital. We investigated predisposing factors, clinical infections and associated fatalities.

Data were derived from screening and from diagnostic samples collected between 2010 and 2019. Risk factors of colonisation were identified by multivariable analysis. Microbiologically verified symptomatic infections and infection-related mortality were recorded during post-transfer hospitalisation.

Colonisation rates proved highest for transfers from Asia (69/96; 71.9%) and lowest for those within Europe (99/524; 18.9%). Of all 698 patients, 208 (29.8%) were colonised; among those, 163 (78.4%) carried ESBL-PE, 28 (13.5%) MDR Acinetobacter species, 25 (12.0%) meticillin-resistant Staphylococcus aureus, 25 (12.0%) vancomycin-resistant Enterococcus, 14 (6.7%) carbapenemase-producing Enterobacteriaceae, and 12 (5.8%) MDR Pseudomonas aeruginosa; 46 strains tested carbapenemase gene-positive. In multivariable analysis, geographical region, intensive care unit (ICU) treatment and antibiotic use abroad proved to be risk factors for colonisation. Clinical MDR infections, two of them fatal (1.0%), were recorded for 22 of 208 (10.6%) MDR carriers.

Colonisation by MDR bacteria was common among patients transferred from foreign hospitals. Region of hospitalisation, ICU treatment and antibiotic use were identified as predisposing factors. Within 30 days after transfer, MDR colonisation manifested as clinical infection in more than 10% of the carriers.

The contribution of healthcare-associated infections (HAI) to mortality can be estimated using statistical methods, but mortality review (MR) is better suited for routine use in clinical settings. The European Centre for Disease Prevention and Control recently introduced MR into its HAI surveillance.

We evaluate validity and reproducibility of three MR measures.

The on-site investigator, usually an infection prevention and control doctor, and the clinician in charge of the patient independently reviewed records of deceased patients with bloodstream infection (BSI), pneumonia, Clostridioides difficile infection (CDI) or surgical site infection (SSI), and assessed the contribution to death using 3CAT: definitely/possibly/no contribution to death; WHOCAT: sole cause/part of causal sequence but not sufficient on its own/contributory cause but unrelated to condition causing death/no contribution, based on the World Health Organization’s death certificate; QUANT: Likert scale: 0 (no contribution) to 10 (definitely cause of death). Inter-rater reliability was assessed with weighted kappa (wk) and intra-cluster correlation coefficient (ICC). Reviewers rated the fit of the measures.

From 2017 to 2018, 24 hospitals (11 countries) recorded 291 cases: 87 BSI, 113 pneumonia , 71 CDI and 20 SSI. The inter-rater reliability was: 3CAT wk 0.68 (95% confidence interval (CI): 0.61–0.75); WHOCAT wk 0.65 (95% CI: 0.58–0.73); QUANT ICC 0.76 (95% CI: 0.71–0.81). Inter-rater reliability ranged from 0.72 for pneumonia to 0.52 for CDI. All three measures fitted ‘reasonably’ or ‘well’ in > 88%.

Feasibility, validity and reproducibility of these MR measures was acceptable for use in HAI surveillance.

France is a low prevalence country for colistin resistance. Molecular and epidemiological events contributing to the emergence of resistance to colistin, one of the 'last-resort' antibiotics to treat multidrug-resistant Gram-negative infections, are important to investigate.

This retrospective (2014 to 2017) observational study aimed to identify risk factors associated with acquisition of colistin-resistant Klebsiella pneumoniae (CRKP) in hospitals in Marseille, France, and to molecularly characterise clinical isolates.

To identify risk factors for CRKP, a matched-case–control (1:2) study was performed in two groups of patients with CRKP or colistin-susceptible K. pneumoniae respectively. Whole-genome-sequences (WGS) of CRKP were compared with 6,412 K. pneumoniae genomes available at the National Center for Biotechnology Information (NCBI).

Multivariate analysis identified male sex and contact with a patient carrying a CRKP as significant independent factors (p < 0.05) for CRKP acquisition, but not colistin administration. WGS of nine of 14 CRKP clinical isolates belonged to the same sequence type (ST)307. These isolates were from patients who had been hospitalised in the same wards, suggesting an outbreak. Comparison of the corresponding strains’ WGS to K. pneumoniae genomes in NCBI revealed that in chromosomal genes likely playing a role in colistin resistance, a subset of five specific mutations were significantly associated with ST307 (p < 0.001).

A ST307 CRKP clone was identified in this study, with specific chromosomal mutations in genes potentially implicated in colistin resistance. ST307 might have a propensity to be or become resistant to colistin, however confirming this requires further investigations.

The mcr-1 gene is a transferable resistance determinant against colistin, a last-resort antimicrobial for infections caused by multi-resistant Gram-negatives.

To study carriage of antibiotic-resistant bacteria in healthy school children as part of a helminth control and antimicrobial resistance survey in the Bolivian Chaco region.

From September to October 2016 we collected faecal samples from healthy children in eight rural villages. Samples were screened for mcr-1- and mcr-2 genes. Antimicrobial susceptibility testing was performed, and a subset of 18 isolates representative of individuals from different villages was analysed by whole genome sequencing (WGS).

We included 337 children (mean age: 9.2 years, range: 7–11; 53% females). The proportion of mcr-1 carriers was high (38.3%) and present in all villages; only four children had previous antibiotic exposure. One or more mcr-1-positive isolates were recovered from 129 positive samples, yielding a total of 173 isolates (171 Escherichia coli, 1 Citrobacter europaeus, 1 Enterobacter hormaechei). No mcr-2 was detected. Co-resistance to other antimicrobials varied in mcr-positive E. coli. All 171 isolates were susceptible to carbapenems and tigecycline; 41 (24.0%) were extended-spectrum β-lactamase producers and most of them (37/41) carried blaCTX-M-type genes. WGS revealed heterogeneity of clonal lineages and mcr-genetic supports.

This high prevalence of mcr-1-like carriage, in absence of professional exposure, is unexpected. Its extent at the national level should be investigated with priority. Possible causes should be studied; they may include unrestricted use of colistin in veterinary medicine and animal breeding, and importation of mcr-1-positive bacteria via food and animals.

Remarkably high carriage prevalence of a community-associated meticillin-resistant Staphylococcus aureus (MRSA) strain of sequence type (ST) 22 in the Gaza strip was reported in 2012. This strain is linked to the pandemic hospital-associated EMRSA-15. The origin and evolutionary history of ST22 in Gaza communities and the genomic elements contributing to its widespread predominance are unknown. Methods: We generated high-quality draft genomes of 61 ST22 isolates from Gaza communities and, along with 175 ST22 genomes from global sources, reconstructed the ST22 phylogeny and examined genotypes unique to the Gaza isolates. Results: The Gaza isolates do not exhibit a close relationship with hospital-associated ST22 isolates, but rather with a basal population from which EMRSA-15 emerged. There were two separate resistance acquisitions by the same MSSA lineage, followed by diversification of other genetic determinants. Nearly all isolates in the two distinct clades, one characterised by staphylococcal cassette chromosome mec (SCCmec) IVa and the other by SCCmec V and MSSA isolates, contain the toxic shock syndrome toxin-1 gene. Discussion: The genomic diversity of Gaza ST22 isolates is not consistent with recent emergence in the region. The results indicate that two divergent Gaza clones evolved separately from susceptible isolates. Researchers should not assume that isolates identified as ST22 in the community are examples of EMRSA-15 that have escaped their healthcare roots. Future surveillance of MRSA is essential to the understanding of ST22 evolutionary dynamics and to aid efforts to slow the further spread of this lineage.

Emergence of colistin resistance has been related to increased use in clinical settings, following global spread of carbapenem-resistant Gram-negative bacteria. Use of colistin in animal production may constitute a further source of spread of resistant strains to humans. We sought to determine risk factors for human colonisation or infection with colistin-resistant Escherichia coli and Klebsiella pneumoniae in a setting where colistin is mainly used for animal production. Methods: This retrospective matched case–control study was performed during a 5-year period at two university-affiliated hospitals in Basel, Switzerland. Conditional univariable logistic regression was used to calculate odds ratios (OR) for colistin resistance. All variables found to be significant in univariable analyses were included in the conditional multivariable regression model using stepwise forward and backward selection. Results: Forty-two cases (33 with colistin-resistant E. coli, 9 with colistin-resistant K. pneumoniae) and 126 matched controls were identified. Baseline characteristics, comorbidities, prior exposure to antibiotics and healthcare settings did not differ between cases and controls, except for prior exposure to carbapenems, hospitalisation and stay abroad during the prior 3 months. In multivariable analyses, only prior exposure to carbapenems remained associated with colistin resistance (OR: 5.00; 95% confidence interval (95% CI): 1.19–20.92; p = 0.028). Conclusion: In a low-endemicity setting for carbapenem resistance, prior exposure to carbapenems was the only risk factor for colonisation or infection with colistin-resistant E. coli or K. pneumoniae. Prior exposure to colistin was not significantly associated with detection of colistin resistance, which mainly occurred in the absence of concurrent carbapenem resistance.

Plasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.6**, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.