The Evolution of Antimicrobial Resistance in Mexico During the Last Decade: Results from the INVIFAR Group

A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources

Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.

Antimicrobial Resistance and Antibiotic Consumption in a Secondary Care Hospital in Mexico

BACKGROUND

Antimicrobial resistance is a global health problem, due to morbidity, mortality, and healthcare costs. The misuse of antimicrobials is the main cause of antimicrobial resistance. The aim of this study was to report antimicrobial resistance and antibiotic consumption in a secondary care hospital in Mexico.

METHODS

Within a cross-sectional study, antimicrobial resistance data on ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and antibiotic consumption from 2020 to 2022 were collected. Antimicrobial resistance was reported based on percentages of resistance and consumption was analyzed using the defined daily dose (DDD)/100 bed days and the AWaRe (Access, Surveillance, Reservation) antibiotic group.

RESULTS

Antibiotic consumption in 2020, 2021 and 2022 was 330, 175 and 175 DDD/100 beds day, respectively. The rate of ceftriaxone resistance in E. coli (n = 526) and K. pneumoniae (n = 80) was 76% and 69%, respectively, the rate of carbapenem resistance in A. baumannii (n = 168) and P. aeruginosa (n = 108) was 92% and 52%, respectively; the rate of oxacillin resistance in S. aureus (n = 208) was 27%; and the rate of vancomycin resistance in E. faecium (n = 68) was 47%.

CONCLUSION

The reported results are congruent with global estimates of antibiotic resistance and consumption, providing an overview that could generate actions for antimicrobial optimization at the local and regional levels.

Acquired blaVIM and blaGES Carbapenemase-Encoding Genes in Pseudomonas aeruginosa: A Seven-Year Survey Highlighting an Increasing Epidemiological Threat

(1) Background: Pseudomonas aeruginosa is a Gram-negative bacterium with several intrinsic and acquired antimicrobial resistance mechanisms. The spread of carbapenemase-encoding genes, an acquired mechanism, enables carbapenem resistance in clinical settings. Detection of the carbapenemase-producer strains is urgent. Therefore, we aimed to characterize carbapenemase production in the clinical strains of P. aeruginosa at a tertiary-care center. (2) Methods: We included clinical strains of P. aeruginosa (from August 2011 to December 2018) with resistance towards at least one carbapenem. Strains were isolated in a tertiary-care center in Mexico City. Antimicrobial susceptibility profiles were determined by broth microdilution. Screening for carbapenemase-encoding genes was performed in all strains. Phenotypic assays (CarbaNP and mCIM) were conducted. Additional modifications to mCIM were also tested. (3) Results: One-hundred seventy-one P. aeruginosa strains out of 192 included in this study were resistant towards at least one of the carbapenems tested. Forty-seven of these strains harbored a carbapenemase-encoding gene. VIM (59.6%) and GES (23.4%) were the most frequently found carbapenemases in our study, followed by IMP (14.9%). (4) Among the most frequent carbapenemase genes identified, metallo-ß-lactamases were the most prevalent, which impair new treatment options. Searching for carbapenemase genes should be performed in resistant isolates to stop transmission and guide antimicrobial treatment.

Bacterial incidence and drug resistance from pathogens recovered from blood, cerebrospinal and pleural fluids in 2019-2020. Results of the Invifar network

Background

Antimicrobial resistance is a global concern. Analysis of sterile fluids is essential because microorganisms are defined as significant in most cases. Blood, cerebrospinal, and pleural fluids are frequently received in the microbiology lab because they are associated with considerable rates of morbi-mortality. Knowledge of epidemiology in these samples is needed to choose proper empirical treatments due to the importance of reducing selection pressure.

Methods

We used retrospective laboratory data of blood, CSF, and pleural fluid collected from patients in Mexico between 2019 and 2020. Each laboratory identified the strains and tested susceptibility using its routine methods. For Streptococcus pneumoniae, a comparative analysis was performed with data from the broth microdilution method.

Results

Forty-five centers participated in the study, with 30,746 clinical isolates from blood, 2,429 from pleural fluid, and 2,275 from CSF. For blood and CSF, Staphylococcus epidermidis was the most frequent. For blood, among gram negatives, the most frequent was Escherichia coli. Among Enterobacterales, 9.8% of K. pneumoniae were carbapenem-resistant. For S. pneumoniae, similar resistance percentages were observed for levofloxacin, cefotaxime, and vancomycin. For CSF, the most frequent gram-negative was E. coli. In Acinetobacter baumannii, carbapenem resistance was 71.4%. The most frequent species detected for pleural fluid was E. coli; in A. baumannii, carbapenem resistance was 96.3%.

Conclusion

Gram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae, the routine, conventional methods showed good agreement in detecting resistance percentages for erythromycin, levofloxacin, and vancomycin.

Comparison of Lateral Flow Immunochromatography and Phenotypic Assays to PCR for the Detection of Carbapenemase-Producing Gram-Negative Bacteria, a Multicenter Experience in Mexico

The identification of carbapenemase-producing Enterobacterales and Pseudomonas aeruginosa is important for treating and controlling hospital infections. The recommended methods for their identification require a long waiting time, technical training, and expertise. Lateral flow immunoassays such as NG-Test CARBA 5^® overcome these needs. We analyzed 84 clinical isolates of carbapenem-resistant Enterobacterales and P. aeruginosa from four different hospitals in a two-year period. Antimicrobial resistance patterns were confirmed with the broth dilution method. Evaluation of KPC, VIM, NDM, IMP, and OXA-48-like enzymes was performed and compared to NG-Test CARBA 5 and phenotypic assays. Enterobacterales represented 69% of isolates and P. aeruginosa represented 31%. Carbapenemase-producing strains were 51 (88%) of Enterobacterales and 23 (88.4%) of P. aeruginosa; 20 (34%) and 23 (88%) were Class B ß-lactamases, respectively. The NG-Test CARBA 5^® assay for Enterobacterales showed high sensitivity (98%), specificity (100%), and PPV (100%); however, it did not for P. aeruginosa. The Kappa concordance coefficient was 0.92 for Enterobacterales and 0.52 for P. aeruginosa. NG-Test CARBA 5^® is a fast and easy-to-use assay. In Enterobacterales, we found excellent agreement in our comparison with molecular tests. Despite the low agreement in P. aeruginosa, we suggest that this test could be used as a complementary tool.

Healthcare System Distrust and Non-Prescription Antibiotic Use: A Cross-Sectional Survey of Adult Antibiotic Users

Antibiotic resistance is a major public health concern driven by antibiotic overuse. Antibiotic stewardship programs are often limited to clinical settings and do little to address non-prescription antibiotic use in community settings. This study investigates the association between non-prescription antibiotic use and healthcare system distrust in the United States and Mexico. An online survey was deployed in the United States and Mexico with enhanced sampling through in-person recruiting in the border region. Non-prescription antibiotic use was defined as having bought or borrowed non-prescription oral or injectable antibiotics within the last 3 years. The survey included a previously validated 10-item scale to measure healthcare system distrust. Logistic regression was used to model the use of non-prescription antibiotics by the level of healthcare system distrust, adjusted for demographic characteristics and antibiotic knowledge. In total, 568 survey participants were included in the analysis, 48.6% of whom had used non-prescription oral or injectable antibiotics in the last 3 years. In the fully adjusted regression model, the odds of using non-prescription antibiotics were 3.2 (95% CI: 1.8, 6.1) times higher for those in the highest distrust quartile versus the lowest. These findings underscore the importance of community-based antibiotic stewardship and suggest that these programs are particularly critical for communities with high levels of healthcare system distrust.

Limited Therapeutic Options in Mexico for the Treatment of Urinary Tract Infections

The rise in antimicrobial resistance (AMR) has complicated the management of urinary tract infections (UTIs). The objective of this study was to evaluate the antimicrobial susceptibility patterns of Escherichia coli and Klebsiella pneumoniae. Design: prospective observational study. Bacteria were classified as susceptible or resistant to ampicillin-sulbactam, amikacin, gentamicin, ciprofloxacin, norfloxacin, nitrofurantoin, trimethoprim-sulfamethoxazole (TMP/SMZ), ertapenem, meropenem, and fosfomycin. The sensitivity to fosfomycin and chloramphenicol was evaluated by the disk diffusion method. Statistical analysis: the chi-square test and Fisher’s exact test were used to compare differences between categories. A p value < 0.05 was considered statistically significant. Isolates were collected from January 2019 to November 2020 from 21 hospitals and laboratories. A total of 238 isolates were received: a total of 156 E. coli isolates and 82 K. pneumoniae isolates. The majority were community-acquired infections (64.1%). Resistance was >20% for beta-lactams, aminoglycosides, fluoroquinolones, and TMP/SMZ. For E. coli isolates, resistance was <20% for amikacin, fosfomycin, and nitrofurantoin; for K. pneumoniae, amikacin, fosfomycin, chloramphenicol, and norfloxacin. All were susceptible to carbapenems. K. pneumoniae isolates registered a higher proportion of extensively drug-resistant bacteria in comparison with E. coli (p = 0.0004). In total, multidrug-resistant bacteria represented 61% of all isolates. Isolates demonstrated high resistance to beta-lactams, fluoro-quinolones, and TMP/SMZ.

Country data on AMR in Mexico in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome

Background

Antimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.

Objectives

To review AMR in Mexico and initiatives addressing it. Identifying any areas where more information is required will provide a call to action to minimize any further rises in AMR and to improve patient outcomes.

Methods

National AMR initiatives in Mexico, antibiotic use and prescribing, and availability of susceptibility data, particularly the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines commonly used in Mexico for specific CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) were also reviewed, along with local antibiotic availability. Insights from a local clinician were sought to contextualize this information.

Conclusions

The Mexican national AMR strategy was published in 2018. This comprised similar objectives to the Global Action Plan from the World Health Assembly (2015) and was compulsory, requiring full compliance from members of the National Health System. Historically, antibiotic consumption in Mexico has been high, however, between 2000 and 2015, consumption fell, in sharp contrast to the majority of countries. Mexico lacks a national surveillance network for AMR, however there are several ongoing global surveillance studies providing local antibiotic susceptibility data. International and local antibiotic prescribing guidelines for CA-RTIs are used. A more standardized inclusive approach in developing local guidelines, using up-to-date local surveillance data of isolates from community-acquired infections, could make guideline use more locally relevant. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development in Mexico and improve patient outcomes.

A case–control study of infections caused by Klebsiella pneumoniae producing New Delhi metallo-beta-lactamase-1: Predictors and outcomes

Introduction

Infections caused by antimicrobial-resistant bacteria are a significant cause of death worldwide, and carbapenemase-producing bacteria are the principal agents. New Delhi metallo-beta-lactamase-1 producing Klebsiella pneumoniae (KP-NDM-1) is an extensively drug-resistant bacterium that has been previously reported in Mexico. Our aim was to conduct a case–control study to describe the risk factors associated with nosocomial infections caused by K. pneumoniae producing NDM-1 in a tertiary-care hospital in Mexico.

Methods

A retrospective case–control study with patients hospitalized from January 2012 to February 2018 at the Hospital Civil de Guadalajara “Fray Antonio Alcalde” was designed. During this period, 139 patients with a culture that was positive for K. pneumoniae NDM-1 (cases) and 486 patients hospitalized in the same department and on the same date as the cases (controls) were included. Data were analyzed using SPSS v. 24, and logistic regression analysis was conducted to calculate the risk factors for KP-NDM-1 infection.

Results

One hundred and thirty-nine case patients with a KP-NDM-1 isolate and 486 control patients were analyzed. In the case group, acute renal failure was a significant comorbidity, hospitalization days were extended, and significantly more deaths occurred. In a multivariate analysis of risk factors, the independent variables included the previous use of antibiotics (odds ratio, OR = 12.252), the use of a urinary catheter (OR = 5.985), the use of a central venous catheter (OR = 5.518), the use of mechanical ventilation (OR = 3.459), and the length of intensive care unit (ICU) stay (OR = 2.334) as predictors of infection with NDM-1 K. pneumoniae.

Conclusion

In this study, the previous use of antibiotics, the use of a urinary catheter, the use of a central venous catheter, the use of mechanical ventilation, and ICU stay were shown to be predictors of infection with NDM-1 K. pneumoniae and were independent risk factors for infection with NDM-1 K. pneumoniae.

Efficacy and In Vitro Activity of Novel Antibiotics for Infections With Carbapenem-Resistant Gram-Negative Pathogens

Infections by Gram-negative multi-drug resistant (MDR) bacterial species are difficult to treat using available antibiotics. Overuse of carbapenems has contributed to widespread resistance to these antibiotics; as a result, carbapenem-resistant Enterobacterales (CRE), A. baumannii (CRAB), and P. aeruginosa (CRPA) have become common causes of healthcare-associated infections. Carbapenems, tigecycline, and colistin are the last resource antibiotics currently used; however, multiple reports of resistance to these antimicrobial agents have been documented worldwide. Recently, new antibiotics have been evaluated against Gram-negatives, including plazomicin (a new aminoglycoside) to treat CRE infection, eravacycline (a novel tetracycline) with in vitro activity against CRAB, and cefiderocol (a synthetic conjugate) for the treatment of nosocomial pneumonia by carbapenem-non-susceptible Gram-negative isolates. Furthermore, combinations of known β-lactams with recently developed β-lactam inhibitors, such as ceftazidime-avibactam, ceftolozane-tazobactam, ceftazidime-tazobactam, and meropenem-vaborbactam, has been suggested for the treatment of infections by extended-spectrum β-lactamases, carbapenemases, and AmpC producer bacteria. Nonetheless, they are not active against all carbapenemases, and there are reports of resistance to these combinations in clinical isolates.This review summarizes and discusses the in vitro and clinical evidence of the recently approved antibiotics, β-lactam inhibitors, and those in advanced phases of development for treating MDR infections caused by Gram-negative multi-drug resistant (MDR) bacterial species.

Antimicrobial Resistance Patterns and Clonal Distribution of E. coli, Enterobacter spp. and Acinetobacter spp. Strains Isolated from Two Hospital Wastewater Plants

The objective of this study was to determine the presence and persistence of antimicrobial-resistant enterobacteria and their clonal distribution in hospital wastewater. A descriptive cross-sectional study was carried out in wastewater from two Mexico City tertiary level hospitals. In February and March of 2020, eight wastewater samples were collected and 26 isolates of enterobacteria were recovered, 19 (73.1%) isolates were identified as E. coli, 5 (19.2%) as Acinetobacter spp. and 2 (7.7%) as Enterobacter spp. Antimicrobial susceptibility profiles were performed using the VITEK 2^® automated system and bacterial identification was performed by the Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS^®). ESBL genes were detected by polymerase chain reaction (PCR) and clonal distributions of isolates were determined by pulsed-field gel electrophoresis (PFGE). E. coli susceptibility to different classes of antimicrobials was analyzed and resistance was mainly detected as ESBLs and fluoroquinolones. One E. coli strain was resistant to doripenem, ertapenem, imipenem and meropenem. The analysis by PCR showed the presence of specific β-lactamases resistance genes (bla_KPC, bla_CTX-M). The PFGE separated the E. coli isolates into 19 different patterns (A–R). PFGE results of Acinetobacter spp. showed the presence of a majority clone A. Surveillance of antimicrobial resistance through hospital wastewater is an important tool for early detection of clonal clusters of clinically important bacteria with potential for dissemination.

Surveillance of Antimicrobial Resistance in Hospital Wastewater: Identification of Carbapenemase-Producing Klebsiella spp

The objective of this study was to investigate the presence and persistence of carbapenemase-producing Klebsiella spp. isolated from wastewater and treated wastewater from two tertiary hospitals in Mexico. We conducted a descriptive cross-sectional study in two hospital wastewater treatment plants, which were sampled in February 2020. We obtained 30 Klebsiella spp. isolates. Bacterial identification was carried out by the Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS^®) and antimicrobial susceptibility profiles were performed using the VITEK2^® automated system. The presence of carbapenem resistance genes (CRGs) in Klebsiella spp. isolates was confirmed by PCR. Molecular typing was determined by pulsed-field gel electrophoresis (PFGE). High rates of Klebsiella spp. resistance to cephalosporins and carbapenems (80%) were observed in isolates from treated wastewater from both hospitals. The molecular screening by PCR showed the presence of bla_KPC and bla_OXA-48-like genes. The PFGE pattern separated the Klebsiella isolates into 19 patterns (A–R) with three subtypes (C1, D1, and I1). Microbiological surveillance and identification of resistance genes of clinically important pathogens in hospital wastewater can be a general screening method for early determination of under-detected antimicrobial resistance profiles in hospitals and early warning of outbreaks and difficult-to-treat infections.

Drug resistance phenotypes and genotypes in Mexico in representative gram-negative species: Results from the infivar network

Aim

This report presents phenotypic and genetic data on the prevalence and characteristics of extended-spectrum β-lactamases (ESBLs) and representative carbapenemases-producing Gram-negative species in Mexico.

Material and methods

A total of 52 centers participated, 43 hospital-based laboratories and 9 external laboratories. The distribution of antimicrobial resistance data for Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae complex, Acinetobacter baumannii complex, and Pseudomonas aeruginosa in selected clinical specimens from January 1 to March 31, 2020 was analyzed using the WHONET 5.6 platform. The following clinical isolates recovered from selected specimens were included: carbapenem-resistant Enterobacteriaceae, ESBL or carbapenem-resistant E. coli, and K. pneumoniae, carbapenem-resistant A. baumannii complex, and P. aeruginosa. Strains were genotyped to detect ESBL and/or carbapenemase-encoding genes.

Results

Among blood isolates, A. baumannii complex showed more than 68% resistance for all antibiotics tested, and among Enterobacteria, E. cloacae complex showed higher resistance to carbapenems. A. baumannii complex showed a higher resistance pattern for respiratory specimens, with only amikacin having a resistance lower than 70%. Among K. pneumoniae isolates, bla_TEM, bla_SHV, and bla_CTX were detected in 68.79%, 72.3%, and 91.9% of isolates, respectively. Among E. coli isolates, bla_TEM, bla_SHV, and bla_CTX were detected in 20.8%, 4.53%, and 85.7% isolates, respectively. For both species, the most frequent genotype was bla_CTX-M-15. Among Enterobacteriaceae, the most frequently detected carbapenemase-encoding gene was bla_NDM-1 (81.5%), followed by bla_OXA-232 (14.8%) and bla_oxa-181(7.4%), in A. baumannii was bla_OXA-24 (76%) and in P. aeruginosa, was bla_IMP (25.3%), followed by bla_GES and bla_VIM (13.1% each).

Conclusion

Our study reports that NDM-1 is the most frequent carbapenemase-encoding gene in Mexico in Enterobacteriaceae with the circulation of the oxacillinase genes 181 and 232. KPC, in contrast to other countries in Latin America and the USA, is a rare occurrence. Additionally, a high circulation of ESBL bla_CTX-M-15 exists in both E. coli and K. pneumoniae.

The epidemiology of carbapenem resistance in Acinetobacter baumannii complex in Germany (2014-2018): an analysis of data from the national Antimicrobial Resistance Surveillance system

Background

Carbapenem-resistant Acinetobacter baumannii complex (CRABC) has globally emerged as a serious public health challenge. This study aimed to describe epidemiological trends and risk factors of carbapenem resistance in A. baumannii complex isolates in Germany between 2014 and 2018.

Methods

We analysed 43,948 clinical A. baumannii complex isolates using 2014 to 2018 data from the German Antimicrobial Resistance Surveillance system. We applied descriptive statistics and uni- and multivariable regression analyses to investigate carbapenem resistance in A. baumannii complex isolates.

Results

The proportion of carbapenem resistance in clinical A. baumannii complex isolates declined from 7.6% (95% confidence interval [95% CI] 4.4–12.7%) in 2014 to 3.5% (95% CI 2.5–4.7%) in 2018 (adjusted OR [aOR] 0.85 [95% CI 0.79–0.93, p ≤ 0.001]). Higher mean CRABC proportions for 2014 to 2018 were observed in secondary care hospitals (4.9% [95% CI 3.2–7.5%], aOR 3.6 [95% CI 2.4–5.3, p ≤ 0.001]) and tertiary care hospitals (5.9% [95% CI 3.0–11.2%], aOR 5.4 [95% CI 2.9–10.0, p ≤ 0.001) compared to outpatient clinics (1.3% [95% CI 1.1–1.6%]). CRABC proportions in hospitals varied between German regions and ranged between 2.4% (95% CI 1.6–3.5%) in the Southeast and 8.8% (95% CI 4.2–17.3%) in the Northwest. Lower CRABC proportions were observed in younger patients (< 1 year: 0.6% [95% CI 0.2–1.3%]; 1–19 years: 1.3% [95% CI 0.7–2.5%]) than adults (20–39 years: 7.7% [95% CI 4.4–13.0%]; 40–59 years: 6.2% [4.2–8.9%]; 60–79 years: 5.8% [95% CI 4.0–8.3%]). In the 20–39 year old patient age group, CRABC proportions were significantly higher for men than for women (14.6% [95% CI 8.6–23.6%] vs. 2.5% [95% CI 1.3–4.5%]). A. baumannii complex isolates from lower respiratory infections were more likely to be carbapenem-resistant than isolates from upper respiratory infections (11.4% [95% CI 7.9–16.2%] vs. 4.0% [95% CI 2.7–6.0%]; adjusted OR: 1.5 [95% CI 1.2–1.9, p ≤ 0.001]).

Conclusions

In contrast to many other regions worldwide, carbapenem resistance proportions among clinical A. baumannii complex isolates are relatively low in Germany and have declined in the last few years. Ongoing efforts in antibiotic stewardship and infection prevention and control are needed to prevent the spread of carbapenem-resistant A. baumannii complex in Germany.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00909-8.