The global outbreak of Mycobacterium chimaera infections in cardiac surgery-a systematic review of whole-genome sequencing studies and joint analysis

Genome-scale analysis of Mycobacterium avium complex isolates from Portugal reveals extensive genetic diversity

Opportunist infections caused by nontuberculous mycobacteria (NTM) have emerged as a significant public health problem. Among these, species of the Mycobacterium avium complex (MAC) are the main responsible for the increase in the number of human disease cases. In order to address the current needs in the detection and surveillance of MAC disease cases, we evaluated different species classification methodologies (BLASTn-based marker-gene approach, Kraken v2, rMLST and MLST databases) and their congruence with a core-SNP phylogenetic approach, based on whole genome sequencing (WGS) data. For this purpose, we used a collection of 142 MAC isolates from Portuguese patients diagnosed between 2014 and 2022. The marker-gene approach (based on the rpoB, hsp65 and groEL genes), showed the best results, allowing the identification of the 142 MAC isolates to the species/subspecies level (M. avium subsp. hominissuis, M. intracellulare, M. intracellulare subsp. chimaera, M. intracellulare subsp. yongonense, M. marseillence and M. colombiense). Additionally, we performed drug susceptibility testing that confirmed clarithromycin efficacy as a first-line treatment for MAC disease, as 93 % of the Portuguese isolates were susceptible. Using a core-SNP approach we also performed an in-depth phylogenetic analysis within each identified species group, and despite the high genetic diversity within the MAC species, we were able to clearly distinguish all the species/subspecies and identify genetic clusters with epidemiological potential. We highlight not only the need for the standardization of an appropriate genotyping approach for species identification and management of MAC disease, but also a more robust large-scale WGS data analysis, in a One Health perspective, in order to identify potential routes of transmission.

The State-of-the-Art of Mycobacterium chimaera Infections and the Causal Link with Health Settings: A Systematic Review

(1) Background. A definition of healthcare-associated infections is essential also for the attribution of the restorative burden to healthcare facilities in case of harm and for clinical risk management strategies. Regarding M. chimaera infections, there remains several issues on the ecosystem and pathogenesis. We aim to review the scientific evidence on M. chimaera beyond cardiac surgery, and thus discuss its relationship with healthcare facilities. (2) Methods. A systematic review was conducted on PubMed and Web of Science on 7 May 2024 according to PRISMA 2020 guidelines for reporting systematic reviews, including databases searches with the keyword "Mycobacterium chimaera". Article screening was conducted by tree authors independently. The criterion for inclusion was cases that were not, or were improperly, consistent with the in-situ deposition of aerosolised M. chimaera. (3) Results. The search yielded 290 eligible articles. After screening, 34 articles (377 patients) were included. In five articles, patients had undergone cardiac surgery and showed musculoskeletal involvement or disseminated infection without cardiac manifestations. In 11 articles, respiratory specimen reanalyses showed M. chimaera. Moreover, 10 articles reported lung involvement, 1 reported meninges involvement, 1 reported skin involvement, 1 reported kidney involvement after transplantation, 1 reported tendon involvement, and 1 reported the involvement of a central venous catheter; 3 articles reported disseminated cases with one concomitant spinal osteomyelitis. (4) Conclusions. The scarce data on environmental prevalence, the recent studies on M. chimaera ecology, and the medicalised sample selection bias, as well as the infrequent use of robust ascertainment of sub-species, need to be weighed up. The in-house aerosolization, inhalation, and haematogenous spread deserve experimental study, as M. chimaera cardiac localisation could depend to transient bacteraemia. Each case deserves specific ascertainment before tracing back to the facility, even if M. chimaera represents a core area for healthcare facilities within a framework of infection prevention and control policies.

Clinical and genomic features of Mycobacterium avium complex: a multi-national European study

BACKGROUND

The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated.

METHODS

Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort.

RESULTS

Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04-0.28, p < 0.001 and OR 0.11 95% CI 0.02-0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%).

CONCLUSIONS

This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence.

Formative evaluation and structural analysis of non-tuberculosis mycobacterial biofilm using material pieces

Non-tuberculosis mycobacteria (NTM) can form biofilms on diverse artificial surfaces. In the present study, we induced NTM biofilm formation on materials used in various medical devices, evaluated the total amount of biofilm, and observed the ultrastructure by scanning electron microscopy.

Construction of a postoperative infection outbreak investigation form: A tool for early detection and control measures

BACKGROUND

To develop an investigation form for postoperative infection outbreak (PIO), and to identify sources of the outbreak in the early stage.

METHODS

After an exhaustive literature review, we used the Delphi method to determine the indicators and relative risk scores of the assessment tools through 2 rounds of specialist consultation and overall consideration of the opinions and suggestions of 20 specialists.

RESULTS

A total of 203 studies of PIO were eligible for inclusion. The mean authority coefficient (Cr) was 0.87. Kendall's W coefficient of the specialist consultation was 0.704 after 2 rounds of consultation (P < .005), suggesting that the specialists had similar opinions. Based on 4 primary items and 19 secondary items of the source of PIO, and tripartite distribution characteristics of infected patients, we constructed the PIO investigation form.

CONCLUSIONS

The PIO investigation form can be used in the investigation of the early-stage cluster of cases, it's a prerequisite for taking effective control measures, avoiding PIO occurrence. However, the effect of the investigation form needs to be further evaluated.

Microbiological Surveillance of Heater-Cooler Units Used in Cardiothoracic Surgery for Detection of Mycobacterium chimaera

Mycobacterium chimaera is a nontuberculous mycobacterium that was identified as causative agent in a global outbreak of severe infections following open-chest cardiothoracic surgery. Heater-cooler units (HCUs), which were contaminated during the manufacturing process, were elucidated as the origin of this outbreak. Regular surveillance of water-containing HCUs used for cardiac surgery was recommended as one preventive measure. We present data on the occurrence of M. chimaera and other mycobacterial pathogens in different HCUs from one surgical center in Germany over a 42-month period. Water samples and swabs from seven different HCUs were taken between 2015 and 2018, and mycobacteria were detected in 50.6% (78/154) of water samples and 21.1% (4/19) of swabs. M. chimaera accounted for the majority of detected pathogens (77/83 isolates in water samples), but other species such as Mycobacterium gordonae were also found. Despite strict adherence to an intensified, regular disinfection procedure, the majority of HCUs remained positive for mycobacteria until the end of the study. In conclusion, additional measures are needed to reduce the risk of intraoperative transmission of M. chimaera, and our observations underscore the inherent infections risks associated with water-containing medical devices.

Environmental Sources and Transmission of Nontuberculous Mycobacteria

The field of environmental nontuberculous mycobacteria (NTM) is benefiting from a new era of genomics that has catapulted our understanding of preferred niches, transmission, and outbreak investigations. The ability to forecast environmental features that promote or reduce environmental NTM prevalence will greatly improve with coordinated environmental sampling and by elevating the necessity for uniform disease notifications. Studies that synergize environmental biology, isolate notifications, and comparative genomics in prospective, longitudinal studies, particularly during climate changes and weather events, will be useful to solve longstanding NTM public health quandaries.

Epidemiological and Molecular Investigation of the Heater-Cooler Unit (HCU)-Related Outbreak of Invasive Mycobacterium chimaera Infection Occurred in Italy

BACKGROUND

From 2013 onwards, a large outbreak of Mycobacterium chimaera (MC) invasive infection, which was correlated with the use of contaminated heater-cooler units (HCUs) during open chest surgery, was reported from all over the world. Here, we report the results of the epidemiological and molecular investigations conducted in Italy after the alarm raised about this epidemic event.

METHODS

MC strains isolated from patients or from HCU devices were characterized by genomic sequencing and molecular epidemiological analysis.

RESULTS

Through retrospective epidemiological analysis conducted between January 2010 and December 2022, 40 possible cases of patients infected with MC were identified. Thirty-six strains isolated from these patients were analysed by whole genome sequencing (WGS) and were found to belong to the genotypes 1.1 or 1.8, which are the genotypes correlated with the outbreak. Most of the cases presented with prosthetic valve endocarditis, vascular graft infection or disseminated infection. Among the cases found, there were 21 deaths. The same analysis was carried out on HCU devices. A total of 251 HCUs were found to be contaminated by MC; genotypes 1.1 or 1.8 were identified in 28 of those HCUs.

CONCLUSIONS

To ensure patients' safety and adequate follow-up, clinicians and general practitioners were made aware of the results and public health measures, and recommendations were issued to prevent further cases in the healthcare settings. The Italian Society of Cardiac Surgery performed a national survey to assess the incidence of HCU-related MC prosthetic infections in cardiac surgery. No cases were reported after HCU replacement or structural modification and disinfection and possibly safe allocation outside surgical rooms.

Clinical characteristics and outcome of Mycobacterium chimaera infections after cardiac surgery: systematic review and meta-analysis of 180 heater-cooler unit-associated cases

OBJECTIVES

Since 2013, heater-cooler unit (HCU) associated Mycobacterium chimaera infections linked to a global outbreak have been described. These infections were characterised by high morbidity and mortality due to delayed diagnosis, as well as challenges in antimycobacterial and surgical therapy. This study aimed to investigate the clinical characteristics and outcome of published cases of HCU-associated M. chimaera infections.

METHODS

We searched PubMed and the Web of Science until 15 June 2022 for case reports, case series, and cohort studies, without language restriction, on patients with M. chimaera infection and a prior history of cardiac surgery. In this systematic review of case reports, no risk of bias assessment could be performed. Clinical, microbiological, and radiological features were recorded. Logistic regression and time-to-event analyses were performed to identify the potential factors associated with better survival.

RESULTS

One hundred eighty patients from 54 publications were included. Most patients underwent surgical aortic valve (67.0%; 118/176 of patients with available data) or combined aortic valve and root replacement (15.3%; 27/176). The median period between the time point of surgery and the first symptoms was 17 months (interquartile range 13-26 months). The overall case fatality rate was 45.5% (80/176), with a median survival of 24 months after the initiation of antimycobacterial therapy or diagnosis. A reoperation (including the removal or exchange of foreign material) was associated with better survival in multivariate logistic regression (OR 0.32 for lethal events; 95% CI 0.12-0.79; p 0.015) and in time-to-event analysis (p 0.0094).

DISCUSSION

This systematic review and meta-analysis confirm the high overall mortality of HCU -associated disseminated M. chimaera infections after cardiac surgery. A reoperation seems to be associated with better survival. Physicians have to stay aware of this infection, as patients might still be present today due to the long latency period.

Clean clothes or dirty clothes? Outbreak investigation of carbapenem-resistant Acinetobacter baumannii related to laundry contamination through multilocus sequence typing (MLST)

OBJECTIVE

To investigate the source in an outbreak of carbapenem-resistant Acinetobacter baumannii (CRA) in a general hospital due to contamination of a laundry evaporative cooler and the laundry environment using multilocus sequence typing (MLST).

METHODS

For CRA culture, clinical samples were collected from infected patients and close contacts, and environmental sampling was performed in patient surroundings and laundry facilities. MLST was used for the molecular typing of representative CRA isolates. Bacterial isolates with identical sequence types were considered epidemiologically linked and attributable to the same source. OXA genes in Acinetobacter baumannii were detected using polymerase chain reaction (PCR).

RESULTS

In total, 58 patients were affected in this outbreak. The mean patient age was 75.3, and 50% were female. The most common diagnoses at admission were skin and soft-tissue infection (n = 12, 20.7%) and pneumonia (n = 12, 20.7%). OXA-23 was positive in 64.7% of isolates. A CRA isolate from the evaporative cooler in the laundry was identical to that of 11 patients across 3 wards, belonging to ST345. Isolates from 3 laundry linen racks were identical to those of 7 patients from 3 wards, classified as ST1145. Isolates found on another linen rack and a pajama shelf were identical to isolates from 3 other patients from 2 wards, belonging to ST2207. There was no significant difference between sequence type distributions of clinical and environmental isolates (P = .12), indicating high likelihood of CRA originating from the same source.

CONCLUSIONS

MLST confirmed that contamination of the laundry evaporative cooler and surrounding environment caused a polyclonal CRA hospital outbreak. Hospital laundry is an important area for infection control and outbreak investigations of CRA.

Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards

Pathogen genomics has transitioned rapidly from the research setting into a powerful tool now routinely used in public health microbiology, for surveillance, outbreak investigations and disease control. As these investigations can have significant public health, treatment and legal impacts, we must ensure the accuracy of these results through validation of testing processes. For laboratories working in this space, it is important to approach this work with a quality and accreditation framework in mind, working towards implementation of quality systems and test validation that meet international regulatory standards. Here we outline the key international standards and processes that lead toward accreditation for pathogen genomics.

M ycobacterium avium complex genomics and transmission in a London hospital

BACKGROUND

Non-tuberculous mycobacteria (NTM) are environmental microorganisms and opportunistic pathogens in individuals with pre-existing lung conditions such as cystic fibrosis (CF) and non-CF bronchiectasis. While recent studies of Mycobacterium abscessus have identified transmission within single CF centres as well as nationally and globally, transmission of other NTM species is less well studied.

METHODS

To investigate the potential for transmission of the Mycobacterium avium complex (MAC) we sequenced 996 isolates from 354 CF and non-CF patients at the Royal Brompton Hospital (London, UK; collected 2013-2016) and analysed them in a global context. Epidemiological links were identified from patient records. Previously published genomes were used to characterise global population structures.

RESULTS

We identified putative transmission clusters in three MAC species, although few epidemiological links could be identified. For M. avium, lineages were largely limited to single countries, while for Mycobacterium chimaera, global transmission clusters previously associated with heater-cooler units (HCUs) were found. However, the immediate ancestor of the lineage causing the major HCU-associated outbreak was a lineage already circulating in patients.

CONCLUSIONS

CF and non-CF patients shared transmission chains, although the lack of epidemiological links suggested that most transmission is indirect and may involve environmental intermediates or asymptomatic carriage in the wider population.

Longitudinal increase in the detection rate of Mycobacterium chimaera in heater-cooler device-derived water samples

BACKGROUND

Colonization with Mycobacterium chimaera and other non-tuberculous mycobacteria (NTM) has been reported for heater-cooler devices (HCDs) produced by several manufacturers. Up until now, exclusively LivaNova (London, UK) HCDs have been associated with M. chimaera infections after cardiac surgery. The vast majority of studies on HCD colonization were cross-sectional.

AIM

We were interested in longitudinal dynamics of mycobacterial growth in HCD water samples and analysed data of a prospective mycobacterial surveillance of five LivaNova 3T HCDs.

METHODS

Five LivaNova HCDs were subjected to prospective mycobacterial surveillance. For each HCD and the total of HCDs, results of mycobacterial detection were analyzed. Logistic regression was applied to model the association between growth of any NTM or M. chimaera and duration of HCD use.

RESULTS

Non-tuberculous mycobacteria were isolated in 319 (48.0%, 21 water samples grew more than one mycobacterial species) of a total of 665 water samples. The most frequently detected species were M. chimaera (N = 247/319, 77.4%), Mycobacterium gordonae (46/319, 14.4%) and Mycobacterium paragordonae (34/319, 10.7%). Detection rates increased prospectively for any NTM (odds ratio (OR) per year in use: 1.60, 95% confidence interval (CI) 1.17-2.24, P<0.001) and for M. chimaera (OR per year in use: 1.67, 95% CI 1.11-2.57, P<0.01).

CONCLUSION

Longer duration of HCD use was associated with higher detection rates for any NTM and M. chimaera, respectively.

Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections

Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.