Quality improvement initiative 'S-A-F-H' to reduce healthcare-associated neonatal sepsis in a tertiary neonatal care unit.

BACKGROUND: Neonatal sepsis is a leading cause of morbidity and mortality among admitted neonates. Healthcare-associated infection (HAI) is a significant contributor in this cohort. LOCAL PROBLEM: In our unit, 16.1% of the admissions developed sepsis during their stay in the unit. METHOD: We formed a team of all stakeholders to address the issue. The problem was analysed using various tools, and the main contributing factor was low compliance with hand hygiene and handling of intravenous lines. INTERVENTIONS: The scrub the hub/aseptic non-touch technique/five moments of hand hygiene/hand hygiene (S-A-F-H) protocol was formulated as a quality improvement initiative, and various interventions were done to ensure compliance with hand hygiene, five moments of hand hygiene, aseptic non-touch technique. The data were collected and analysed regularly with the team members, and actions were planned accordingly. RESULTS: Over a few months, the team could reduce the incidence of HAI by 50%, which has been sustained for over a year. The improvement in compliance with the various aspects of S-A-F-H increased. CONCLUSIONS: Compliance with hand hygiene steps, five moments of hand hygiene and an aseptic non-touch technique using quality improvement methodology led to a reduction in neonatal sepsis incidence in the unit. Regular reinforcement is required to maintain awareness of asepsis practices and implementation in day-to-day care and to bring about behavioural changes.

Compliance of healthcare workers in a psychiatric inpatient ward to infection control practices during the COVID-19 pandemic: a participant observation study supplemented with a self-reported survey.

BACKGROUND: As an emerging infectious disease with a heterogenous and uncertain transmission pattern, coronavirus disease 2019 (COVID-19) has created a catastrophe in healthcare-associated infections (HAIs) and posed a significant challenge to infection control practices (ICPs) in healthcare settings. While the unique characteristics of psychiatric patients and clinical settings may make the implementation of ICPs difficult, evidence is lacking for compliance with ICPs among healthcare workers (HCWs) in a psychiatric setting during the COVID-19 pandemic. METHODS: A cross-sectional multi-method study based on participant unobtrusive observation coupled with the completion of a self-administered ICP survey was conducted to assess compliance with ICPs among HCWs in a psychiatric inpatient ward in a regional hospital. An online checklist, called eRub, was used to record the performance of HCWs in hand hygiene (HH) and other essential ICPs. Furthermore, a well-validated questionnaire (i.e., Compliance with Standard Precautions Scale, CSPS) was used to collect the participants' self-reported ICP compliance for later comparison. RESULTS: A total of 2,670 ICP opportunities were observed from January to April 2020. The overall compliance rate was 42.6%. HCWs exhibited satisfactory compliance to the wearing of mask (91.2%) and the handling of clinical waste (87.5%); suboptimal compliance to the handling of sharp objects (67.7%) and linen (72.7%); and poor compliance to HH (3.3%), use of gloves (40.9%), use of personal protective equipment (20%), and disinfection of used surface/area (0.4%). The compliance rates of the nurses and support staff to HH were significantly different (χ2 = 123.25, p < 0.001). In the self-reported survey, the overall compliance rate for ICPs was 64.6%. CONCLUSION: The compliance of HCWs in a psychiatric inpatient ward to ICPs during the COVID-19 pandemic ranged from poor to suboptimal. This result was alarming. Revisions of current ICP guidelines and policies that specifically target barriers in psychiatric settings will be necessary.

Gram-negative bacterial infections in surgical intensive care unit patients following abdominal surgery: high mortality associated with Stenotrophomonas maltophilia infection.

BACKGROUND: Stenotrophomonas maltophilia, a multidrug-resistant gram-negative bacteria (GNB), is an emerging nosocomial pathogen. This study assessed the clinical outcomes of GNB infections in surgical intensive care unit (SICU) patients post-abdominal surgery, focusing on the differences between S. maltophilia and other GNBs, including Pseudomonas aeruginosa. METHODS: A retrospective study was conducted on SICU patients at Kaohsiung Chang Gung Memorial Hospital from 2010 to 2020, who developed GNB infections following abdominal surgery. RESULTS: Of 442 patients, 237 had S. maltophilia and 205 had non-S. maltophilia GNB infections (including 81 with P. aeruginosa). The overall mortality rate was 44.5%, and S. maltophilia infection emerged as a significant contributor to the mortality rate in patients with GNB infections. S. maltophilia patients had longer mechanical ventilation and SICU stays, with a 30-day mortality rate of 35.4%, higher than the non-S. maltophilia GNB (22.9%) and P. aeruginosa (21%) groups. In-hospital mortality was also higher in the S. maltophilia group (53.2%) compared to the non-S. maltophilia GNB (34.6%) and P. aeruginosa groups (29.6%). Risk factors for acquiring S. maltophilia included a higher Sequential Organ Failure Assessment score and prior broad-spectrum antibiotics use. Older age, polymicrobial infections, and elevated bilirubin were associated with increased 30-day mortality in S. maltophilia patients. CONCLUSION: S. maltophilia infections in post-abdominal surgery patients are linked to higher mortality than non-S. maltophilia GNB and P. aeruginosa infections, emphasizing the need for early diagnosis and treatment to improve outcomes.

Association of institutional masking policies with healthcare-associated SARS-CoV-2 infections in Swiss acute care hospitals during the BA.4/5 wave (CH-SUR study): a retrospective observational study.

BACKGROUND: In the initial phase of the SARS-CoV-2 pandemic, masking has been widely accepted in healthcare institutions to mitigate the risk of healthcare-associated infection. Evidence, however, is still scant and the role of masks in preventing healthcare-associated SARS-CoV-2 acquisition remains unclear.We investigated the association of variation in institutional mask policies with healthcare-associated SARS-CoV-2 infections in acute care hospitals in Switzerland during the BA.4/5 2022 wave. METHODS: SARS-CoV-2 infections in hospitalized patients between June 1 and September 5, 2022, were obtained from the "Hospital-based surveillance of COVID-19 in Switzerland"-database and classified as healthcare- or community-associated based on time of disease onset. Institutions provided information regarding institutional masking policies for healthcare workers and other prevention policies. The percentage of healthcare-associated SARS-CoV-2 infections was calculated per institution and per type of mask policy. The association of healthcare-associated SARS-CoV-2 infections with mask policies was tested using a negative binominal mixed-effect model. RESULTS: We included 2'980 SARS-CoV-2 infections from 13 institutions, 444 (15%) were classified as healthcare-associated. Between June 20 and June 30, 2022, six (46%) institutions switched to a more stringent mask policy. The percentage of healthcare-associated infections subsequently declined in institutions with policy switch but not in the others. In particular, the switch from situative masking (standard precautions) to general masking of HCW in contact with patients was followed by a strong reduction of healthcare-associated infections (rate ratio 0.39, 95% CI 0.30-0.49). In contrast, when compared across hospitals, the percentage of health-care associated infections was not related to mask policies. CONCLUSIONS: Our findings suggest switching to a more stringent mask policy may be beneficial during increases of healthcare-associated SARS-CoV-2 infections at an institutional level.

A Multidisciplinary Approach to Enhancing Sterilization Processes for Pleuravideoscopes in a Pulmonary Clinic.

PURPOSE/OBJECTIVES: The Centers for Disease Control and Prevention has highlighted the strong association between healthcare-associated infections and the reprocessing of flexible endoscopes. This process improvement project provided an evidence-based workflow analysis of pleuravideoscope reprocessing to validate and implement safe practices in the pulmonary clinic and sterile processing department. DESCRIPTION OF THE PROJECT/PROGRAM: A multidisciplinary team created an audit tool to complete infection control risk assessment using Lean Six Sigma methodology. OUTCOME: The risk assessment identified gaps in clinical practice, prompting corrective measures using a shared decision-making approach. The organization updated standard operating procedures, provided training and competency assessments, and purchased single-use pleuravideoscopes. These initiatives addressed the deficiencies and reinforced a culture of continuous process improvement and patient safety. CONCLUSION: Multidisciplinary teams should perform comprehensive reviews of facility processes and assess the risks related to infection control to identify optimal pleuravideoscope workflows for the healthcare institution. The involvement of a clinical nurse specialist is advantageous, as they possess the expertise necessary to facilitate collaborative efforts among team members spanning various departments. By leveraging the insights and skills of diverse professionals, healthcare organizations can optimize their reprocessing programs and enhance patient safety.

Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.

BACKGROUND: A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings. RESULTS: We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2. CONCLUSIONS: This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.

Whole-genome sequencing analysis of multidrug-resistant Serratia marcescens isolates in an intensive care unit in Brazil.

INTRODUCTION: Serratia marcescens is an opportunistic pathogen found ubiquitously in the environment and associated with a wide range of nosocomial infections. This multidrug-resistant bacterium has been a cause of concern for hospitals and healthcare facilities due to its ability to spread rapidly and cause outbreaks. Next generation sequencing genotyping of bacterial isolates has proven to be a valuable tool for tracking the spread and transmission of nosocomial infections. This has allowed for the identification of outbreaks and transmission chains, as well as determining whether cases are due to endogenous or exogenous sources. Evidence of nosocomial transmission has been gathered through genotyping methods. The aim of this study was to investigate the genetic diversity of carbapenemase-producing S. marcescens in an outbreak at a public hospital in Cuiaba, MT, Brazil. METHODOLOGY: Ten isolates of S. marcenses were sequenced and antibiotic resistance profiles analyzed over 12 days. RESULTS: The isolates were clonal and multidrug resistant. Gentamycin and tigecycline had sensitivity in 90% and 80% isolates, respectively. Genomic analysis identified several genes that encode ß-lactamases, aminoglycoside-modifying enzymes, efflux pumps, and other virulence factors. CONCLUSIONS: Systematic surveillance is crucial in monitoring the evolution of S. marcescens genotypes, as it can lead to early detection and prevention of outbreaks.

Disinfection of sink drains to reduce a source of three opportunistic pathogens, during Serratia marcescens clusters in a neonatal intensive care unit.

OBJECTIVE: Evaluate the effects of five disinfection methods on bacterial concentrations in hospital sink drains, focusing on three opportunistic pathogens (OPs): Serratia marcescens, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. DESIGN: Over two years, three sampling campaigns were conducted in a neonatal intensive care unit (NICU). Samples from 19 sink drains were taken at three time points: before, during, and after disinfection. Bacterial concentration was measured using culture-based and flow cytometry methods. High-throughput short sequence typing was performed to identify the three OPs and assess S. marcescens persistence after disinfection at the genotypic level. SETTING: This study was conducted in a pediatric hospitals NICU in Montréal, Canada, which is divided in an intensive and intermediate care side, with individual rooms equipped with a sink. INTERVENTIONS: Five treatments were compared: self-disinfecting drains, chlorine disinfection, boiling water disinfection, hot tap water flushing, and steam disinfection. RESULTS: This study highlights significant differences in the effectiveness of disinfection methods. Chlorine treatment proved ineffective in reducing bacterial concentration, including the three OPs. In contrast, all other drain interventions resulted in an immediate reduction in culturable bacteria (4-8 log) and intact cells (2-3 log). Thermal methods, particularly boiling water and steam treatments, exhibited superior effectiveness in reducing bacterial loads, including OPs. However, in drains with well-established bacterial biofilms, clonal strains of S. marcescens recolonized the drains after heat treatments. CONCLUSIONS: Our study supports thermal disinfection (>80°C) for pathogen reduction in drains but highlights the need for additional trials and the implementation of specific measures to limit biofilm formation.

Investigation of multiple nosocomial infections using a semi-Markov multi-state model.

BACKGROUND: The prevalence of multiple nosocomial infections (MNIs) is on the rise, however, there remains a limited comprehension regarding the associated risk factors, cumulative risk, probability of occurrence, and impact on length of stay (LOS). METHOD: This multicenter study includes all hospitalized patients from 2020 to July 2023 in two sub-hospitals of a tertiary hospital in Guangming District, Shenzhen. The semi-Markov multi-state model (MSM) was utilized to analyze risk factors and cumulative risk of MNI, predict its occurrence probability, and calculate the extra LOS of nosocomial infection (NI). RESULTS: The risk factors for MNI include age, community infection at admission, surgery, and combined use of antibiotics. However, the cumulative risk of MNI is lower than that of single nosocomial infection (SNI). MNI is most likely to occur within 14 days after admission. Additionally, SNI prolongs LOS by an average of 7.48 days (95% Confidence Interval, CI: 6.06-8.68 days), while MNI prolongs LOS by an average of 15.94 days (95% CI: 14.03-18.17 days). Furthermore, the more sites of infection there are, the longer the extra LOS will be. CONCLUSION: The longer LOS and increased treatment difficulty of MNI result in a heavier disease burden for patients, necessitating targeted prevention and control measures.

Plasmid genomic epidemiology of carbapenem-hydrolysing class D ß-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021.

Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.

Compliance and adherence to hand hygiene practices for effective infection control.

Hand hygiene (HH) is the most effective way to curb the spread of healthcare-associated infections. Nonetheless, healthcare personnel encounter difficulties in adhering to WHO HH recommendations. This study aimed to investigate HH compliance and adherence after the implementation of an action plan in a municipal hospital in Moscow. An initial evaluation of HH compliance among clinical health workers was carried out in June 2022 according to the WHO HH guidelines followed by a 3-month re-audit of HH practices. The results were compared to the baseline to evaluate compliance and adherence to HH among healthcare personnel. From June to September 2022, there were 2,732 moments of contact with patients or their immediate surroundings. The HH total compliance rate significantly (p < 0.05) increased from 52.3% in June 2022 to 83.3% in September 2022 with a 75% overall total compliance rate. The profession-specific total compliance rate was highest among nurses (79.6%) and lowest among ancillary staff (69.7%). Staff were also more adherent to the before-moments compared to the after-moments of the HH guidelines. Monthly re-audits and providing feedback resulted in a significant improvement in compliance and adherence with HH guidelines after implementation of the action plan.

A Quality Improvement Project to Increase Infection Control Compliance Among Endoscopy Staff at a Large Urban Medical Center.

Although nurses and other healthcare professionals play a key role in preventing hospital-associated infections, studies show that infection control compliance rates have remained low. The purpose of this quality improvement project was to increase infection control compliance of hand hygiene and procedure room disinfection among endoscopy staff at a large urban medical center in Cincinnati, Ohio. This quality improvement project provided an education session on current evidence-based infection control guidelines to 20 participants, including registered nurses and technicians within the endoscopy department. Direct observational audits were conducted 4 weeks before and 4 weeks after the education session, measuring compliance with hand sanitizer, soap and water, and procedure room disinfection, over a period of 150 days. The project goals were met, as hand sanitizer compliance improved by 12%-83%; overall soap and water compliance improved by 20%-75%; and endoscopy procedure room disinfection compliance improved by 14%-92%.

A Trial of Automated Outbreak Detection to Reduce Hospital Pathogen Spread.

BACKGROUND: Detection and containment of hospital outbreaks currently depend on variable and personnel-intensive surveillance methods. Whether automated statistical surveillance for outbreaks of health care-associated pathogens allows earlier containment efforts that would reduce the size of outbreaks is unknown. METHODS: We conducted a cluster-randomized trial in 82 community hospitals within a larger health care system. All hospitals followed an outbreak response protocol when outbreaks were detected by their infection prevention programs. Half of the hospitals additionally used statistical surveillance of microbiology data, which alerted infection prevention programs to outbreaks. Statistical surveillance was also applied to microbiology data from control hospitals without alerting their infection prevention programs. The primary outcome was the number of additional cases occurring after outbreak detection. Analyses assessed differences between the intervention period (July 2019 to January 2022) versus baseline period (February 2017 to January 2019) between randomized groups. A post hoc analysis separately assessed pre-coronavirus disease 2019 (Covid-19) and Covid-19 pandemic intervention periods. RESULTS: Real-time alerts did not significantly reduce the number of additional outbreak cases (intervention period versus baseline: statistical surveillance relative rate [RR]=1.41, control RR=1.81; difference-in-differences, 0.78; 95% confidence interval [CI], 0.40 to 1.52; P=0.46). Comparing only the prepandemic intervention with baseline periods, the statistical outbreak surveillance group was associated with a 64.1% reduction in additional cases (statistical surveillance RR=0.78, control RR=2.19; difference-in-differences, 0.36; 95% CI, 0.13 to 0.99). There was no similarly observed association between the pandemic versus baseline periods (statistical surveillance RR=1.56, control RR=1.66; difference-in-differences, 0.94; 95% CI, 0.46 to 1.92). CONCLUSIONS: Automated detection of hospital outbreaks using statistical surveillance did not reduce overall outbreak size in the context of an ongoing pandemic. (Funded by the Centers for Disease Control and Prevention; ClinicalTrials.gov number, NCT04053075. Support for HCA Healthcare's participation in the study was provided in kind by HCA.).

Ochrobactrum Anthropi; an Unusual Cause of Bacteremia and Pneumonia: A Case Report and a Brief Review of the Literature.

Background: Ochrobactrum anthropi spp. is a non-enteric, aerobic gram-negative bacillus that has been reported to cause sepsis and occasionally bacteremia in both immunocompetent and immunocompromised hosts. This bacterium is capable of surviving in various habitats, but due to its affinity for aqueous environments, O. anthropi is hypothesized to have an affinity for indwelling plastic devices and other foreign bodies.

Case Presentation: We report a case of a 66 y/o male with a history of polysubstance abuse disorder admitted for toxic metabolic encephalopathy and found to have bronchopneumonia and bacteremia secondary to O. anthropi infection resulting in sepsis and cardiopulmonary arrest.

Discussion: Ochrobactrum spp. is an unusual pathogen of low virulence and has been noted to cause bacteremia and occasionally sepsis in both immunocompetent and immunosuppressed patients. Isolation of this pathogen in the appropriate setting should be considered a true pathogen and treated as such to avoid sequela of this infection.

Conclusion: This case report and literature review suggest that Ochrobactrum anthropi appears more frequently as a pathogen in nosocomial infections than suggested in the literature.

Point-of-Care Electrochemical Immunosensor Applied against Nosocomial Infection: Staphylococcus aureus Detection in Human Hand Skin.

Staphylococcus aureus is an important pathogen that causes nosocomial infections, resulting in unacceptable morbidity and mortality rates. In this work, we proposed the construction of a nanostructured ZnO-based electrochemical immunosensor for qualitative and semiquantitative detection of S. aureus using simple methods for growing zinc oxide nanorods (ZnO NRs) on a sensor board and immobilizing the anti-S. aureus antibody on ZnO NRs through cystamine and glutaraldehyde. The immunosensor detected S. aureus in the 103-107 colony-forming unit (CFU) mL-1 range and showed a limit of detection (LoD) around 0.792 × 103 CFU mL-1. Beyond a satisfactory LoD, the developed immunosensor presented other advantages, such as high versatility for point-of-care assays and a suitable selective factor that admits the detection of the S. aureus concentration range in human hand skin after washing. Moreover, the immunosensor showed the potential to be an excellent device to control nosocomial infection by detecting the presence of S. aureus in human hand skin.

[Automated surveillance and risk prediction with the aim of risk-stratified infection control and prevention (RISK PRINCIPE)]. / Automatisierte Surveillance und Risikovorhersage mit dem Ziel einer risikostratifizierten Infektionskontrolle und -prävention (RISK Prediction for Risk-stratified Infection Control and Prevention).

Healthcare-associated infections (HCAIs) represent an enormous burden for patients, healthcare workers, relatives and society worldwide, including Germany. The central tasks of infection prevention are recording and evaluating infections with the aim of identifying prevention potential and risk factors, taking appropriate measures and finally evaluating them. From an infection prevention perspective, it would be of great value if (i) the recording of infection cases was automated and (ii) if it were possible to identify particularly vulnerable patients and patient groups in advance, who would benefit from specific and/or additional interventions.To achieve this risk-adapted, individualized infection prevention, the RISK PRINCIPE research project develops algorithms and computer-based applications based on standardised, large datasets and incorporates expertise in the field of infection prevention.The project has two objectives: a) to develop and validate a semi-automated surveillance system for hospital-acquired bloodstream infections, prototypically for HCAI, and b) to use comprehensive patient data from different sources to create an individual or group-specific infection risk profile.RISK PRINCIPE is based on bringing together the expertise of medical informatics and infection medicine with a focus on hygiene and draws on information and experience from two consortia (HiGHmed and SMITH) of the German Medical Informatics Initiative (MII), which have been working on use cases in infection medicine for more than five years.

Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis.

We identified 23 cases of Mycobacterium immunogenum respiratory acquisition linked to a colonized plumbing system at a new hospital addition. We conducted a genomic and epidemiologic investigation to assess for clonal acquisition of M. immunogenum from hospital water sources and improve understanding of genetic distances between M. immunogenum isolates. We performed whole-genome sequencing on 28 M. immunogenum isolates obtained from August 2013 to July 2021 from patients and water sources on four intensive care and intermediate units at an academic hospital. Study hospital isolates were recovered from 23 patients who experienced de novo respiratory isolation of M. immunogenum and from biofilms obtained from five tap water outlets. We also analyzed 10 M. immunogenum genomes from previously sequenced clinical (n = 7) and environmental (n = 3) external control isolates. The 38-isolate cohort clustered into three clades with pairwise single-nucleotide polymorphism (SNP) distances ranging from 0 to 106,697 SNPs. We identified two clusters of study hospital isolates in Clade 1 and one cluster in Clade 2 for which clinical and environmental isolates differed by fewer than 10 SNPs and had less than 0.5% accessory genome variation. A less restrictive combined threshold of 40 SNPs and 5% accessory genes reliably captured additional isolates that met clinical criteria for hospital acquisition, but 12 (4%) of 310 epidemiologically unrelated isolate pairs also met this threshold. Core and accessory genome analyses confirmed respiratory acquisition of multiple clones of M. immunogenum from hospital water sources to patients. When combined with epidemiologic investigation, genomic thresholds accurately distinguished hospital acquisition.