Serratia marcescens Colonization in a Neonatal Intensive Care Unit Has Multiple Sources, with Sink Drains as a Major Reservoir

Keeping Your Neonatal Intensive Care Unit Clean: The Hospital Environment as a Potential Source of Health Care-Associated Infections

The patient's environment is an important (and often overlooked) source of pathogen exposure for patients in the neonatal intensive care unit (NICU) setting. Environmental surfaces in the NICU, including those frequently touched during the course of patient care, may be contaminated with potential pathogens. In this review, we highlight environmental reservoirs that lead to health care-associated infection risks in the NICU environment and provide examples from medical literature. Finally, we provide a few suggested interventions to mitigate these environmental risks in your NICU.

Longitudinal bacterial community dynamics and sodium hypochlorite intervention in a newly built university building

Urbanisation and building advancements have increased microbial growth in indoor environments, altering human interactions with these microorganisms. Restrooms and their sinks harbour diverse bacterial communities, that differ from those found in natural environments, that could have negative implications for human health. Over two and a half years, this study examined the diversity, temporal dynamics, and resilience of bacterial communities in restroom sink P-traps in a newly built university building. Structured into two phases, the first phase consisted of continuous monitoring of bacterial community dynamics for two years (n = 352), while the second phase involved an intervention with sodium hypochlorite (bleach) and subsequent sampling (n = 132). In the first phase, we show that sink communities converge, becoming more compositionally similar to other sinks within the building. Bacterial families such as Rhodocyclaceae and Flavobacteriaceae dominated across the sinks, and others such as Comamonadaceae, Moraxellaceae and Enterbacteriaceae were highly prevalent. When comparing bacterial structure and composition to other sinks located on the university campus, the mean bacterial dissimilarity decreased over time, indicating compositional similarity, particularly with the newer buildings on campus. The second phase demonstrated resilience by the bacterial sink communities. Following bleach treatments, a distinct increase in Acinetobacter was observed. However, by the fourth week after bleach invention, bacterial communities had re-established to levels observed prior to treatment. This study had the unique opportunity to sample a newly built building before occupancy and for the subsequent two and a half years. The findings provide crucial insights into the development and resilience of sink P-trap bacterial communities in restrooms, laying the groundwork for more targeted approaches to disinfection strategies.

Serratia marcescens outbreak in a neonatal intensive care unit associated with contaminated handwashing sinks

PURPOSE

This article describes the origin of a S. marcescens outbreak in a neonatal intensive care unit (NICU).

MATERIALS AND METHODS

A retrospective case-control study including 12 S. marcescens-positive and 22 S. marcescens-negative neonates in the NICU was performed to identify the source of the outbreak. S. marcescens isolates were collected during the outbreak and analyzed using whole-genome sequencing (WGS). IQ-Tree software, BEAST2 software package and SCOTTI software were used to construct a phylogenetic tree and a propagation path map.

RESULTS

The index case occurred on February 21st and outbreak ended on March 9th, 2021, affecting a total of 12 neonates (2 with S. marcescens infection and 10 with S. marcescens colonization). Multivariate logistic regression identified that the distance of <0.8 m between the bed unit and the sink (odds ratio [OR], 20.50; 95 % confidence interval [CI], 1.09-384.86), a large number of rotating nurses within a week (OR 2.58, 95 % CI, 1.09-6.11) and use of humidification water in the incubator (OR 189.70, 95 % CI, 2.76-13027.31) were significant increased risk factors for S. marcescens infection or colonization in the outbreak. WGS sifted out a predominant clone between contaminated handwashing sinks and patients, suggesting that cross-transmission was involved in the dissemination of S. marcescens.

CONCLUSION

Contaminated handwashing sinks can be a communication intermediary of S. marcescens infection or colonization of neonates in the NICU. A distance of <0.8 m between the bed unit and the sink, and a large number of rotating nurses might play important roles in this outbreak. Attention should be paid to sinks contamination and contact transmission to prevent outbreaks.

The drainome: longitudinal metagenomic characterization of wastewater from hospital ward sinks to characterize the microbiome and resistome and to assess the effects of decontamination interventions

BACKGROUND

Hospital drains and water interfaces are implicated in nosocomial transmission of pathogens. Metagenomics can assess the microbial composition and presence of antimicrobial resistance genes in drains ('the drainome') but studies applying these methods longitudinally and to assess infection control interventions are lacking.

AIM

To apply long-read metagenomics coupled with microbiological measurements to investigate the drainome and assess the effects of a peracetic-acid-containing decontamination product.

METHODS

Twelve-week study in three phases: a baseline phase, an intervention phase of enhanced decontamination with peracetic acid, and a post-intervention phase. Five hospital sink drains on an intensive care unit were sampled twice weekly. Each sample had: (1) measurement of total viable count (TVC); (2) metagenomic analyses including (i) taxonomic classification of bacteria and fungi (ii), antibiotic resistance gene detection, (iii) plasmid identification; and (3) immunochromatographic detection of antimicrobial residues.

FINDINGS

Overall TVCs remain unchanged in the intervention phase (+386 cfu/mL, SE 705, P = 0.59). There was a small but significant increase in the microbial diversity in the intervention phase (-0.07 in Simpson's index, SE 0.03, P = 0.007), which was not sustained post-intervention (-0.05, SE 0.03, P = 0.08). The intervention was associated with increased relative abundance of the Pseudomonas genus (18.3% to 40.5% (+22.2%), SE 5.7%, P < 0.001). Extended spectrum β-lactamases were found in all samples, with NDM-carbapenemase found in three drains in six samples. Antimicrobial residues were detected in a large proportion of samples (31/115, 27%), suggesting use of sinks for non-handwashing activities.

CONCLUSION

Metagenomics and other measurements can determine the composition of the drainome and assess the effectiveness of decontamination interventions.

Antimicrobial Resistance Pattern, Predisposing Factors, and Outcome of Serratia Infection in Patients Treated at a Secondary-Care Hospital in Oman: A 5-Year Retrospective Study

Background

Serratia has emerged as an important nosocomial opportunistic pathogen, often associated with serious infections. We investigated the antimicrobial resistance trends, predisposing factors, and infection outcomes associated with Serratia species isolated in a secondary-care hospital in Oman.

Materials and Methods

A retrospective study was conducted at a secondary-care hospital in the northern region of Oman after receiving approval from the research ethics and approval committee of Oman. The relevant data of patients diagnosed with Serratia infection during 2017-2021 was extracted from the Sohar Hospital health records. We statistically analyzed the data using the statistical software STATA version 14.

Results

A total of 257 non-duplicate Serratia strains were studied. S. marcescens was the predominant (79.4%) isolated species. Serratia strains were more frequently isolated from males (51.4%). The most affected were older people aged > 60 years (29.4%), infants (28%), and patients treated at critical care units. Serratia has demonstrated high resistance to beta-lactams. The susceptibility rates of Serratia strains to tigecycline, ciprofloxacin, trimethoprim-sulfamethoxazole, gentamicin, amikacin, piperacillin-tazobactam, imipenem, and meropenem was high. Septicemia, pneumonia, mechanical ventilation, and hemodialysis were the independent risk factors for increased mortality among studied subjects (P < 0.05).

Conclusions

Our study results recommend empirical therapy with trimethoprim-sulfamethoxazole, piperacillin-tazobactam, aminoglycosides, and ciprofloxacin as first-line drugs for Serratia infection. The emergence of ESBL producers and carbapenem-resistant strains is worrisome. Regular updating of physicians' knowledge about antimicrobial profiles, antibiotic prescription policies, and infection control measures is necessary to combat antimicrobial resistance and improve outcomes.

A narrative review and update on drain-related outbreaks

BACKGROUND

Outbreaks linked to hospital drainage systems are well reported, and continue to present challenges to incident management teams. Such outbreaks can be protracted and complex, with multi-modal strategies being required for remediation.

AIM

To summarize recent drain-related outbreaks, investigate whether multi-modal control measures are being implemented, and determine any antecedent factors.

METHODS

Databases were searched for drain-related outbreaks over a 5-year period. Search terms employed included 'healthcare drainage outbreaks', 'drain outbreaks', 'drainage system outbreaks', 'sink outbreaks' and 'shower outbreaks'. Information was collected on country of origin, pathogens involved, unit affected, drain types, patient numbers, drainage system interventions, type of drain disinfectant, infection control interventions, typing method, outcomes and any antecedent factors.

FINDINGS

Nineteen drain-related outbreak studies were reviewed. The majority of incidents were due to carbapenemase-producing Enterobacterales, and were from critical care settings. Most (16/19) studies recognized the need for a multi-modal approach. Information on the success of interventions was not documented for all incidents, but 13/19 studies reported no further cases after control measures. Variation in the choice of agent and frequency of application exists with regards to drain disinfection. Seven studies discussed antecedent factors.

CONCLUSION

Despite drain-related outbreaks being reported for the last 24 years and review articles on the subject, outbreaks continue to pose significant challenges. There is currently no UK guidance on the management of drain-related outbreaks or the design of new buildings to mitigate the risk. Addressing the challenges from hospital drainage systems should be considered a priority by agencies and guidance developers.

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.

Nosocomial outbreak caused by disinfectant-resistant Serratia marcescens in an adult intensive care unit, Hungary, February to March 2022

In 2022, an outbreak with severe bloodstream infections caused by Serratia marcescens occurred in an adult intensive care unit (ICU) in Hungary. Eight cases, five of whom died, were detected. Initial control measures could not stop the outbreak. We conducted a matched case-control study. In univariable analysis, the cases were more likely to be located around one sink in the ICU and had more medical procedures and medications than the controls, however, the multivariable analysis was not conclusive. Isolates from blood cultures of the cases and the ICU environment were closely related by whole genome sequencing and resistant or tolerant against the quaternary ammonium compound surface disinfectant used in the ICU. Thus, S. marcescens was able to survive in the environment despite regular cleaning and disinfection. The hospital replaced the disinfectant with another one, tightened the cleaning protocol and strengthened hand hygiene compliance among the healthcare workers. Together, these control measures have proved effective to prevent new cases. Our results highlight the importance of multidisciplinary outbreak investigations, including environmental sampling, molecular typing and testing for disinfectant resistance.

A rare case of successful treatment of peritoneal dialysis patient with Serratia marcescens peritonitis without catheter removal: case report and literature review

Serratia marcescens, as a Gram-negative opportunistic pathogen, is a rare cause of peritonitis and has worse clinical outcomes than Gram-positive peritonitis. In this case report, we describe a case of Serratia marcescens associated peritonitis that was successfully cured without catheter removal. A 40-year-old male patient with peritoneal dialysis who worked in the catering industry was admitted to the hospital for 16 hours after the discovery of cloudy peritoneal dialysate and abdominal pain. Ceftazidime and cefazolin sodium were immediately given intravenously as an empirical antibiotic regimen. After detecting Serratia marcescens in the peritoneal diasate culture, the treatment was switched to ceftazidime and levofloxacin. The routine examination of peritoneal dialysate showed a significant decrease in white blood cells, the peritoneal dialysate became clear, and the peritoneal dialysis catheter was retained. The patient was treated for 2 weeks and treated with oral antibiotics for 1 week. It is necessary to further strengthen the hygiene of work environment to prevent Serratia marcescens infection in peritoneal dialysis patients. We recommend that patients with Serratia marcescens associated peritonitis should be treated with a combination of antibiotics as early as possible empirically, and at the same time, the peritoneal dialysis fluid culture should be improved, and the antibiotic regimen should be timely adjusted according to the drug sensitivity results. For patients with clinical symptoms for more than 3 days, considering the strong virulence of Serratia marcescens, whether to use meropenem directly or not can provide a reference for clinical decision-making. Further clinical studies are needed to achieve more precise anti-infective treatment.

The ICU environment contributes to the endemicity of the "Serratia marcescens complex" in the hospital setting

Serratia marcescens is an opportunistic pathogen historically associated with sudden outbreaks in intensive care units (ICUs) and the spread of carbapenem-resistant genes. However, the ecology of S. marcescens populations in the hospital ecosystem remains largely unknown. We combined epidemiological information of 1,432 Serratia spp. isolates collected from sinks of a large ICU that underwent demographic and operational changes (2019-2021) and 99 non-redundant outbreak/non-outbreak isolates from the same hospital (2003-2019) with 165 genomic data. These genomes were grouped into clades (1-4) and subclades (A and B) associated with distinct species: Serratia nematodiphila (1A), S. marcescens (1B), Serratia bockelmannii (2A), Serratia ureilytica (2B), S. marcescens/Serratia nevei (3), and S. nevei (4A and 4B). They may be classified into an S. marcescens complex (SMC) due to the similarity between/within subclades (average nucleotide identity >95%-98%), with clades 3 and 4 predominating in our study and publicly available databases. Chromosomal AmpC β-lactamase with unusual basal-like expression and prodigiosin-lacking species contrasted classical features of Serratia. We found persistent and coexisting clones in sinks of subclades 4A (ST92 and ST490) and 4B (ST424), clonally related to outbreak isolates carrying blaVIM-1 or blaOXA-48 on prevalent IncL/pB77-CPsm plasmids from our hospital since 2017. The distribution of SMC populations in ICU sinks and patients reflects how Serratia species acquire, maintain, and enable plasmid evolution in both "source" (permanent, sinks) and "sink" (transient, patients) hospital patches. The results contribute to understanding how water sinks serve as reservoirs of Enterobacterales clones and plasmids that enable the persistence of carbapenemase genes in healthcare settings, potentially leading to outbreaks and/or hospital-acquired infections.IMPORTANCEThe "hospital environment," including sinks and surfaces, is increasingly recognized as a reservoir for bacterial species, clones, and plasmids of high epidemiological concern. Available studies on Serratia epidemiology have focused mainly on outbreaks of multidrug-resistant species, overlooking local longitudinal analyses necessary for understanding the dynamics of opportunistic pathogens and antibiotic-resistant genes within the hospital setting. This long-term genomic comparative analysis of Serratia isolated from the ICU environment with isolates causing nosocomial infections and/or outbreaks within the same hospital revealed the coexistence and persistence of Serratia populations in water reservoirs. Moreover, predominant sink strains may acquire highly conserved and widely distributed plasmids carrying carbapenemase genes, such as the prevalent IncL-pB77-CPsm (pOXA48), persisting in ICU sinks for years. The work highlights the relevance of ICU environmental reservoirs in the endemicity of certain opportunistic pathogens and resistance mechanisms mainly confined to hospitals.

Cultivation and sequencing-free protocol for Serratia marcescens detection and typing

Serratia marcescens is an opportunistic pathogen that survives in inhospitable environments causing large outbreaks, particularly in neonatal intensive care units (NICUs). Genomic studies revealed that most S. marcescens nosocomial infections are caused by a specific clone (here "Infectious clone"). Whole genome sequencing (WGS) is the only portable method able to identify this clone, but it requires days to obtain results. We present a cultivation-free hypervariable-locus melting typing (HLMT) protocol for the fast detection and typing of S. marcescens, with 100% detection capability on mixed samples and a limit of detection that can reach the 10 genome copies. The protocol was able to identify the S. marcescens infectious clone with 97% specificity and 96% sensitivity when compared to WGS, yielding typing results portable among laboratories. The protocol is a cost and time saving method for S. marcescens detection and typing for large environmental/clinical surveillance screenings, also in low-middle income countries.

Achromobacter species (sp.) outbreak caused by hospital equipment containing contaminated water: risk factors for infection

BACKGROUND

Nosocomial outbreaks of urinary tract infections caused by Achromobacter spp. have been rare in recent decades.

AIM

To identify the origin of an Achromobacter sp. outbreak, conduct multi-modal infection control measures, and finally to stop the outbreak. To this end, an epidemiological outbreak investigation and risk factor analysis were performed.

METHODS

Achromobacter sp. was detected in 22 patients in our urology wards and six environmental cultures of specimens obtained from the operating rooms. Strains isolated were submitted for antimicrobial susceptibility testing. An on-site epidemiological investigation, evaluation of patient medical records, and environmental sampling were performed to identify the source of the outbreak, and implementation of infection control intervention. A case-control study was performed to analyse the potential risk factors.

FINDINGS

Environmental sampling showed that the source of the infection for 22 patients was an ISA-IIIA-type medical pressurizer containing contaminated water. A case-control analysis showed that the risk factors for infection were: diagnosis of kidney/ureteral stones, surgery, placement of a double-J stent, and history of hospitalization in the past three months.

CONCLUSION

It was concluded that the outbreak occurred in patients who underwent internal lithotripsy and double-J stent placement, due to contact transmission with the contaminated sensor and connecting tubes of the ISA-IIIA-type medical pressurizer.

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

BACKGROUND

Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking.

AIMS

To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing.

METHODS

Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22 °C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0).

FINDINGS

The limits of detection for each antibiotic were: 3 μg/L (ampicillin), 10 μg/L (doxycycline), 20 μg/L (sulfamethoxazole) and 8 μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22 °C for up to five days.

CONCLUSIONS

Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.

High-Throughput Short Sequence Typing Schemes for Pseudomonas aeruginosa and Stenotrophomonas maltophilia Pure Culture and Environmental DNA

Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.