Trends in antibiotic susceptibility and incidence of late-onset Klebsiella pneumoniae neonatal sepsis over a six-year period in a neonatal intensive care unit in Karachi, Pakistan

Antibiotic resistance in the Middle East and Southern Asia: a systematic review and meta-analysis

Introduction

Despite global surveillance efforts, antibiotic resistance (ABR) is difficult to address in low- and middle-income countries (LMICs). In the absence of country-wide ABR surveillance data, peer-reviewed literature is the next most significant source of publicly available ABR data. Médecins Sans Frontières conducted this review in hopes of using the pooled findings to inform treatment choices in the studied countries where sufficient local ABR data are unavailable.

Methods

A systematic literature review reporting ABR rates for six infection sites in nine countries in the Middle East and Southern Asia was conducted. PubMed was used to identify literature published between January 2012 and August 2022. A meta-analysis of the included studies (n = 694) was conducted, of which 224 are reviewed in this paper. The JBI critical appraisal tool was used to evaluate risk of bias for included studies.

Results

This paper focuses on sepsis, burns and wound infections, specifically, with the largest number of papers describing data from Iran, Türkiye and Pakistan. High (>30%) resistance to recommended first-line antibiotics was found. Gram-negative resistance to ceftriaxone, aminoglycosides and carbapenems was high in burn-related infections; colistin resistance among Klebsiella pneumoniae isolates in Pakistan was alarmingly high (81%).

Conclusions

High-quality data on ABR in LMIC settings remain difficult to obtain. While peer-reviewed literature is a source of publicly available ABR data, it is of inconsistent quality; the field also lacks agreed reporting standards, limiting the capacity to pool findings. Nonetheless, high resistance to first-line antibiotics underscores the need for improved localized surveillance and stewardship.

Gender and sex hormone effects on neonatal innate immune function

OBJECTIVES

Scientific evidence provides a widened view of differences in immune response between male and female neonates. The X-chromosome codes for several genes important in the innate immune response and neonatal innate immune cells express receptors for, and are inhibited by, maternal sex hormones. We hypothesized that sex differences in innate immune responses may be present in the neonatal population which may contribute to the increased susceptibility of premature males to sepsis. We aimed to examine the in vitro effect of pro-inflammatory stimuli and hormones in neutrophils and monocytes of male and female neonates, to examine the expression of X-linked genes involved in innate immunity and the miRNA profiles in these populations.

METHODS

Preterm infants (n = 21) and term control (n = 19) infants were recruited from the Coombe Women and Infants University Hospital Dublin with ethical approval and explicit consent. The preterm neonates (eight female, 13 male) were recruited with a mean gestation at birth (mean ± SD) of 28 ± 2 weeks and corrected gestation at the time of sampling was 30 + 2.6 weeks. The mean birth weight of preterm neonates was 1084 ± 246 g. Peripheral blood samples were used to analyze immune cell phenotypes, miRNA human panel, and RNA profiles for inflammasome and inflammatory genes.

RESULTS

Dividing neutrophil results by sex showed no differences in baseline CD11b between sexes among either term or preterm neonates. Examining monocyte CD11b by sex shows, that at baseline, total and classical monocytes have higher CD11b in preterm females than preterm males. Neutrophil TLR2 did not differ between sexes at baseline or following lipopolysaccharide (LPS) exposure. CD11b expression was higher in preterm male non-classical monocytes following Pam3CSK treatment when compared to females, a finding which is unique to our study. Preterm neonates had higher TLR2 expression at baseline in total monocytes, classical monocytes and non-classical monocytes than term. A sex difference was evident between preterm females and term females in TLR2 expression only. Hormone treatment showed no sex differences and there was no detectable difference between males and females in X-linked gene expression. Two miRNAs, miR-212-3p and miR-218-2-3p had significantly higher expression in preterm female than preterm male neonates.

CONCLUSIONS

This study examined immune cell phenotypes and x-linked gene expression in preterm neonates and stratified according to gender. Our findings suggest that the responses of females mature with advancing gestation, whereas male term and preterm neonates have very similar responses. Female preterm neonates have improved monocyte activation than males, which likely reflects improved innate immune function as reflected clinically by their lower risk of sepsis. Dividing results by sex showed changes in preterm and term infants at baseline and following LPS stimulation, a difference which is reflected clinically by infection susceptibility. The sex difference noted is novel and may be limited to the preterm or early neonatal population as TLR2 expression on monocytes of older children does not differ between males and females. The differences shown in female and male innate immune cells likely reflect a superior innate immune defense system in females with sex differences in immune cell maturation. Existing human studies on sex differences in miRNA expression do not include preterm patients, and most frequently use either adult blood or cord blood. Our findings suggest that miRNA profiles are similar in neonates of opposite sexes at term but require further investigation in the preterm population. Our findings, while novel, provide only very limited insights into sex differences in infection susceptibility in the preterm population leaving many areas that require further study. These represent important areas for ongoing clinical and laboratory study and our findings represent an important contribution to exiting literature.

Bacteriological Profile and Antibiotic Susceptibility of Neonatal Sepsis Cases in the Neonatal Intensive Care Unit of a Tertiary Hospital in Türkiye

OBJECTIVE

We aimed to determine the demographic data, mortality, and morbidity of early- and late-neonatal sepsis cases, the etiologic agents in these cases, and the antibiotic susceptibility of these agents.

METHODS

This study was conducted retrospectively in a tertiary neonatal intensive care unit (NICU). The demographic, clinical, and laboratory data of newborns diagnosed with culture-proven sepsis within 24 months were evaluated.

RESULTS

Two hundred and eleven culture data points belonging to 197 infants were evaluated. Forty percent of the infants had a history of premature birth. The most common clinical findings were respiratory distress and feeding intolerance. Coagulase-negative staphylococci (CoNS) were detected most frequently as early- and late-sepsis agents. The most common Gram-negative bacteria detected as late-sepsis agents were Klebsiella spp. and Escherichia coli (E. coli). The overall mortality rate was 10%.

CONCLUSIONS

Neonatal sepsis continues to have high mortality rates in tertiary NICUs. CoNS was the most common agent, highlighting the importance of developing and maintaining personnel training and handwashing practices. It will be important to consider the resistance rates of Klebsiella spp., the most common Gram-negative agent in late-onset sepsis (LOS) cases, to commonly used antibiotics in empirical treatments.

Vaccine value profile for Klebsiella pneumoniae

Klebsiella pneumoniae causes community- and healthcare-associated infections in children and adults. Globally in 2019, an estimated 1.27 million (95% Uncertainty Interval [UI]: 0.91-1.71) and 4.95 million (95% UI: 3.62-6.57) deaths were attributed to and associated with bacterial antimicrobial resistance (AMR), respectively. K. pneumoniae was the second leading pathogen in deaths attributed to AMR resistant bacteria. Furthermore, the rise of antimicrobial resistance in both community- and hospital-acquired infections is a concern for neonates and infants who are at high risk for invasive bacterial disease. There is a limited antibiotic pipeline for new antibiotics to treat multidrug resistant infections, and vaccines targeted against K. pneumoniae are considered to be of priority by the World Health Organization. Vaccination of pregnant women against K. pneumoniae could reduce the risk of invasive K.pneumoniae disease in their young offspring. In addition, vulnerable children, adolescents and adult populations at risk of K. pneumoniae disease with underlying diseases such as immunosuppression from underlying hematologic malignancy, chemotherapy, patients undergoing abdominal and/or urinary surgical procedures, or prolonged intensive care management are also potential target groups for a K. pneumoniae vaccine. A 'Vaccine Value Profile' (VVP) for K.pneumoniae, which contemplates vaccination of pregnant women to protect their babies from birth through to at least three months of age and other high-risk populations, provides a high-level, holistic assessment of the available information to inform the potential public health, economic and societal value of a pipeline of K. pneumoniae vaccines and other preventatives and therapeutics. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public-private partnerships, and multi-lateral organizations, and in collaboration with stakeholders from the WHO. All contributors have extensive expertise on various elements of the K.pneumoniae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.

Examining the impact and response to an outbreak of carbapenemase-producing Enterobacterales in a neonatal unit in the United Kingdom: An outbreak report

Background

Carbapenemase-producing Enterobacterales (CPE) are a group of Gram-negative bacteria causing global concern due to their resistance to carbapenems. In this report, we detail the learning points from a CPE outbreak in a tertiary neonatal unit (NU) in the UK.

Methods

Routine surveillance screening (rectal swabs) of babies on the NU identified a potential cluster of CPE carriage. Samples were sent to a reference laboratory for confirmatory testing. Environmental screening and cot mapping were undertaken to determine movements of babies within the unit. Regular audits of cleaning standards, hand hygiene, and maternal hygiene when expressing breast milk were carried out.

Results

The outbreak lasted 19 weeks. During the outbreak, there were 360 admissions, with 11 babies being colonised with the outbreak strain. Once the outbreak was declared, there were enhanced Infection Prevention and Control (IPC) precautions (including increased environmental and equipment cleaning frequency). CPE screening frequency was increased and cot capacity was reduced. Hand hygiene compliance improved from 92% at the start of the outbreak to 100% by its close. Cleaning standards remained compliant. Maternal hygiene standards varied from 78% to 100%, but no cross-infection links were identified. Environmental screening was negative. No route of cross-infection was identified. Notably, no babies developed invasive CPE infection.

Conclusion

This is the first report of a CPE outbreak in a UK NU. Although no specific mode of cross-transmission was identified and the outbreak's end cannot be attributed to any single intervention, the bundle of interventions proved successful after a 5-month period.

Microbial Pattern of Neonatal Sepsis in the Neonatal Intensive Care Unit of dr. Ramelan Navy Central Hospital

Background

The morbidity and mortality rates from neonatal sepsis remain high. However, there is limited information about the microbial pattern of neonatal sepsis in Indonesia. Microbial patterns can give an overview of the hygiene of an environment and act as a determinant for choosing definitive antibiotic treatment in neonatal sepsis patients. The organisms that cause neonatal sepsis differ from unit to unit and from time to time within the same unit.

Objectives

This study is aimed at discovering the microbial pattern of neonatal sepsis in the Neonatal Intensive Care Unit (NICU), dr. Ramelan Navy Central Hospital, in 2021-2022.

Methods

This is a retrospective, cross-sectional study that takes secondary data from the NICU and clinical microbiology department of dr. Ramelan Navy Central Hospital. Data that met the inclusion and exclusion criteria available between January 1, 2021, and December 31, 2022, were collected. Patients whose blood cultures were positive for bacterial growth and diagnosed with sepsis were selected as the study sample.

Results

Out of 174 samples, 93 (53.4%) were found positive for bacterial infection and diagnosed as neonatal sepsis. Gram-negative isolates (96.8%) were predominant. Sixty-point-two percent of Klebsiella pneumoniae XDR, 19.4% of Klebsiella pneumoniae ESBL, and 8.6% of Burkholderia cepacia XDR were identified. The gram-positive isolates found in this study were only 3 samples (3.2%). Two-point-one percent of MRSA and 1.1% of Staphylococcus haemolyticus MDR were identified.

Conclusion

The most common microorganisms causing neonatal sepsis in our NICU were gram-negative bacteria, particularly Klebsiella pneumoniae XDR. Following the recommended infection control procedures, practicing good hand hygiene, and having access to basic supplies and equipment are important to prevent and reduce the incidence of sepsis.

Exploring the resistome, virulome, and mobilome of multidrug-resistant Klebsiella pneumoniae isolates: deciphering the molecular basis of carbapenem resistance

BACKGROUND

Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has become highly resistant to antibiotics due to the widespread acquisition of genes encoding a variety of enzymes such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases. We collected Klebsiella pneumoniae isolates from a local tertiary care hospital from February 2019-February 2021. To gain molecular insight into the resistome, virulome, and genetic environment of significant genes of multidrug-resistant K. pneumoniae isolates, we performed the short-read whole-genome sequencing of 10 K. pneumoniae isolates recovered from adult patients, neonates, and hospital tap water samples.

RESULTS

The draft genomes of the isolates varied in size, ranging from 5.48 to 5.96 Mbp suggesting the genome plasticity of this pathogen. Various genes conferring resistance to different classes of antibiotics e.g., aminoglycosides, quinolones, sulfonamides, tetracycline, and trimethoprim were identified in all sequenced isolates. The highest resistance was observed towards carbapenems, which has been putatively linked to the presence of both class B and class D carbapenemases, blaNDM, and blaOXA, respectively. Moreover, the biocide resistance gene qacEdelta1 was found in 6/10 of the sequenced strains. The sequenced isolates exhibited a broad range of sequence types and capsular types. The significant antibiotic resistance genes (ARGs) were bracketed by a variety of mobile genetic elements (MGEs). Various spontaneous mutations in genes other than the acquired antibiotic-resistance genes were observed, which play an indirect role in making these bugs resistant to antibiotics. Loss or deficiency of outer membrane porins, combined with ESBL production, played a significant role in carbapenem resistance in our sequenced isolates. Phylogenetic analysis revealed that the study isolates exhibited evolutionary relationships with strains from China, India, and the USA suggesting a shared evolutionary history and potential dissemination of similar genes amongst the isolates of different origins.

CONCLUSIONS

This study provides valuable insight into the presence of multiple mechanisms of carbapenem resistance in K. pneumoniae strains including the acquisition of multiple antibiotic-resistance genes through mobile genetic elements. Identification of rich mobilome yielded insightful information regarding the crucial role of insertion sequences, transposons, and integrons in shaping the genome of bacteria for the transmission of various resistance-associated genes. Multi-drug resistant isolates that had the fewest resistance genes exhibited a significant number of mutations. K. pneumoniae isolate from water source displayed comparable antibiotic resistance determinants to clinical isolates and the highest number of virulence-associated genes suggesting the possible interplay of ARGs amongst bacteria from different sources.

A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan

Background

Carbapenem resistance is epidemic worldwide, these last resort antimicrobials are listed in the WHO 'watch group' with higher resistance potential. During the years 2017-18 Pakistan Antimicrobial Resistance Surveillance System reported an increase in carbapenem resistance. However, a comprehensive information on prevalence and molecular epidemiology of carbapenem resistance in Pakistan is not available. This systematic review and meta-analysis is aimed to report the current carbapenem resistance situation in Pakistan and its treatment options.

Methods

In this systematic review and meta-analysis, we investigated the pooled prevalence (PPr) of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae by organizing available data, from Web of Science and PubMed by April 2, 2020, in various groups and subgroups including species, years, provinces, extended spectrum β-lactamase production, clinical presentation, carbapenemase and metallo-β-lactamase production, and New Delhi metallo-β-lactamase (NDM) prevalence. Literature review was updated for the studies publisehd by December 07, 2023. Moreover, we descriptively reviewed the molecular epidemiology of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae in Pakistan. Lastly, we statistically explored different treatment options available for carbapenem resistant infections. We used R package 'metafor' for performing meta-analysis and influence diagnostics and determining treatment options.

Results

From two academic databases Web of Science and PubMed we identified 343 studies. Eighty-eight studies were selected for the systematic review and meta-analysis. Seventy-four studies were selected for phenotypic analysis, 36 for genotypic analysis, and 31 for available treatment options. PPr-ID of 12% [0.12 (0.07, 0.16)] was observed for phenotypic carbapenem resistance in Enterobacteriaceae with more prevalence recorded in Klebsiella pneumoniae 24% [0.24 (0.05, 0.44)] followed by 9% [0.09 (-0.03, 0.20)] in Escherichia coli. During the last two decades we observed a striking increase in carbapenem resistance PPr i.e., from 0% [0.00 (-0.02, 0.03)] to 36% [0.36 (0.17, 0.56)]. blaNDM with PPr 15% [0.15 (0.06, 0.23)] in naive isolates was found to be the fundamental genetic determinant for carbapenem resistance in Enterobacteriaceae in Pakistan. Polymyxin B, colistin, tigecycline, and fosfomycin were identified as the suggested treatment options available for multidrug resistant infections not responding to carbapenems. Various studies reported carbapenem resistance from human, animal, and environment sources.

Conclusion

In conclusion, we found that NDM-1 producing carbapenem resistant Enterobacteriaceae are increasing in Pakistan. Meta-analysis showed that metallo-β-lactamases producing E. coli ST405 and K. pneumoniae sequence type11 are the major resistant clones. Number of reported studies in various subgroups and inconsistency in following CLSI guidelines are the potential limitations of this meta-analysis. A National antimicrobial resistance (AMR) surveillance strategy based on One Health is urgently needed to check any future AMR crisis in Pakistan.

The Interaction between Human Microbes and Advanced Glycation End Products: The Role of Klebsiella X15 on Advanced Glycation End Products' Degradation

Previous studies have shown that advanced glycation end products (AGEs) are implicated in the occurrence and progression of numerous diseases, with dietary AGEs being particularly associated with intestinal disorders. In this study, methylglyoxal-beta-lactoglobulin AGEs (MGO-β-LG AGEs) were utilized as the exclusive nitrogen source to investigate the interaction between protein-bound AGEs and human gut microbiota. The high-resolution mass spectrometry analysis of alterations in peptides containing AGEs within metabolites before and after fermentation elucidated the capacity of intestinal microorganisms to enzymatically hydrolyze long-chain AGEs into short-chain counterparts. The 16S rRNA sequencing revealed Klebsiella, Lactobacillus, Escherichia-Shigella, and other genera as dominant microbiota at different fermentation times. A total of 187 potential strains of AGE-metabolizing bacteria were isolated from the fermentation broth at various time points. Notably, one strain of Klebsiella exhibited the most robust growth capacity when AGEs served as the sole nitrogen source. Subsequently, proteomics was employed to compare the changes in protein levels of Klebsiella X15 following cultivation in unmodified proteins and proteins modified with AGEs. This analysis unveiled a remodeled amino acid and energy metabolism pathway in Klebsiella in response to AGEs, indicating that Klebsiella may possess a metabolic pathway specifically tailored to AGEs. This study found that fermenting AGEs in healthy human intestinal microbiota altered the bacterial microbiota structure, especially by increasing Klebsiella proliferation, which could be a key factor in AGEs' role in causing diseases, particularly intestinal inflammation.

Retrospective analysis of pediatric sepsis and the burden of antimicrobial resistance in Duhok, Kurdistan Region of Iraq

Introduction: Sepsis is a life-threatening complication in pediatric patients. This study primarily aimed to investigate sepsis-causing bacteria and their antimicrobial resistance profile and check the change in the antimicrobial resistance trend for some selected bacteria. In addition, we evaluated the incidence of sepsis, the related mortality rate, and the effectiveness and outcome of the treatment regimes in sepsis pediatric patients. Methods: A retrospective analysis was conducted on 4-year data (2018-2021) collected from three intensive care units at the Hevi Pediatric Teaching Hospital. Sepsis screening involved clinical detection and confirmation by blood culture. Results: A total of 520 out of 1,098 (47.35%) blood samples showed positive microbial growth. A decrease in sepsis rate was observed during the COVID-19 pandemic. Coagulase-negative Staphylococci (CoNS) and Klebsiella pneumonia were the most commonly isolated bacteria. A notable variation in the antimicrobial resistance trend was observed among sepsis-causing bacteria. The empirical sepsis treatment recommended by the WHO was ineffective, as certain bacteria exhibited 100% resistance to every antibiotic tested. The mortality rate significantly increased from 1.3% in 2018 to 16.5% in 2021. Discussion: The antimicrobial resistance profile of sepsis causing bacteria is of concerns, indicating a potentially serious situation. Thus, to avoid treatment failure, the monitoring of antimicrobial resistance in pediatric patients is essential.

Can Clean Delivery Kits Prevent Infections? Lessons from Traditional Birth Attendants in Nigeria

Background

In resource-poor settings, perinatal infections contribute significantly to maternal and neonatal deaths, and the use of clean delivery kits (CDKs) has been proposed as a tool to reduce the risk of infection-related deaths. This study aims to assess the acceptability and effectiveness of CDKs in preventing infections in deliveries attended by traditional birth attendants (TBAs) in Abeokuta, Nigeria.

Methods

The study was a cluster-randomized trial with 67 birth centres/clusters, 453 births/mothers, and 457 babies randomized to intervention or control arms; intervention involved supplementation of delivery with JANMA CDKs. Interviews were conducted at the birth homes, and the primary outcomes were neonatal infection and puerperal fever. The association between infection and perinatal risk factors was tested using the Chi-square and Fisher's exact tests.

Results

CDKs were well accepted by TBAs. The incidence of puerperal fever and neonatal infection was 1.1% and 11.2%, respectively. Concurrent infection was found in 1 (0.22%) of the mother-neonate pair. There was no significant association between any of the sociodemographic factors and infection for both mothers and neonates. PROM and prolonged labour were significantly associated with puerperal infection. All mothers with puerperal fever were from the control group. Compared to the control group, the relative risk of puerperal infection and neonatal infection in the intervention group was 0.08 (0.004 -1.35, p = 0.079) and 0.64 (0.37 to 1.1, p = 0.10), respectively.

Conclusion

CDKs hold promising results in attenuating maternal infections in resource-poor settings. Larger studies with greater statistical power are required to establish statistically reliable information.

Antibiotics resistance as a major public health concern: A pharmaco-epidemiological study to evaluate prevalence and antibiotics susceptibility-resistance pattern of bacterial isolates from multiple teaching hospitals

BACKGROUND

Multi Drugs Resistance (MDR) is among the most worrisome healthcare issues resulting from inappropriate and indiscriminate utilization of antimicrobial agents which has compromised the efficacy and reliability of antimicrobial agents (AMAs). This has not only put a huge burden on the health care system but also is a major cause of morbidity and mortality. This project was designed to evaluate the prevalence of various microbial strains among patients admitted to various teaching hospitals and to assess their susceptibility and resistance towards clinically approved antibiotics.

METHODS

The study was conducted during August 2021-February 2022 to determine the prevalence of common resistant strains of bacteria and to analyze their susceptibility pattern to the commonly prescribed antibiotics using standard procedures. One hundred and thirty biological samples including urine, blood, cerebrospinal fluid (CSF), wound swabs, pus and sputum were collected from the site of infection from the patients admitted at different wards of North West General Hospital (NWGH), Peshawar, Pakistan, Khyber Teaching Hospital (KTH), Peshawar Pakistan, and Hayat Abad Medical Complex (HMC) Peshawar Pakistan. Samples were collected and cultured following standard hospital procedures. The cultured samples were subjected to identification procedures including Gram staining, morphological characterization of bacterial colonies and biochemical assessments. The identified bacteria were tested for their susceptibility using Kirby-Bauer disc diffusion method. The diameter of Inhibitory Zones (DIZ) was analyzed following Clinical and Laboratory Standards Institute (CLSI) criteria. Minimum Inhibitory Concentrations (MICs) were evaluated using agar dilution method. Antimicrobials sensitivity were presented as antibiogram following CLSI M39 standard.

RESULTS

A total of one hundred and thirty biological samples were collected, out of which one hundred and nine samples were positive for bacterial growth and were further processed for detailed analysis. The frequency and type of bacteria isolated from various cultures indicated that Gram negative bacteria (n = 92/109) were more dominant than Gram-positive (n = 17/109) pathogens. The most prevalent bacteria isolated was Escherichia coli (29.35 %), followed by Staphylococcus aureus (15.59 %), and Klebsiella spp, (12.84 %). In addition, other pathogens including, Enterobacter spp, Citrobacter spp, and Acinetobacter spp. showed a prevalence of 9.175 %, 8.25 %, and 5.50 % respectively. As indicated in the antbiogram, several organisms exhibited considerble decline in the sensitivies towards various antibiotics. A high percentage of resistance was observed against some antibiotics including trimethoprim, co-trimoxazole, amoxicillin/clavulanate, ciprofloxacin, piperacillin/tazobactam, cefotaxime and ceftazidime.

CONCLUSION

The prevalence of resistant strains of pathogens is increasing day by day, while the antibiotics commonly prescribed against them are losing their efficacy, which is pushing the world to the era of pre-antibiotics. Unfortunately, the discovery of novel antibiotics is limited and researchers speculate that the is pushing towards pre-antibiotics era. Subsequently, efforts must be directed towards ensuring rational antibiotics use to prevent emergence of MDR pathogens. Our findings indicated that Gram negative bacteria including Escherichia coli was most prevalent. Other bacterial strains including S. aureus, Klebsiella spp, Enterobacter spp, Citrobacter spp, and Acinetobacter spp. were found among the causative agents. Unfortunately, considerable decline in the sensitivities of various bacterial isolated were observed towards the tested antibiotics. Previous studies reported the high prevalence of E. coli and S. aureus in clinical samples of Pakistani hospitals including hospitals in Peshawar and thus our findings are in agreement with the previous reports. Pharmacists being experts can play their role by promoting the optimal use of antimicrobial agents and educating healthcare professionals, patients and the public.

Sex differences in neonatal brain injury and inflammation

Neonatal brain injury and associated inflammation is more common in males. There is a well-recognised difference in incidence and outcome of neonatal encephalopathy according to sex with a pronounced male disadvantage. Neurodevelopmental differences manifest from an early age in infancy with females having a lower incidence of developmental delay and learning difficulties in comparison with males and male sex has consistently been identified as a risk factor for cerebral palsy in epidemiological studies. Important neurobiological differences exist between the sexes with respect to neuronal injury which are especially pronounced in preterm neonates. There are many potential reasons for these sex differences including genetic, immunological and hormonal differences but there are limited studies of neonatal immune response. Animal models with induced neonatal hypoxia have shown various sex differences including an upregulated immune response and increased microglial activation in males. Male sex is recognized to be a risk factor for neonatal hypoxic ischemic encephalopathy (HIE) during the perinatal period and this review discusses in detail the sex differences in brain injury in preterm and term neonates and some of the potential new therapies with possible sex affects.

Infection control measures against multidrug-resistant Gram-negative bacteria in children and neonates

The increase in infections caused by multidrug-resistant (MDR) Gram-negative bacteria in neonatal and pediatric intensive care units over recent years is alarming. MDR Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii have constituted the main causes of the MDR Gram-negative bacteria problem. The implementation of infection control measures such as hand hygiene, cohorting of patients, contact precautions, active surveillance and environmental cleaning could diminish their spread. Recently, water safety has been identified as a major component of infection control policies. The aim of the current review is to highlight the effectiveness of these infection control measures in managing outbreaks caused by MDR Gram-negative bacteria in neonatal and pediatric intensive care units and highlight future perspectives on the topic.

Antimicrobial resistance pattern, virulence determinants and molecular analysis of carbapenem-resistant Klebsiella pneumoniae isolated from clinical samples in Iran

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as an important global threat in recent years. The objective of the present study was to characterize the molecular characteristics, antibiotic resistance pattern and the distribution of virulence factors in CRKP isolated from different clinical specimens. A total of 60 clinical CRKP isolates were collected from clinical samples. Based on Clinical Laboratory Standards Institute guidelines, antimicrobial susceptibility testing was assessed by the disk diffusion method. Carbapenem and aminoglycoside resistance determinants in addition to virulence genes were inspected by PCR. Molecular characteristics of CRKP isolates were analyzed by random amplified polymorphic DNA (RAPD) PCR and enterobacterial repetitive intergenic consensus (ERIC) PCR. All isolates were resistant to imipenem, meropenem, cefoxitin, levofloxacin, cefotaxime, ceftazidime and ciprofloxacin. Resistance to tetracycline, gentamicin and kanamycin were detected in 53%, 75% and 72% of isolates, respectively. The most common carbapenem resistance genes were OXA-48 (28.5%) and NDM (22%). The most common aminoglycosides resistance genes were aac6´Ib (57%) and aac(3)-IVa (28%). The most prevalent virulence genes were mrkD (82%), entB (62%) and ybts (58%). ERIC and RAPD analyses revealed 55 and 53 different patterns of CRKP isolates, respectively. We conclude that CRKP infections have been associated with different genotypes and that the carbapenemase type (OXA-48) and AME gene (aac6´-Ib) were widely distributed in CRKP isolates in our hospital. Continued compliance with existing phenotypes and genotypes, and strict enforcement of infection control guidelines, are recommended approaches for the prevention and dissemination of these strains.

Contemporary Trends in Global Mortality of Sepsis Among Young Infants Less Than 90 Days: A Systematic Review and Meta-Analysis

Objective

Current knowledge on the global burden of infant sepsis is limited to population-level data. We aimed to summarize global case fatality rates (CFRs) of young infants with sepsis, stratified by gross national income (GNI) status and patient-level risk factors.

Methods

We performed a systematic review and meta-analysis on CFRs among young infants < 90 days with sepsis. We searched PubMed, Cochrane Central, Embase, and Web of Science for studies published between January 2010 and September 2019. We obtained pooled CFRs estimates using the random effects model. We performed a univariate analysis at patient-level and a meta-regression to study the associations of gestational age, birth weight, onset of sepsis, GNI, age group and culture-proven sepsis with CFRs.

Results

The search yielded 6314 publications, of which 240 studies (N = 437,796 patients) from 77 countries were included. Of 240 studies, 99 were conducted in high-income countries, 44 in upper-middle-income countries, 82 in lower-middle-income countries, 6 in low-income countries and 9 in multiple income-level countries. Overall pooled CFR was 18% (95% CI, 17-19%). The CFR was highest for low-income countries [25% (95% CI, 7-43%)], followed by lower-middle [25% (95% CI, 7-43%)], upper-middle [21% (95% CI, 18-24%)] and lowest for high-income countries [12% (95% CI, 11-13%)]. Factors associated with high CFRs included prematurity, low birth weight, age less than 28 days, early onset sepsis, hospital acquired infections and sepsis in middle- and low-income countries. Study setting in middle-income countries was an independent predictor of high CFRs. We found a widening disparity in CFRs between countries of different GNI over time.

Conclusion

Young infant sepsis remains a major global health challenge. The widening disparity in young infant sepsis CFRs between GNI groups underscore the need to channel greater resources especially to the lower income regions.

Systematic Review Registration

[www.crd.york.ac.uk/prospero], identifier [CRD42020164321].

Efficacy of empiric antibiotic treatment of late-onset neonatal sepsis caused by Enterobacteriaceae: A Systematic Review

Neonatal sepsis is a serious condition, where an adequate empiric antibiotic treatment is crucial. The objective of this systematic review is to assess whether the World Health Organisation's recommended treatment regime remains applicable for late-onset neonatal sepsis caused by Enterobacteriaceae, in the time of increased antimicrobial resistance. PubMed was searched for articles from 2009 to 2020. A total of 49 articles were eligible for inclusion. The review was carried out in accordance with PRISMA guidelines. For Klebsiella spp. 100%, 68%, and 63% of the studies found sensitivity to ampicillin, gentamicin, and third generation cephalosporin in <50% of the isolates. For Escherichia coli the corresponding values were 88%, 50%, and 42% respectively, whilst for Enterobacter spp. 100%, 70% and 94% of the studies found <50% sensitivity to these antibiotics. Overall, there is low sensitivity to all agents in the WHO's recommended empiric treatment regimes (WHO recommends ampicillin plus gentamicin as first line treatment and third generation cephalosporin as second line treatment). A revised guideline for empiric antibiotic treatment of neonatal sepsis is urgently needed due to increased threat of antimicrobial resistant Enterobacteriaceae causing neonatal sepsis.

Molecular Epidemiological Surveillance of CTX-M-15-producing Klebsiella pneumoniae from the patients of a teaching hospital in Sindh, Pakistan

Background 

The presence of Extended-spectrum β-lactamase positive bacteria in hospital setting is an aggravating influential factor for hospitalized patients, and its consequences may be hazardous. Therefore, there is a need for rapid detection methods for newly emerging drug-resistant bacteria. This study was aimed at the molecular characterization of Extended-spectrum β-lactamase -positive  Klebsiella pneumoniae isolates recovered from the patients of a teaching hospital in Sindh, Pakistan.  

Methods 

A total of 513  K. pneumoniae isolates were obtained from various clinical samples during June 2019 to May 2020. The collected isolates were investigated for antimicrobial susceptibility (antibiogram), and PCR and DNA sequencing were performed to analyse the ESBL genes.  

Results 

Among the 513 isolates, as many as 359 (69.9%) were Extended-spectrum β-lactamase producers and 87.5% were multi-drug resistant, while none had resistance to imipenem. PCR scored 3% blaTEM, 3% blaSHV, and 60% blaCTX-M-15 genes for the tested isolates.  

Conclusion 

The study showed that CTX-M-15 was the major prevalent Extended-spectrum β-lactamase type among the isolates. Additionally, all the isolates were susceptible to carbapenems. Screening and detection of Extended-spectrum β-lactamase tests are necessary among all isolates from the enterobacteriaceae family in routine microbiology laboratory to prevent associated nosocomial infections. A larger study is essential to understand molecular epidemiology of Extended-spectrum β-lactamase producing organisms to minimize morbidities due to these multidrug resistant organisms.

Antimicrobial resistance among GLASS priority pathogens from Pakistan: 2006-2018

Background

In 2018 Pakistan initiated its national antimicrobial resistance (AMR) surveillance aligned with Global Antimicrobial Surveillance System (GLASS). To complement this surveillance, we conducted a situational analysis of AMR rates among GLASS organisms in the country. Data from published studies and from antibiograms was compared and role of antibiograms as potential contributors to national AMR surveillance explored.

Methods

AMR rates for GLASS specified pathogen/antimicrobials combination from Pakistan were reviewed. Data sources included published studies (2006–2018) providing AMR rates from Pakistan (n = 54) as well as antibiograms (2011–2018) available on the Pakistan Antimicrobial Resistance Network (PARN) website. Resistance rates were categorized as follows: Very low: 0–10%, Low: 11–30%, Moderate: 30–50% and High: > 50%.

Results

Published data from hospital and community/laboratory-based studies report resistance rates of > 50% and 30–50% respectively to 3rd generation cephalosporins, fluoroquinolones and cotrimoxazole amongst Klebsiella pneumoniae and Escherichia coli. Carbapenem resistance rates amongst these organisms remained below 30%. High (> 50%) resistance was reported in Acinetobacter species to aminoglycosides and carbapenems among hospitalized patients. The evolution of ceftriaxone resistant Salmonella Typhi and Shigella species is reported. The data showed > 50% to fluoroquinolones amongst Neisseria gonorrhoeae and the spread of methicillin resistant Staphylococcus aureus (< 30%; 2008) to (> 50%; 2010) in hospital settings. Resistance reported in published studies aligned well with antibiogram data. The latter also captured a clear picture of evolution of resistance over the study period.

Conclusion

Both published studies as well antibiograms suggest high rates of AMR in Pakistan. Antibiogram data demonstrating steady increase in AMR highlight its potential role towards supplementing national AMR surveillance efforts particularly in settings where reach of national surveillance may be limited.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06795-0.

Carbapenem-Resistant Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit: Risk Factors for Mortality

AIM

The aim of our study was to determine the factors associated with mortality in neonates with carbapenem-resistant Klebsiella pneumoniae (CRKP).

MATERIAL AND METHODS

This retrospective, single-center study was conducted in the Neonatal Intensive Care Unit of Harran University Faculty of Medicine between January 2017 and July 2018 who had CRKP growth in their blood, urine or cerebrospinal fluid cultures. The discharged group was designated as the control group (Group 1), whereas the group that faced mortality was classified as the case group (Group 2). The demographic data, clinical findings and laboratory and microbiological results of the two groups were compared to identify risk factors.

RESULTS

A total of 58 patients (36 in Group 1 and 22 in Group 2) exhibited CRKP growth during the study period. Low birth weight (p = 0.039), previous antifungal (p = 0.002) or amikacin use (p = 0.040), congenital anomalies (p = 0.002), total parenteral nutrition (TPN) administration (p = 0.002), surgery (p = 0.035), thrombocytopenia (p = 0.007), low platelet mass index (p = 0.011), elevated C-reactive protein (p = 0.004), high carbapenem minimum inhibitory concentration (MIC) (p = 0.029) and high amikacin MIC (p = 0.019) were associated with mortality. In a multivariate regression analysis, previous antifungal use (p = 0.028), congenital anomalies (p = 0.032) and TPN use (p = 0.013) were independent factors in predicting mortality.

CONCLUSION

Previous antifungal use, congenital anomalies and TPN use were found to be independent risk factors for mortality in neonates with CRKP infection.

Risk factors for, and molecular epidemiology and clinical outcomes of, carbapenem- and polymyxin-resistant Gram-negative bacterial infections in pregnant women, infants, and toddlers: a systematic review and meta-analyses

In the following systematic review and meta-analyses, we report several conclusions about resistance to carbapenem and polymyxin last-resort antibiotics for treating multidrug-resistant bacterial infections among pregnant women and infants. Resistance to carbapenems and polymyxins is increasing, even in otherwise vulnerable groups such as pregnant women, toddlers, and infants, for whom therapeutic options are limited. In almost all countries, carbapenem-/polymyxin-resistant Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii infect and/or colonize neonates and pregnant women, causing periodic outbreaks with very high infant mortalities. Downregulation of plasmid-borne bla_NDM , bla_KPC , bla_OXA-48 , bla_IMP, bla_VIM , bla_GES-5 , and ompK35/36 in clonal strains accelerates the horizontal and vertical transmissions of carbapenem resistance among these pathogens. New Delhi metallo-β-lactamase (NDM)-positive isolates in infants/neonates have been mainly detected in China and India, while OXA-48-positive isolates in infants/neonates have been mainly detected in Africa. NDM-positive isolates in pregnant women have been found only in Madagascar. Antibiotic therapy, prolonged hospitalization, invasive procedures, mechanical ventilation, low birth weight, and preterm delivery have been common risk factors associated with carbapenem/polymyxin resistance. The use of polymyxins to treat carbapenem-resistant infections may be selecting for resistance to both agents, restricting therapeutic options for infected infants and pregnant women. Currently, low- and middle-income countries have the highest burden of these pathogens. Antibiotic stewardship, periodic rectal and vaginal screening, and strict infection control practices in neonatal ICUs are necessary to forestall future outbreaks and deaths.

Meropenem-induced pancytopenia in a preterm neonate: a case report

BACKGROUND

A post-marketing surveillance study has reported an association between meropenem use and the incidence of hematologic abnormalities, including leukopenia, thrombocytopenia, hemolysis, and neutropenia, but the precise incidence in neonates is unknown. Here, we report meropenem-induced pancytopenia in a preterm neonate.

CASE PRESENTATION

A preterm newborn Pakistani received intravenous meropenem 40 mg/kg every 8 hours to treat Klebsiella pneumoniae in blood cultures and suspected meningitis. The baby developed severe thrombocytopenia, with a platelet count of 22 × 103 cells/mm3, low hemoglobin level of 9.7 g/dl, and low absolute neutrophil count (ANC) of 816 cells/mm3 on days 3, 14, and 17 of meropenem therapy, respectively. Based on the blood culture and institutional guidelines, meropenem treatment was continued with monitoring and supportive care for a total of 19 days. After discontinuation of meropenem, the baby was monitored continuously for hematological changes, and low counts persisted for 3 days. ANC improved to > 1500 cells/mm3 on the fourth day, and the platelet count reached > 150 × 103 cells/mm3 for the first time on the seventh day of meropenem discontinuation. All subsequent complete blood count (CBC) reports showed improving trends. The baby was discharged on the 48th day of life (DOL), with follow-up monitoring of CBC. The baby was kept on iron supplements, and hemoglobin level of 11.2 g/dl was observed on the 59th DOL.

CONCLUSION

Neonatal pancytopenia may lead to serious health complications; therefore, clinicians and pharmacists need to vigilantly monitor CBC in this vulnerable population, even when administering meropenem in septic doses for the recommended duration.

Treatment outcomes, antibiotic use and its resistance pattern among neonatal sepsis patients attending Bahawal Victoria Hospital, Pakistan

BACKGROUND

Sepsis is one of the major causes of neonatal mortality in Pakistan. This study aimed to investigate the treatment outcomes, antibiotic use and its resistance pattern among neonatal sepsis patients attending a tertiary care hospital in Pakistan. We also aimed to identify the factors affecting mortality in neonatal sepsis patients.

METHODS

A descriptive, cross-sectional study was conducted in the pediatric wards of the Bahawal Victoria Hospital, Bahawalpur, Pakistan. All eligible neonatal sepsis patients who were registered at the study site from January 1, 2019 to June 30, 2019 were included in the study. The data collection form included information on patient's characteristics, antibiotic use and its sensitivity pattern, laboratory and microbiological data, and final treatment outcomes. Treatment outcomes included, discharged (with treatment success), leave against medical advice (LAMA), discharged on request (DOR) and death. Multivariable binary logistic regression analysis was used to find the independent factors associated with death. A p-value of less than 0.05 was considered statistically significant.

RESULTS

Among the total 586 patients, 398 (67.9%) were male, 328 (56%) were preterm, 415 (70.8%) were diagnosed with early onset sepsis, 299 (51%) were born with low birth weight. Most of the patients (n = 484, 82.6%) were treated with amikacin+cefotaxime at the start of treatment. Culture was positive in 52 (8.9%) patients and the most commonly identified bacteria included, Klebsiella species (n = 19, 36.5%) followed by E. coli (n = 15, 28.5%) and Staphylococcus aureus (n = 8, 15.4%). The identified bacterial isolates showed high level of resistance against the antibiotics initiated at the start of the treatment, while resistance against piperacillin+tazobactam, imipenem, vancomycin and linezolid was very low. Just under half of the patients (n = 280, 47.8%) successfully completed the treatment (i.e., discharged with treatment success), while 123 (21%) patients died during treatment. In multivariable binary logistic regression, the factors which still remained significantly associated with neonatal death included, preterm delivery (AOR 9.59; 95% CI 4.41, 20.84), sub-optimal birth weight (AOR 5.13; 95% CI 2.19, 12.04), early onset sepsis (AOR 2.99; 95% CI 1.39, 6.41) and length of hospital stay (AOR 0.76; 95% CI 0.67, 0.88).

CONCLUSION

The mortality rate associated with sepsis was high in our study cohort. The bacterial isolates showed high level of resistance against the antibiotics started as the empiric therapy. Rational use of antibiotics can decrease the adverse outcomes in neonatal sepsis patients.

A risk score based on pediatric sequential organ failure assessment predicts 90-day mortality in children with Klebsiella pneumoniae bloodstream infection

Background

Klebsiella pneumoniae bloodstream infection (Kp-BSI) is a serious threat to pediatric patients. The objective of this study was to explore the risk factors, validate the prediction efficiency of pediatric Sequential Organ Failure Assessment (SOFA) and establish better early predictors of mortality in pediatric patients with Kp-BSI.

Methods

All children diagnosed with Kp-BSI were included in this retrospective cohort study from January 2009 to June 2019. Basic characteristics, symptoms and physical examinations, treatments, laboratory statistics, and SOFA at the onset of Kp-BSI were recorded. The Cox proportional hazard model and receiver operating characteristic curves were used to assess the association between the variables and the 90-day mortality and their predictive value. DeLong’s test of receiver operating characteristic curves and integrated discrimination improvement index were used to determine the improvement in predictive capacity of the modified SOFA models. A predictive score was developed using multivariate logistic regression.

Results

Of the 146 children enrolled, 33 (22.6%) patients died within 90 days. Hospitalization in the last 6 months, intra-abdominal source of infection, presence of organ failure, and altered levels of blood biomarkers, including C-reactive protein, albumin, and lactate were significant risk factors for 90-day mortality. The area under the curve (AUC) of SOFA for predicting 90-day mortality was 0.80 (95% CI 0.71–0.89). Moreover, we found that a prediction model combining SOFA with two other parameters, namely hospitalization in the last 6 months and intra-abdominal source of infection, was better at predicting mortality (AUC = 0.89, 95% CI 0.82–0.96; sensitivity = 0.86; specificity = 0.84). According to this novel risk model, we defined three statistically different groups: low-risk, medium-risk and high-risk groups, with an observed 90-day mortality of 5.4, 35.7, and 72.0%, respectively. With reference to the low-risk patients, the medium-risk and high-risk groups had a higher mortality, with hazard ratios of 8.36 (95% CI 3.60–27.83) and 20.27 (95% CI 7.47–54.95), respectively.

Conclusions

The modified SOFA may be better than the original score to predict 90-day mortality in pediatric patients with Kp-BSI. Future prospective studies are required to validate this novel scoring system in external cohorts.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-020-05644-w.

Nanotechnological strategies for systemic microbial infections treatment: A review

Systemic infections is one of the major causes of mortality worldwide, and a shortage of drug approaches applied for the rapid and necessary treatment contribute to increase the levels of death in affected patients. Several drug delivery systems based in nanotechnology such as metallic nanoparticles, liposomes, nanoemulsion, microemulsion, polymeric nanoparticles, solid lipid nanoparticles, dendrimers, hydrogels and liquid crystals can contribute in the biological performance of active substances for the treatment of microbial diseases triggered by fungi, bacteria, virus and parasites. In the presentation of these statements, this review article present and demonstrate the effectiveness of these drug delivery systems for the treatment of systemic diseases caused by several microorganisms, through a review of studies on scientific literature worldwide that contributes to better information for the most diverse professionals from the areas of health sciences. The studies demonstrated that the drug delivery systems described can contribute to the therapeutic scenario of these diseases, being classified as safe, active platforms and with therapeutic versatility.

Draft genome sequence of an extensively drug-resistant neonatal Klebsiella pneumoniae isolate harbouring multiple plasmids contributing to antibiotic resistance

OBJECTIVES

Klebsiella pneumoniae is a notorious nosocomial pathogen that has become a significant cause of neonatal infections causing morbidity and mortality. A multidrug-resistant K. pneumoniae isolate (K184) was isolated from a 5-day-old infant admitted to the neonatal intensive care unit of a local hospital in Rawalpindi, Pakistan. Whole-genome analysis of the isolated strain was performed to gain a better understanding of the genetic basis of antimicrobial resistance and virulence determinants.

METHODS

K. pneumoniae isolate K184 was sequenced on an Illumina HiSeq 2500 platform. The genome was assembled using SPAdes with 30× coverage and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.4.3. Characterisation of the strain was performed using MLST 2.0 server. Plasmids, antimicrobial resistance determinants and virulence factors were identified using PlasmidFinder v.2.0, the Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors Database (VFDB), respectively.

RESULTS

Neonatal K. pneumoniae isolate K184 has a considerably large genome with a size of 6,686,067 bp and a GC content of 55.6%. The isolate possesses three plasmids actively contributing to antimicrobial resistance, which classifies it as heavily loaded genome, along with three prophage regions. With 15 antimicrobial resistance determinants and various virulence factors, the neonatal isolate belongs to ST2096.

CONCLUSION

The genome of neonatal isolate K184 studied here provides an insight into antibiotic resistance and virulence determinants. This draft genome can be used to compare antimicrobial-resistant K. pneumoniae strains isolated from the neonatal population.

Efficacy of colistin in multidrug-resistant neonatal sepsis: experience from a tertiary care center in Karachi, Pakistan

OBJECTIVE

Infections with multidrug-resistant organisms (MDROs) such as Gram-negative bacteria have high morbidity and mortality with limited treatment options. Colistin, an antibiotic active against MDRO, was rarely used due to frequent adverse effects, but its use has now been recommended among adults. In this study, we determined the efficacy of colistin for the treatment of sepsis in neonates.

DESIGN/SETTING/PATIENTS/OUTCOMES

We conducted a retrospective record review of all neonates admitted to the neonatal intensive care unit of Aga Khan University Hospital, Karachi, Pakistan, between June 2015 and June 2018, who had sepsis and received colistin by intravenous, inhalation and/or intrathecal routes. Predictors of colistin efficacy, for neonatal survival and microbial clearance, were assessed using multiple logistic regression.

RESULTS

153 neonates received colistin; 120 had culture-proven sepsis; and 93 had MDR-GNB (84 colistin-sensitive). 111 (72.5%) neonates survived and were discharged from hospital; 82.6% had microbial clearance. Neonates with colistin-sensitive bacteria (adjusted OR (AOR)=3.2, 95% CI 2.8 to 4.0), and those in which colistin therapy started early (AOR=7.2, 95% CI 3.5 to 13.6) were more likely to survive. Neonates with increased gestational age (AOR=1.9, 95% CI 1.5 to 3.0), higher weight (AOR=5.4, 95% CI 3.3 to 11.8) and later onset of sepsis (AOR=4.3, 95% CI 2.0 to 9.0) had higher survival. Adverse events included nephrotoxicity in 5.2%; 13.7% developed seizures and 18.3% had electrolyte imbalance.

CONCLUSIONS

Colistin therapy was associated with survival among neonates suffering from MDR-GNB sepsis. The frequency of side effects was moderate.

Factors associated with culture proven neonatal sepsis in the Ho municipality 2016

Introduction

Neonatal Sepsis (NNS) is a public health problem which causes death or disability unless appropriate antibiotic treatment is given promptly. Globally, sepsis is an important cause of morbidity and mortality in neonates despite recent progress in health care delivery. We assessed the factors associated with culture proven sepsis among neonates in the Ho Municipality, Ghana.

Methods

a cross-sectional study was conducted in two public hospitals in the Ho Municipality between January and May, 2016. All neonates who were clinically suspected with sepsis in the Neonatal Intensive Care Unit (NICU) and their mothers were recruited. A 2ml blood sample was taken aseptically and dispensed into a mixture of thioglycollate and tryptone soy broth in a 1: 10 dilution and microbiological procedures performed. Case notes of both neonates and their mothers were reviewed and interviews conducted to collect both clinical and socio-demographic data. We determined the factors associated with culture proven neonatal sepsis using logistic regression model and statistical significance was determined at 95% confidence intervals.

Results

out of 150 neonates, 26 (17%) had laboratory confirmed sepsis. The most common pathogen isolated was Staphylococcus epidermidis 14, (54%). Neonates whose mothers were primigravida (OR=2.74; 95% CI: 1.12-6.68), and those who attended antenatal clinics (ANC) fewer than three schedules (OR=2.90; 95% CI: 1.06-7.96) had higher odds of developing culture proven sepsis.

Conclusion

neonates who were the first babies of their mothers were more likely to develop laboratory confirmed sepsis. Also, neonates of mothers who attended ANC less than 3 times were more likely to develop laboratory confirmed sepsis. High index of suspicion is required to diagnose neonatal sepsis among neonates of primigravida mothers and mothers who attend fewer than three ANC schedules.

Late-onset neonatal sepsis in Suzhou, China

Background

This study aimed to describe the causative organisms of neonatal late-onset sepsis (LOS) and their antimicrobial resistance in Suzhou, Southeast China over a 7-year period.

Methods

We performed a retrospective study on neonates with LOS from Jan1, 2011 to Dec 31, 2017. The demographic, clinical, and laboratory data of neonates with LOS were analyzed. Logistic regression was used to investigate the risk factors with mortality.

Results

During the study period, 202 neonates with LOS were finally identified. The most common pathogens were Escherichia coli (29.2%), followed by Klebsiella pneumoniae (19.3%), and Coagulase-negative Staphylococcus (CoNS) (16.8%). Nearly 90% of the K. pneumoniae were resistant to cefazolin and 71.8% to ceftazidime. Thirty-four patients (16.8%) died. Multivariable logistic regression showed that significant predictors of mortality were birth weight < 1500 g, respiratory distress and convulsions.

Conclusions

Gram-negative organisms have an important role in LOS in our region, with high levels of resistance to third-generation cephalosporins. These data may help in the selection of antibiotics for empirical treatment of neonates with sepsis.

Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission

Antimicrobial resistance (AMR) is a growing public health challenge that is expected to disproportionately burden lower- and middle-income countries (LMICs) in the coming decades. Although the contributions of human and veterinary antibiotic misuse to this crisis are well-recognized, environmental transmission (via water, soil or food contaminated with human and animal faeces) has been given less attention as a global driver of AMR, especially in urban informal settlements in LMICs-commonly known as 'shanty towns' or 'slums'. These settlements may be unique hotspots for environmental AMR transmission given: (1) the high density of humans, livestock and vermin living in close proximity; (2) frequent antibiotic misuse; and (3) insufficient drinking water, drainage and sanitation infrastructure. Here, we highlight the need for strategies to disrupt environmental AMR transmission in urban informal settlements. We propose that water and waste infrastructure improvements tailored to these settings should be evaluated for their effectiveness in limiting environmental AMR dissemination, lowering the community-level burden of antimicrobial-resistant infections and preventing antibiotic misuse. We also suggest that additional research is directed towards developing economic and legal incentives for evaluating and implementing water and waste infrastructure in these settings. Given that almost 90% of urban population growth will occur in regions predicted to be most burdened by the AMR crisis, there is an urgent need to build effective, evidence-based policies that could influence massive investments in the built urban environment in LMICs over the next few decades.

Klebsiella pneumoniae: an increasing threat to public health

OBJECTIVES

This review fills the paucity of information on K. pneumoniae as a nosocomial pathogen by providing pooled data on epidemiological risk factors, resistant trends and profiles and resistant and virulent genes of this organism in Asia.

METHODS

Exhaustive search was conducted using PubMed, Web of Science, and Google scholar for most studies addressing the prevalence, risk factors, drug resistant-mediated genes and/or virulent factors of K. pneumoniae in Asia. Data extracted for meta-analysis were analyzed using comprehensive meta-analysis version 3. Trends data for the isolation rate and resistance rates were entered into Excel spread sheet and the results were presented in graphs.

RESULTS

The prevalence rate of drug resistance in K. pneumoniae were; amikacin (40.8%) [95% CI 31.9-50.4], aztreonam (73.3%) [95% CI 59.9-83.4], ceftazidime (75.7%) [95% CI 65.4-83.6], ciprofloxacin (59.8%) [95% CI 48.6-70.1], colistin (2.9%) [95% CI 1.8-4.4], cefotaxime (79.2%) [95% CI 68.0-87.2], cefepime (72.6) [95% CI 57.7-83.8] and imipenem (65.6%) [95% CI 30.8-89.0]. TEM (39.5%) [95% CI 15.4-70.1], SHV-11 (41.8%) [95% CI 16.2-72.6] and KPC-2 (14.6%) [95% CI 6.0-31.4] were some of the resistance mediated genes observed in this study. The most virulent factors utilized by K. pneumoniae are; hypermucoviscous phenotype and mucoviscosity-related genes, genes for biosynthesis of lipopolysaccharide, iron uptake and transport genes and finally, adhesive genes.

CONCLUSION

It can be concluded that, antimicrobial resistant in K. pneumoniae is a clear and present danger in Asia which needs strong surveillance to curb this menace. It is very important for public healthcare departments to monitor and report changes in antimicrobial-resistant isolates.

A review of -multidrug-resistant Enterobacteriaceae in a neonatal unit in Johannesburg, South Africa

Background

Multi-drug resistant organisms are an increasingly important cause of neonatal sepsis.

Aim

This study aimed to review neonatal sepsis caused by multi-drug resistant Enterobacteriaceae (MDRE) in neonates in Johannesburg, South Africa.

Methods

This was a cross sectional retrospective review of MDRE in neonates admitted to a tertiary neonatal unit between 1 January 2013 and 31 December 2015.

Results

There were 465 infections in 291 neonates. 68.6% were very low birth weight (< 1500 g). The median age of infection was 14.0 days. Risk factors for MDRE included prematurity (p = 0.01), lower birth weight (p = 0.04), maternal HIV infection (p = 0.02) and oxygen on day 28 (p < 0.001). The most common isolate was Klebsiella pneumoniae (66.2%). Total MDRE isolates increased from 0.39 per 1000 neonatal admissions in 2013 to 1.4 per 1000 neonatal admissions in 2015 (p < 0.001). There was an increase in carbapenem-resistant Enterobacteriaceae (CRE) from 2.6% in 2013 to 8.9% in 2015 (p = 0.06). Most of the CRE were New Delhi metallo—β lactamase- (NDM) producers.

The all-cause mortality rate was 33.3%. Birth weight (p = 0.003), necrotising enterocolitis (p < 0.001) and mechanical ventilation (p = 0.007) were significantly associated with mortality. Serratia marcescens was isolated in 55.2% of neonates that died.

Conclusions

There was a significant increase in MDRE in neonatal sepsis during the study period, with the emergence of CRE. This confirms the urgent need to intensify antimicrobial stewardship efforts and address infection control and prevention in neonatal units in LMICs. Overuse of broad- spectrum antibiotics should be prevented.

Complete genome analysis of a Siphoviridae phage TSK1 showing biofilm removal potential against Klebsiella pneumoniae

Multidrug-resistant Klebsiella pneumoniae is a nosocomial pathogen, produces septicemia, pneumonia and UTI. Excessive use of antibiotics contributes towards emergence of multidrug-resistance. Bacteriophage-therapy is a potential substitute of antibiotics with many advantages. In this investigation, microbiological and genome characterization of TSK1 bacteriophage and its biofilm elimination capability are presented. TSK1 showed narrow host range and highest stability at pH 7 and 37 °C. TSK1 reduced the growth of K. pneumoniae during the initial 14 hours of infection. Post-treatment with TSK1 against different age K. pneumoniae biofilms reduced 85-100% biomass. Pre-treatment of TSK1 bacteriophage against the biofilm of Klebsiella pneumoniae reduced > 99% biomass in initial 24 hr of incubation. The genome of TSK1 phage comprised 49,836 base pairs with GC composition of 50.44%. Total seventy-five open reading frames (ORFs) were predicted, 25 showed homology with known functional proteins, while 50 were called hypothetical, as no homologs with proved function exists in the genome databases. Blast and phylogenetic analysis put it in the Kp36 virus genus of family Siphoviridae. Proposed packaging strategy of TSK1 bacteriophage genome is headful packaging using the pac sites. The potential of TSK1 bacteriophage could be used to reduce the bacterial load and biofilm in clinical and non-clinical settings.

Predictors of Mortality in Neonates and Infants Hospitalized With Sepsis or Serious Infections in Developing Countries: A Systematic Review

Background: Neonates and infants comprise the majority of the 6 million annual deaths under 5 years of age around the world. Most of these deaths occur in low/middle income countries (LMICs) and are preventable. However, the clinical identification of neonates and infants at imminent risk of death is challenging in developing countries. Objective: To systematically review the literature on clinical risk factors for mortality in infants under 12 months of age hospitalized for sepsis or serious infections in LMICs. Methods: MEDLINE and EMBASE were systematically searched using MeSH terms through April 2017. Abstracts were independently screened by two reviewers. Subsequently, full-text articles were selected by two independent reviewers based on PICOS criteria for inclusion in the final analysis. Study data were qualitatively synthesized without quantitative pooling of data due to heterogeneity in study populations and methodology. Results: A total of 1,139 abstracts were screened, and 169 full-text articles were selected for text review. Of these, 45 articles were included in the analysis, with 21 articles featuring neonatal populations (under 28 days of age) exclusively. Most studies were from Sub-Saharan Africa and South Asia. Risk factors for mortality varied significantly according to study populations. For neonatal deaths, prematurity, low birth-weight and young age at presentation were most frequently associated with mortality. For infant deaths, malnutrition, lack of breastfeeding and low oxygen saturation were associated with mortality in the highest number of studies. Conclusions: Risk factors for mortality differ between the neonatal and young infant age groups and were also dependant on the study population. These data can serve as a starting point for the development of individualized predictive models for in-hospital and post-discharge mortality and for the development of interventions to improve outcomes among these high-risk groups.

First Report of bla CTX-M-15-Type ESBL-Producing Klebsiella pneumoniae in Wild Migratory Birds in Pakistan

We investigated wild migratory birds faecal swabs for extended-spectrum β-lactamases-producing Klebsiella pneumoniae (ESBL-K. pneumoniae) from wetland habitats in Pakistan. ESBL-K. pneumoniae were analysed for MDR phenotype, ESBL genotype and genetic diversity. A total of 13 (8.6%) ESBL-K. pneumoniae were recovered. Of these, 8 (61%) isolates were MDR. DNA sequencing confirmed bla _CTX-M-15 as the dominant ESBL genotype. BOX-PCR fingerprints showed most of the isolates are unrelated. This study is the first to report the wildlife contamination of CTX-M-15-producing K. pneumoniae in Pakistan. Due to long-range migration, these birds could be responsible for trans-boundary spread of multidrug-resistant bacteria.

Characteristics of carbapenemase-producing Klebsiella pneumoniae as a cause of neonatal infection in Shandong, China

The goal of the present study was to examine the characteristics of carbapenem-resistant Klebsiella pneumoniae as a cause of neonatal infection. A total of 37 carbapenem-resistant Klebsiella pneumoniae-positive newborns hospitalized in Shandong Provincial Hospital, China between April 2011 and October 2013 were examined. Antibiotic susceptibility testing was performed using the agar dilution method and the Etest. Resistance genes were assessed by polymerase chain reaction (PCR) and sequencing. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were used to determine the genotypes and homology of these isolates. Plasmids were analyzed by PFGE and conjugation experiments. The outer membrane proteins were examined by PCR and SDS-PAGE. All of the isolates were revealed to be resistant to the third and fourth generation cephalosporins and piperacillin-tazobactam. Tigecycline, colistin, levofloxacin and amikacin were successful against all of the isolates. The antibiotic resistance rates of aztreonam, gentamicin, trimethoprim-sulfamethoxazole and fosfomycin were 13.51, 48.64, 78.38 and 86.49%, respectively. Of the 37 cases, 25 isolates (67.57%) were bla_NDM-1 positive, 13 isolates (35.14%) were bla_IMP-4 positive and 1 isolate (2.70%) was bla_IMP-8 positive. Two isolates carried both bla_NDM-1 and bla_IMP-4. The isolate carrying 2-4 plasmids and bla_NDM-1 and bla_IMP-4 was transferable between strains. SDS-PAGE data indicated that outer membrane proteins remained present. PFGE revealed 7 distinct clusters, and MLST reported the presence of ST20, ST17, ST54, ST705 and ST290 sequences, which indicated that there was clone and plasmid spread between newborns. The main resistance mechanism of carbapenem-resistant Klebsiella pneumoniae was that the isolates expressed the carbapenemase resistance of bla_NDM-1 and bla_IMP-4 genes. The current study indicates that early detection of these genes may be helpful in infection prevention and control.

Carbapenem-Resistant Enterobacteriaceae Infections in Children

Carbapenem-resistant Enterobacteriaceae (CRE) are an emerging global public health threat. Infections due to CRE are associated with significant morbidity and mortality. Few therapeutic options are available for treatment of these infections, and optimal antibiotic treatment regimens are unclear. Along with the rapidly increasing prevalence of CRE in the USA and worldwide, several studies have described the epidemiology of CRE in the adult population. While CRE are now also reported sporadically in children, there is a significant lack of data on the epidemiology, risk factors, treatment, and outcomes in this population. This article provides a comprehensive review of what is known to date about CRE, including clinical and molecular epidemiology, microbiologic diagnosis, antibiotic treatment options, and outcomes. In particular, this review will focus on the available data on CRE in the pediatric population.

Platelet Mass Predicts Intracranial Hemorrhage in Neonates With Gram-negative Sepsis

Neonatal sepsis due to gram-negative bacteria is associated with severe hemorrhagic conditions, such as intracranial hemorrhage (ICH). The aim of the study was to investigate the significance of platelet (PLT) count and platelet mass (PM) in predicting promptly neonatal ICH. Demographics, species, PLT, PM, ICH, and outcome for neonates with gram-negative sepsis for the period 2005 to 2012 were retrospectively recorded. Eighty-four infants were enrolled with median gestational age 30 weeks, median birthweight 1481.5 g, and median age at sepsis diagnosis 23 days. The most frequently isolated bacteria were Enterobacter spp. (38.1%). ICH occurred in 16 neonates (19%), whereas the mortality rate was 25% (21 neonates). The median PLT count and PM at days 1, 2, and 3 after diagnosis of gram-negative sepsis was significantly associated with the presence of ICH. Regression analysis revealed the cutoff predictive value of 355 fL/nL for the PM at day 3 (area under the curve: 75, sensitivity 90%, P=0.002). PM levels could play an important role in predicting the occurrence of ICH in high-risk neonates.

Inhibition of aminoglycoside 6'-N-acetyltransferase type Ib-mediated amikacin resistance in Klebsiella pneumoniae by zinc and copper pyrithione

The in vitro activity of the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] was inhibited by CuCl2 with a 50% inhibitory concentration (IC50) of 2.8 μM. The growth of an amikacin-resistant Klebsiella pneumoniae strain isolated from a neonate with meningitis was inhibited when amikacin was supplemented by the addition of Zn(2+) or Cu(2+) in complex with the ionophore pyrithione. Coordination complexes between cations and ionophores could be developed for their use, in combination with aminoglycosides, to treat resistant infections.

Profile of ceftolozane/tazobactam and its potential in the treatment of complicated intra-abdominal infections

Drug-resistant pathogens have gained a foothold especially in the most vulnerable patient populations, hospitalized and immunocompromised individuals. Furthermore, extended-spectrum β-lactamase and carbapenemase-producing organisms are finding their way even into the community, with patients presenting to the hospital with established colonization and infection with resistant Enterobacteriaceae in particular. Recently, a novel antipseudomonal cephalosporin in combination with an established Class A β-lactamase inhibitor, ceftolozane/tazobactam has been approved by the FDA for use in the treatment of complicated urinary tract infections and complicated intra-abdominal infections. Ceftolozane is a uniquely potent antipseudomonal cephalosporin because of its high affinity for the penicillin-binding proteins of Pseudomonas aeruginosa, its low affinity for the intrinsic Class C β-lactamases of P. aeruginosa, its ability to enter P. aeruginosa through the outer membrane without the utilization of OprD protein, and the fact that it is not a substrate of the often upregulated MexAB/OprM efflux system of P. aeruginosa. The biological chemistry, pharmacokinetics/pharmacodynamics, microbiologic spectrum, and clinical trials that led to the approval of ceftolozane is reviewed. A discussion regarding its potential role in the treatment of complicated intra-abdominal infections and other infectious disease syndromes associated with drug-resistant pathogens follows.

Antibiotic stewardship programmes in intensive care units: Why, how, and where are they leading us

Antibiotic usage and increasing antimicrobial resistance (AMR) mount significant challenges to patient safety and management of the critically ill on intensive care units (ICU). Antibiotic stewardship programmes (ASPs) aim to optimise appropriate antibiotic treatment whilst minimising antibiotic resistance. Different models of ASP in intensive care setting, include “standard” control of antibiotic prescribing such as “de-escalation strategies”through to interventional approaches utilising biomarker-guided antibiotic prescribing. A systematic review of outcomes related studies for ASPs in an ICU setting was conducted. Forty three studies were identified from MEDLINE between 1996 and 2014. Of 34 non-protocolised studies, [1 randomised control trial (RCT), 22 observational and 11 case series], 29 (85%) were positive with respect to one or more outcome: These were the key outcome of reduced antibiotic use, or ICU length of stay, antibiotic resistance, or prescribing cost burden. Limitations of non-standard antibiotic initiation triggers, patient and antibiotic selection bias or baseline demographic variance were identified. All 9 protocolised studies were RCTs, of which 8 were procalcitonin (PCT) guided antibiotic stop/start interventions. Five studies addressed antibiotic escalation, 3 de-escalation and 1 addressed both. Six studies reported positive outcomes for reduced antibiotic use, ICU length of stay or antibiotic resistance. PCT based ASPs are effective as antibiotic-stop (de-escalation) triggers, but not as an escalation trigger alone. PCT has also been effective in reducing antibiotic usage without worsening morbidity or mortality in ventilator associated pulmonary infection. No study has demonstrated survival benefit of ASP. Ongoing challenges to infectious disease management, reported by the World Health Organisation global report 2014, are high AMR to newer antibiotics, and regional knowledge gaps in AMR surveillance. Improved AMR surveillance data, identifying core aspects of successful ASPs that are transferable, and further well-conducted trials will be necessary if ASPs are to be an effective platform for delivering desired patient outcomes and safety through best antibiotic policy.

Multidrug-resistant Gram-negative bacteria: a product of globalization

Global trade and mobility of people has increased rapidly over the last 20 years. This has had profound consequences for the evolution and the movement of antibiotic resistance genes. There is increasing exposure of populations all around the world to resistant bacteria arising in the emerging economies. Arguably the most important development of the last two decades in the field of antibiotic resistance is the emergence and spread of extended-spectrum β-lactamases (ESBLs) of the CTX-M group. A consequence of the very high rates of ESBL production among Enterobacteriaceae in Asian countries is that there is a substantial use of carbapenem antibiotics, resulting in the emergence of plasmid-mediated resistance to carbapenems. This article reviews the emergence and spread of multidrug-resistant Gram-negative bacteria, focuses on three particular carbapenemases--imipenem carbapenemases, Klebsiella pneumoniae carbapenemase, and New Delhi metallo-β-lactamase--and highlights the importance of control of antibiotic use.

First report of a Klebsiella pneumoniae ST466 strain causing neonatal sepsis harbouring the blaCTX-M-15 gene in Rabat, Morocco

Klebsiella pneumoniae is one of the Gram-negative bacilli most commonly found in urine of pregnant women and causing neonatal sepsis. The aim of this study was to analyse in terms of epidemiology and antimicrobial resistance of 23 K. pneumoniae isolates collected from vaginal swabs or urine of pregnant women, from pharyngeal and ear swabs of apparently healthy newborns and from peripheral cultures and hemocultures of newborns with suspected invasive neonatal infection in Rabat, Morocco. The prevalence of K. pneumoniae was 0.6 and 0.9% among pregnant women and neonates, respectively. These strains showed lower antimicrobial resistance levels regarding the developed countries. Thus, only one strain from a neonate presented an ESBL. This is the first report of a K. pneumoniae strain causing neonatal sepsis harbouring the blaCTX-M-15 gene in an IncFII plasmid and belonging to ST466 in this area.

Multi-drug resistant gram negative infections and use of intravenous polymyxin B in critically ill children of developing country: retrospective cohort study

Background

Patients in pediatric intensive care Units (PICU) are susceptible to infections with antibiotic resistant organisms which increase the morbidity, mortality and cost of care.

To describe the clinical characteristics and mortality in patients with Multi-Drug Resistant (MDR) gram negative organisms. We also report safety of Polymyxin B use in these patients.

Methods

Files of patients admitted in PICU of Aga Khan University Hospital, from January 2010 to December 2011, one month to 15 years of age were reviewed. Demographic and clinical features of patients with MDR gram negative infections, antibiotic susceptibility pattern of isolates, discharge disposition and adverse effects of Polymyxin B were recorded.

Results

A total of 44.8/1000(36/803) admitted patients developed MDR gram negative infections, of which 47.2%(17/36) were male, with mean age of 3.4 yrs(+/−4.16). Acinetobacter Species (25.5%) was the most frequently isolated MDR organisms followed by Klebsiella Pneumoniae (17%). Sensitivity of isolates was 100% to Polymyxin B, followed by Imipenem (50%), and piperacillin/tazobactem (45%). The crude mortality rate of patients with MDR gram negative infections was 44.4% (16/36). Fourteen of 36 patients received Polymyxin B and 57.1%; (8/14) of them were cured. Nephrotoxicity was observed in 21.4% (3/14) cases, none of the patients showed signs of neuropathy.

Conclusion

Our study highlights high rates of Carbapenem resistant gram negative isolates, leading to increasing use of Polymyxin B as the only drug to combat against these critically ill children. Therefore, we emphasizeon Stewardship of Antibiotics and continuous surveillance system as strategies in overall management of these critically ill children.

Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness

We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a "commensal lifestyle." However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.

IMPORTANCE

During critical illness, the normal gut microbiota becomes disrupted in response to host physiologic stress and antibiotic treatment. Here we demonstrate that the community structure of the gut microbiota during prolonged critical illness is dramatically changed such that in many cases only two-member pathogen communities remain. Most of these ultra-low-membership communities display low virulence when grouped together (i.e., a commensal lifestyle); individually, however, they can express highly harmful behaviors (i.e., a pathogenic lifestyle). The commensal lifestyle of the whole community can be shifted to a pathogenic one in response to host factors such as opioids that are released during physiologic stress and critical illness. This shift can be prevented by using compounds such as Pi-PEG15-20 that interrupt bacterial virulence expression. Taking the data together, this report characterizes the plasticity seen with respect to the choice between a commensal lifestyle and a pathogenic lifestyle among ultra-low-diversity pathogen communities that predominate in the gut during critical illness and offers novel strategies for prevention of sepsis.