Increase in isolation of extended spectrum beta lactamase producing multidrug resistant non typhoidal Salmonellae in Pakistan

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.

A secular trend in invasive non-typhoidal Salmonella in South India, 2000-2020: Identification challenges and antibiogram

PURPOSE

Invasive non-typhoidal Salmonella (iNTS) disease is an important cause of morbidity and mortality in African countries. However, the incidence in Indian subcontinent remains poorly documented. This study has assessed the incidence of iNTS in India with a perspective on its AMR profiles and serovar distribution for a period of 21 years from 2000 to 2020 from a tertiary care centre in South India.

METHODS

A total of 461 iNTS isolates were subjected to serotyping and antimicrobial susceptibility testing (AST). A subset of isolates was genotyped by multi locus sequence typing (MLST) and results were compared to serotyping to predict the accuracy.

RESULTS

Overall, 461 iNTS isolates were characterised mostly comprising of S. Typhimurium (49.2%) and S. Enteritidis (28.8%). Proportion of isolates resistant to first line antibiotics such as ampicillin, chloramphenicol and trimethoprim/sulphamethoxazole were 6.7%, 1.7% and 3.6% respectively. Isolates resistant to third generation cephalosporin are at a gradual rise while decreased susceptibility to quinolones was most common. The incidence of iNTS infection was maximum in the age group of >15 years. MLST analysis showed discrepancies in assigning the serovars by serotyping as three S. Saintpaul were identified as S. Typhimurium.

CONCLUSION

The clinical epidemiology, serovar distribution and antimicrobial susceptibility patterns of invasive Salmonella isolates from India suggest that there is only a small burden of iNTS disease. However the gradual emergence of AMR in iNTS isolates indicates serious risk for public health warranting the importance enhanced molecular surveillance.

Association between Non-Typhoidal Salmonella Infection and Growth in Children under 5 Years of Age: Analyzing Data from the Global Enteric Multicenter Study

Non-typhoidal Salmonella (NTS) is one of the less focused on infections and is often associated with faulty child nutrition in the developing world. This study aimed to evaluate the association of NTS infection with growth faltering among children under the age of five. We analyzed data from 378 fecal NTS positive children with both moderate-to-severe diarrhea (MSD) and asymptomatic infection from the seven countries of South Asia and sub-Saharan Africa during enrolment and on day 60 follow up in the Global Enteric Multicenter Study (GEMS) for the period of December 2007 to March 2011. Children not associated with fecal NTS (n = 1134) were randomly selected from the same dataset (1:3 ratio) as a comparison group. The association between an explanatory variable and the outcome variable was longitudinally tested using generalized estimating equations (GEE), where the dependent variables were height-for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ) z-score, and the independent variable was the presence of fecal NTS. The GEE multivariable model identified a negative association between fecal NTS and WAZ (coefficient: -0.19; 95% CI (confidence interval): -0.33, -0.04, and p value = 0.010), WHZ (coef: -0.19; 95% CI: -0.34, -0.05, and p value = 0.007), and HAZ (coef: -0.13; 95% CI: -0.27, -0.01, and p value = 0.073) after adjusting for age, gender, diarrhea, breastfeeding status, mothers' education, number of children under the age of five, household size by the number of people regularly sleep at the home, handwashing practice, source of drinking water, wealth index, presence of co-pathogens, comorbidity, and study sites. In the GEMS, where children were followed during 50-90 days of enrolment, the presence of fecal NTS harmed the child's anthropometric outcomes. Minimizing potential exposure to NTS is needed to curb worsening child undernutrition.

Characterisation of antibiotic resistance of Salmonella isolated from dog treats in Japan

Dog treats might be contaminated with Salmonella. In Canada and the USA, outbreaks of human salmonellosis related to exposure to animal-derived dog treats were reported. Consequently, surveillance data on Salmonella contamination of dog treats have been gathered in many countries, but not in Japan. In the current study, we investigated whether dog treats in Japan were contaminated with Salmonella. Overall, 303 dog treats (of which 255 were domestically produced) were randomly collected and the presence of Salmonella investigated. Seven samples were positive for Salmonella enterica subsp. enterica. Among these isolates, three were identified as serovar 4,5,12:i:–; two were serovar Rissen; and two were serovar Thompson. All serovar 4,5,12:i:– and Thompson isolates were resistant to one or more drugs. Two serovar Rissen isolates were fully susceptible to all tested antimicrobial agents. All Salmonella isolates were susceptible to cefotaxime, ciprofloxacin and nalidixic acid. The gene bla_TEM was detected in two serovar 4,5,12:i:– isolates. The bla_CTX−M and bla_CMY genes were not detected in any isolates. This study demonstrated that dog treats in Japan could constitute a potential source of dog and human Salmonella infections, including multidrug-resistant Salmonella isolates.

Effect of Bismuth Subsalicylate vs Placebo on Use of Antibiotics Among Adult Outpatients With Diarrhea in Pakistan: A Randomized Clinical Trial

IMPORTANCE

Many of the 4.5 billion annual episodes of diarrhea are treated unnecessarily with antibiotics; prevalence of antibiotic resistance among diarrheal pathogens is increasing. Knowledge-based antibiotic stewardship interventions typically yield little change in antibiotic use.

OBJECTIVE

To compare antibiotic use among adult outpatients with diarrhea given bismuth subsalicylate (BSS) or placebo.

DESIGN, SETTING, AND PARTICIPANTS

This randomized clinical trial took place from April to October 2014. Participants were patients aged 15 to 65 years with acute, nonbloody diarrhea from 22 outpatient clinics in Karachi, Pakistan. Participants were interviewed about symptoms and health care utilization during the 5 days after enrollment. Group assignment was concealed from participants, field staff, and the statistician. Primary analysis occurred from August to September 2015.

INTERVENTIONS

Participants were randomly assigned (1:1) to receive BSS or placebo for 48 hours or less.

MAIN OUTCOMES AND MEASURES

Use of systemic antibiotics within 5 days of enrollment. Secondary outcomes included measures of duration and severity of illness.

RESULTS

Among eligible patients, 39 declined to participate, 440 enrolled, and 1 enrolled participant was lost to follow-up, for a total of 439 patients included in the analysis. Median (interquartile range) participant age was 32 (23-45) years and 187 (43%) were male. Two hundred twenty patients were randomized to BSS and 220 were randomized to placebo. Overall, 54 participants (12%) used systemic antibiotics (16% in the placebo group and 9% in the BSS group); all antibiotic use followed consultation with a physician. Use of any antibiotic was significantly lower in the BSS group (20 of 220 vs 34 of 219 patients; odds ratio [OR], 0.54; 95% CI, 0.30-0.98), as was use of fluoroquinolones (8 of 220 vs 20 of 219 patients; OR, 0.38; 95% CI, 0.16-0.88). Rates of care seeking and hospitalization were similar between groups and no difference was detected in timing of diarrhea resolution. However, those in the BSS group less commonly received intravenous rehydration (14 of 220 vs 27 of 219 patients; OR, 0.48; 95% CI, 0.25-0.95) and missed less work (median [interquartile range], 0 [0-1] vs 1 [0-1] day; P = .04) during follow-up.

CONCLUSIONS AND RELEVANCE

This study found less antibiotic use among participants given BSS for acute diarrhea in a setting where antibiotics are commonly used to treat diarrhea. Encouraging health care professionals in such settings to recommend BSS as frontline treatment for adults with diarrhea, and promoting BSS for diarrhea self-management, may reduce antibiotic use and rates of antibiotic resistance globally.

TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT02047162.

Prevalence of extended-spectrum-β-lactamase-producing Enterobacteriaceae: first systematic meta-analysis report from Pakistan

Background

South-Asia is known as a hub for multidrug-resistant (MDR) bacteria. Unfortunately, proper surveillance and documentation of MDR pathogens is lacking in Pakistan. The alarming increase in the prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a serious problem. From this perspective, we analysed published data regarding ESBL-producing Enterobacteriaceae in different regions of Pakistan.

Methods

A meta-analysis was performed to determine the prevalence of ESBL-producing Enterobacteriaceae in Pakistan. A Web-based search was conducted in electronic databases, including PubMed, Scopus and PakMedi Net (for non-indexed Pakistani journals). Articles published (in either indexed or non-indexed journals) between January 2002 and July 2016 were included in the study. Relevant data were extracted, and statistical analysis was performed using the Metaprop command of STATA version 14.1.

Results

A total of 68 studies were identified from the electronic data base search, and 55 of these studies met our inclusion criteria. Pakistan’s overall pooled proportion of ESBL-producers was 0.40 (95% CI: 0.34–0.47). The overall heterogeneity was significant (I2 = 99.75%, p < 0.001), and significant ES = 0 (Z = 18.41, p < 0.001) was found. OXA, SHV, TEM and CTX-M were the most commonly found gene variants for ESBLs in these studies.

Conclusion

The prevalence of ESBL-producing Enterobacteriaceae is high in Pakistan. Little is known about the annual frequency of ESBLs and their prevalence in different provinces of Pakistan. No data are available regarding ESBL frequency in Baluchistan. This underscores an urgent demand for regular surveillance to address this antimicrobial resistance problem. Surveillance to better understand the annual ESBL burden is crucial to improve national and regional guidelines.

Detection of Salmonella spp. with the BACTEC 9240 Automated Blood Culture System in 2008 - 2014 in Southern Iran (Shiraz): Biogrouping, MIC, and Antimicrobial Susceptibility Profiles of Isolates

Background

Human salmonellosis continues to be a major international problem, in terms of both morbidity and economic losses. The antibiotic resistance of Salmonella is an increasing public health emergency, since infections from resistant bacteria are more difficult and costly to treat.

Objectives

The aims of the present study were to investigate the isolation of Salmonella spp. with the BACTEC automated system from blood samples during 2008 - 2014 in southern Iran (Shiraz). Detection of subspecies, biogrouping, and antimicrobial susceptibility testing by the disc diffusion and agar dilution methods were performed.

Patients and Methods

A total of 19 Salmonella spp. were consecutively isolated using BACTEC from blood samples of patients between 2008 and 2014 in Shiraz, Iran. The isolates were identified as Salmonella, based on biochemical tests embedded in the API-20E system. In order to characterize the biogroups and subspecies, biochemical testing was performed. Susceptibility testing (disc diffusion and agar dilution) and extended-spectrum β-lactamase (ESBL) detection were performed according to the clinical and laboratory standards institute (CLSI) guidelines.

Results

Of the total 19 Salmonella spp. isolates recovered by the BACTEC automated system, all belonged to the Salmonella enterica subsp. houtenae. Five isolates (26.5%) were resistant to azithromycin. Six (31.5%) isolates with the disc diffusion method and five (26.3%) with the agar dilution method displayed resistance to nalidixic acid (minimum inhibitory concentration [MIC] > 32 μg/mL). All nalidixic acid-resistant isolates were also ciprofloxacin-sensitive. All isolates were ESBL-negative. Twenty-one percent of isolates were found to be resistant to chloramphenicol (MIC ≥ 32 μg/mL), and 16% were resistant to ampicillin (MIC ≥ 32 μg/mL).

Conclusions

The results indicate that multidrug-resistant (MDR) strains of Salmonella are increasing in number, and fewer antibiotics may be useful for treating S. enterica infections. Routine investigation and reporting of antibiotic MICs in patients presenting with Salmonella infections is suggested.

Screening of soil actinomyectes against Salmonella serovar Typhi NCTC 5761 and characterization of the prominent active strains

BACKGROUND AND OBJECTIVES

Annual incidence of infection with S. Typhi is estimated to be about 17 million cases worldwide. A systematic search among actinomycete isolates from soil of Iran aimed at finding active actinomycetes against the causative agent of typhoid fever, Salmonella Typhi was carried out during this study.

MATERIALS AND METHODS

Our anti-Salmonella screening program resulted in nine highly active actinomycete isolates. All nine antibiotic producing strains showed broad-spectrum antibacterial activity, as five strains showed antifungal activity as well. Based on microscopic morphology and cell wall analysis, all nine active actinomycete strains were representatives of the genus Streptomyces. Three of the producing strains including the isolates HG87, HG116 and HG443 with inhibition zone of >20 mm, were selected for further identification and investigation of cytotoxic effects.

RESULTS AND CONCLUSION

None of the producing strains showed cytotoxicity on HEK and USSC cell lines, while strain HG116 showed excellent antitumor activity on T47D cancer cell lines. Isolates HG87, HG116 and HG443 can be distinguished from the related species by some phenotypic and biochemical characteristics. Our results demonstrate the broad-range biological activity exhibited by bioactive compounds of soil actinomycetes from Iran.

Serotype profile and molecular characterization of antimicrobial resistance in non-typhoidal Salmonella isolated from gastroenteritis cases over nine years

Resistance to third-generation cephalosporins in non-typhoidal Salmonella (NTS) is emerging worldwide. We report the occurrence of extended-spectrum beta-lactamase (ESBL) phenotypes in 53.4 % of NTS isolated over a period of nine years from gastroenteritis cases. ESBL and AmpC co-production was observed in 21 % of the isolates. Occurrence of blaCTX-M-15 and blaCMY-2 resistance genes was observed in 11.6 % and 37 % of the isolates respectively. Overall, Salmonella enterica serovar Senftenberg was the predominant serovar carrying blaCTX-M-15 and blaCMY-2 resistance genes. We report for the first time from India, one isolate each of S. enterica serovar Thompson, S. enterica serovar Infantis and S. enterica serovar Newport, carrying the blaCTX-M-15 gene. We also report for the first time from India, a case of gastroenteritis due to S. enterica serovar Thompson.

Non-typhoidal Salmonella gastroenteritis at a diarrheal hospital in Dhaka, Bangladesh, 1996-2011

Data on non-typhoidal Salmonella (NTS) infection in South Asia are limited. We used data gathered prospectively from 1996 to 2011 as part of a hospital surveillance system in Dhaka, Bangladesh, to identify diarrheal patients with NTS isolated from stool. NTS was isolated in 1.3% (468 of 37,439) of diarrheal patients; 47% of total cases of NTS were in children < 5 years of age, although older adults (≥ 60 years) had the highest isolation rates. NTS isolation peaked in the monsoon months of July and August. Over the study period, rates of multidrug resistance decreased, whereas rates of decreased susceptibility to ciprofloxacin increased. Compared with control patients, NTS patients were older and wealthier; however, no differences in type of housing or exposure to animals were found. NTS patients had increased inflammatory cells in stool and required more fluid resuscitation.

Salmonella infections: an update on epidemiology, management, and prevention

Salmonella species are a group of Gram-negative enterobacteria and known human pathogens in developing as well as industrialized countries. Despite significant advances in sanitation, provision of potable water, and highly controlled food chain surveillance, transmission of Salmonella spp. continues to affect communities, preferentially children, worldwide. This review summarizes updated concepts on typhoidal and non-typhoidal Salmonella infections, starting with a historical perspective that implicates typhoid Salmonella as a significant human pathogen since ancient times. We describe the epidemiology of this pathogen with emphasis on the most recent non-typhoidal Salmonella outbreaks in industrialized countries and continued outbreaks of typhoid Salmonella in underserved countries. An overview of clinical aspects of typhoid and non-typhoid infections in developing and industrialized countries, respectively, is provided, followed by a description on current treatment concepts and challenges treating multidrug-resistant Salmonella infections. We conclude with prevention recommendations, and recent research studies on vaccine prevention.

When and how to cover for resistant gram-negative bacilli in severe sepsis and septic shock

In the 80s and 90s, increasing antibiotic resistance was met by the introduction of new effective agents with broader antibacterial spectra for the empirical treatment of severe infections. In recent years, however, few novel antimicrobials have been developed, and this has critically weakened our strength in the fight against resistant bacteria, especially Gram-negative bacilli. It has been well proven that mortality increases if initial empirical antibiotic treatment for severe infection is inappropriate due to resistance of the pathogen. Physicians are already faced with the increasing challenge of untreatable or almost untreatable Gram-negative infections due to antibiotic resistance. Empirical treatment with broader spectra and high antibiotic pressure both in- and outside hospital is the driving force behind resistance. Since new efficient drugs against Gram-negative bacilli will not be available for some time, the best we can do to stop infections caused by multidrug-resistant bacteria is to improve infection control and choice of antibiotics, which should be based on surveillance of local antibiotic consumption and resistance. We must learn more about the revived antibacterial agents colistin and fosfomycin, and the few next generation Gram-negative antibiotics that have been developed. The aim of this review is to give an update on present therapeutic options in the fight against multidrug-resistant Gram-negative bacteria.

Increasing Trend of Resistance to Penicillin, Tetracycline, and Fluoroquinolone Resistance in Neisseria gonorrhoeae from Pakistan (1992-2009)

Emergence and spread of drug resistant Neisseria gonorrhoeae is global concern. We evaluated trends of antimicrobial resistance in Neisseria gonorrhoeae over years 1992–2009 in Pakistan. Resistance rates were compared between years (2007–2009) and (1992–2006). Antimicrobial susceptibility testing was performed and interpreted according to Clinical Laboratory Standards Institute (CLSI) criteria using the disk diffusion methodology against penicillin, ceftriaxone, tetracycline and ofloxacin. Additional antibiotics tested in 100 strains isolated during 2007–2009, included cefotaxime, cefoxitin, cefuroxime, cefipime, ceftazidime, ceftizoxime, cefixime, cefpodoxime, spectinomycin and azithromycin. Neisseria gonorrhoeae ATCC 49226 was used as control. Chi-square for trend analysis was conducted to assess resistance trend over the study period. During study period significant increase in combined resistance to penicillin, tetracycline and ofloxacin was observed (P value <0.01). Resistance rates during the two study period also increased significantly (P value <0.01). Ceftriaxone resistance was not observed. None of the isolates were found to be resistant or with intermediate sensitivity to additional antibiotics. Our findings suggest that penicillin, ciprofloxacin, tetracycline should not be used in the empirical treatment of gonorrhea in Pakistan. Ceftriaxone and cefixime should be the first line therapy; however periodic MICs should be determined to identify emergence of strains with reduced susceptibility.

Fluoroquinolone resistance among Mycobacterium tuberculosis strains from Karachi, Pakistan: data from community-based field clinics

A fluoroquinolone (FQ) resistance rate of 5.9% is reported in 205 Mycobacterium tuberculosis isolates from patients presenting to field clinics in Karachi, Pakistan (2006 to 2009). FQ resistance among multidrug-resistant (MDR) strains was 11.1% (5/45), and it was 4.9% (5/103) in M. tuberculosis strains susceptible to all first-line agents. Spoligotyping of resistant strains did not show dominance of one strain type. Our data reflect considerable FQ-resistant M. tuberculosis isolates and the need to consider inclusion of FQ within first-line sensitivity testing in such settings.